[1] "ofn"        "-oTLUSC-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/LUSC-TP/15084586/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/15093660/transformed.cor.cli.txt"

nPatients in clinical file=495, in cluster file=501, common to both=493
[1]  83 493
[1] "AMP PEAK  1(1Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                          254                           239 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                          254                           239 
[1] "AMP PEAK  2(2P16.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                          269                           224 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                          269                           224 
[1] "AMP PEAK  3(2Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                          170                           323 
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                          170                           323 
[1] "AMP PEAK  4(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           444                             49 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           444                             49 
[1] "AMP PEAK  5(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                        117                         376 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                        117                         376 
[1] "AMP PEAK  6(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           382                            111 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           382                            111 
[1] "AMP PEAK  7(5P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                        349                         144 
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                        349                         144 
[1] "AMP PEAK  8(6P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                          163                           330 
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                          163                           330 
[1] "AMP PEAK  9(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                        150                         343 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                        150                         343 
[1] "AMP PEAK 10(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          252                           241 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          252                           241 
[1] "AMP PEAK 11(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                          260                           233 
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                          260                           233 
[1] "AMP PEAK 12(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                           235                            258 
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                           235                            258 
[1] "AMP PEAK 13(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           349                            144 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           349                            144 
[1] "AMP PEAK 14(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          132                           361 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          132                           361 
[1] "AMP PEAK 15(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           182                            311 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           182                            311 
[1] "AMP PEAK 16(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                            251                             242 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                            251                             242 
[1] "AMP PEAK 17(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                         173                          320 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                         173                          320 
[1] "AMP PEAK 18(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          86                          407 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          86                          407 
[1] "AMP PEAK 19(14Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                           157                            336 
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                           157                            336 
[1] "AMP PEAK 20(14Q32.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                            155                             338 
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                            155                             338 
[1] "AMP PEAK 21(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                           175                            318 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                           175                            318 
[1] "AMP PEAK 22(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                           231                            262 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                           231                            262 
[1] "AMP PEAK 23(18P11.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                            178                             315 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                            178                             315 
[1] "AMP PEAK 24(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           150                            343 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           150                            343 
[1] "AMP PEAK 25(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         219                          274 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         219                          274 
[1] "AMP PEAK 26(19Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                           231                            262 
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                           231                            262 
[1] "AMP PEAK 27(20P12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           274                            219 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           274                            219 
[1] "AMP PEAK 28(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                            301                             192 
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                            301                             192 
[1] "AMP PEAK 29(22Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                            251                             242 
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                            251                             242 
[1] "AMP PEAK 30(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                        121                         372 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                        121                         372 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           223                            270 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           223                            270 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          216                           277 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          216                           277 
[1] "DEL PEAK  3(2P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           49                           444 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           49                           444 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          129                           364 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          129                           364 
[1] "DEL PEAK  5(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          154                           339 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          154                           339 
[1] "DEL PEAK  6(3P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                          390                           103 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                          390                           103 
[1] "DEL PEAK  7(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                        426                          67 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                        426                          67 
[1] "DEL PEAK  8(3P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          419                            74 
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          419                            74 
[1] "DEL PEAK  9(3P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                          413                            80 
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                          413                            80 
[1] "DEL PEAK 10(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                           78                           415 
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                           78                           415 
[1] "DEL PEAK 11(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          312                           181 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          312                           181 
[1] "DEL PEAK 12(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          280                           213 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          280                           213 
[1] "DEL PEAK 13(4Q32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                          321                           172 
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                          321                           172 
[1] "DEL PEAK 14(4Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          323                           170 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          323                           170 
[1] "DEL PEAK 15(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          362                           131 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          362                           131 
[1] "DEL PEAK 16(5Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                          379                           114 
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                          379                           114 
[1] "DEL PEAK 17(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                          132                           361 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                          132                           361 
[1] "DEL PEAK 18(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                           121                            372 
  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                           121                            372 
[1] "DEL PEAK 19(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                        132                         361 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                        132                         361 
[1] "DEL PEAK 20(7Q11.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                            46                            447 
  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                            46                            447 
[1] "DEL PEAK 21(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                          101                           392 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                          101                           392 
[1] "DEL PEAK 22(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          336                           157 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          336                           157 
[1] "DEL PEAK 23(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        325                         168 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        325                         168 
[1] "DEL PEAK 24(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          381                           112 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          381                           112 
[1] "DEL PEAK 25(9P21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                          320                           173 
  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                          320                           173 
[1] "DEL PEAK 26(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           248                            245 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           248                            245 
[1] "DEL PEAK 27(10P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                           216                            277 
  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                           216                            277 
[1] "DEL PEAK 28(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            264                             229 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            264                             229 
[1] "DEL PEAK 29(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           242                            251 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           242                            251 
[1] "DEL PEAK 30(11Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                           159                            334 
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                           159                            334 
[1] "DEL PEAK 31(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                         182                          311 
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                         182                          311 
[1] "DEL PEAK 32(12Q24.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                             83                             410 
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                             83                             410 
[1] "DEL PEAK 33(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            329                             164 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            329                             164 
[1] "DEL PEAK 34(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           340                            153 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           340                            153 
[1] "DEL PEAK 35(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                           172                            321 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                           172                            321 
[1] "DEL PEAK 36(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           165                            328 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           165                            328 
[1] "DEL PEAK 37(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                           168                            325 
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                           168                            325 
[1] "DEL PEAK 38(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                           184                            309 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                           184                            309 
[1] "DEL PEAK 39(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           204                            289 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           204                            289 
[1] "DEL PEAK 40(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           268                            225 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           268                            225 
[1] "DEL PEAK 41(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           131                            362 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           131                            362 
[1] "DEL PEAK 42(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                           101                            392 
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                           101                            392 
[1] "DEL PEAK 43(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                         231                          262 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                         231                          262 
[1] "DEL PEAK 44(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           229                            264 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           229                            264 
[1] "DEL PEAK 45(19Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                            144                             349 
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                            144                             349 
[1] "DEL PEAK 46(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           241                            252 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           241                            252 
[1] "DEL PEAK 47(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                           274                            219 
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                           274                            219 
[1] "DEL PEAK 48(22Q11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                             93                             400 
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                             93                             400 
[1] "DEL PEAK 49(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                            125                             368 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                            125                             368 
[1] "DEL PEAK 50(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                          151                           342 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                          151                           342 
[1] "DEL PEAK 51(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                          148                           345 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                          148                           345 
[1] "DEL PEAK 52(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                          144                           349 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                          144                           349 
[1] "DEL PEAK 53(XQ22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                          111                           382 
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                          111                           382 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "COMPLETENESS_OF_RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCH_NUMBER"                          

Input Data has 23 rows and 493 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=188,	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=324,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=10,	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=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=109,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=106,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH_NUMBER':	nDistinctValues=36,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 493 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY_PERFORMANCE_SCORE"           
 [8] "HISTOLOGICAL_TYPE"                     
 [9] "RADIATIONS_RADIATION_REGIMENINDICATION"
[10] "NUMBER_PACK_YEARS_SMOKED"              
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[12] "COMPLETENESS_OF_RESECTION"             
[13] "RACE"                                  
[14] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=45, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=10, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
111 290  69  23 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
111 290  69  23 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
111 290  69  23 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
111 290  69  23 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
312 131  39   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
312 131  39   5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
312 131  39   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
312 131  39   5 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=8, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=5, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=106, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=55, binary=FALSE, numeric=TRUE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q21.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1Q21.2) MUTATED   148 100
  AMP PEAK  1(1Q21.2) WILD-TYPE 133  96
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                          248                           229 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                          100                            96 
$`AMP PEAK  1(1Q21.2) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
       75.75       117.57        23.54        92.15        31.99        36.07 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
      154.32        49.94       119.54        46.88        99.16        70.16 
TCGA-21-1077 TCGA-21-1081 TCGA-21-1082 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
       34.78         9.34       119.80        41.69        33.93        10.82 
TCGA-22-0940 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
       21.99         1.74        14.10        27.02        48.82        20.48 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 
       48.33        24.13         0.56        38.17        34.75        19.30 
TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       31.73        63.55        14.63        54.28        71.34        79.20 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 
       18.84        30.12        62.86        22.06       133.74        98.01 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 
      174.08       103.53       151.27        14.07        54.44        27.02 
TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 
        4.70         6.94       110.99        44.19        27.16         2.63 
TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 
       61.61        28.96        32.88        65.23        23.24        12.00 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 
       18.15         1.12         4.04        20.91         3.95         0.39 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        8.12         7.46         7.82         6.81         0.39         3.39 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5034 TCGA-39-5035 
       74.07        68.58        55.20        70.03        36.39        15.58 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       35.70        17.06        40.21        38.66        27.02        33.11 
TCGA-43-6143 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V 
       12.36         7.76        66.51        11.61         9.73        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 
        9.99        10.65         0.39         0.39        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 
       30.35         8.75        27.45        18.25         2.04         0.99 
TCGA-56-7730 TCGA-56-8308 TCGA-56-8504 TCGA-56-8622 TCGA-56-A4BX TCGA-58-8388 
        6.51        17.00        16.77         1.81        13.32        13.55 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       16.47        34.78        34.36        56.65        35.24        29.92 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2706 TCGA-60-2708 TCGA-60-2711 TCGA-60-2715 
       21.11        10.22        92.71        80.45        41.42        35.34 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB 
       32.32        29.85        35.90        26.83        11.77       102.67 
TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MU 
       66.61        59.97        45.57        89.29        78.28        25.41 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2755 TCGA-66-2756 
       16.96        43.10         2.01        21.07         0.92         0.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
       21.01        25.05         0.99        23.01         3.02         2.01 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 TCGA-66-2791 TCGA-66-2793 
        3.98        12.00         1.97        40.01         5.03        10.06 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        4.01        49.05         2.73        13.35        16.18        14.73 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 
       73.12        23.28        11.18        89.98        20.78         0.49 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
      106.95         0.16        15.75        86.76        53.95        37.81 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8145 TCGA-77-8148 TCGA-77-8156 
       53.92        39.09       104.09         6.97         9.63         0.33 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
      117.57        22.29        42.41        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 
       38.86        11.97        12.99         6.41        36.53        32.91 
TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
        1.38        29.95        25.15        19.04        24.13        31.56 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 
       16.87        10.09        16.77         5.29         3.09         0.72 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QQ 
        0.10        15.62        25.68        19.33        14.96        18.18 
TCGA-85-A50M TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7964 
       12.56        14.96        12.39         3.65         2.93        14.07 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       20.22        22.62        10.59         3.48         4.01         5.26 
TCGA-92-8065 TCGA-94-7557 TCGA-94-7943 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 
        2.30         0.16        11.70         5.03        14.14        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       49.87        18.31        19.36        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-MF-A522 
       27.16        18.58        20.71        19.10        16.11        11.84 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HN 
        0.07        64.08        51.78         1.22        13.74        37.22 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52N 
       24.00        14.73        29.75        83.57         0.43        33.07 
TCGA-O2-A52S TCGA-O2-A5IB 
       12.72        11.18 

$`AMP PEAK  1(1Q21.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3419 
       12.20         7.46        79.46         4.80        11.34         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-5595 TCGA-21-1076 TCGA-21-1078 
       86.96         6.18         2.79        27.19        60.89        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-A5DI 
       31.73       122.43        43.23        31.63        88.11        32.19 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-4593 TCGA-22-4604 
        7.33        14.93         4.31        64.21        35.08        13.12 
TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 TCGA-22-5477 TCGA-22-5478 
       32.02         9.57        11.77        64.93        44.25         0.79 
TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4547 TCGA-33-4589 
       11.74        56.32        16.64         7.63        79.53         1.55 
TCGA-33-6737 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASJ TCGA-34-2604 TCGA-34-2609 
       19.76         0.30        36.62       118.36        31.50        31.27 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 
       67.79        56.38         9.07        16.93        30.94         4.96 
TCGA-34-8454 TCGA-34-8456 TCGA-37-3789 TCGA-37-4129 TCGA-39-5011 TCGA-39-5019 
       27.19        26.43         0.43         6.58        47.80        44.75 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 
       60.79         1.71        24.33         1.94        27.39        35.64 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
       17.88        22.49        18.38        27.91        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
        5.46         3.81        19.59        13.38        11.77         2.93 
TCGA-43-A56U TCGA-46-6026 TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 TCGA-56-6546 
       14.20        13.91        29.95        28.96         0.10         0.62 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 
        0.99         0.43         1.45         1.32         0.85         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 
       17.49         3.48        26.89        14.07         1.35        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.18        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
       19.23        17.85        21.04        18.74         0.13         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J 
        2.76         0.03        13.25        29.95        71.24        85.12 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2709 
        3.58        12.23        96.82        37.94        21.93        49.48 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       66.54         9.01        56.91        50.33        48.49        42.64 
TCGA-60-2720 TCGA-60-2724 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN 
        3.19        23.57        70.62        58.65        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2744 
       25.28        16.37        36.16        53.88        34.59         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
        1.02         2.01        43.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 
        2.01         7.07        19.00        19.00        12.03        24.95 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 
       25.97        22.98         4.04        22.98        30.02        54.08 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-77-6842 TCGA-77-6844 TCGA-77-7142 
        6.64         6.94         8.02        29.56        75.09        42.28 
TCGA-77-7335 TCGA-77-7463 TCGA-77-8007 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 
       70.13        46.78         6.51        82.92        12.59        17.72 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       11.54        26.40        27.39        54.41        65.49        35.90 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-85-6175 TCGA-85-7697 TCGA-85-7698 
      126.18       132.36         5.92         9.67        34.95        31.30 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
        1.15        18.94        14.07        34.52         0.76        13.22 
TCGA-85-8350 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       22.45        32.71         2.01         7.76        14.63        13.94 
TCGA-85-8584 TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 
       12.59        17.72        24.36        19.73        16.21        15.85 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-92-7340 TCGA-94-7033 
        0.79        24.92         9.50        11.77         2.70        21.04 
TCGA-94-8035 TCGA-94-8491 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL 
        4.01        26.63        16.14        57.07        17.46        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
        8.42         2.76         3.88        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF 
       21.21        20.32        12.89        13.18        13.41         4.54 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HT 
       45.37         4.21         2.89        39.85        30.58        22.78 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W 
       65.49         3.65        16.80         3.72        43.89         8.58 
TCGA-XC-AA0X 
        0.20 

  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                       174.08                        132.36 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                        21.04                         17.72 
[1] "0.1 - 174.1 (21.0)" "0.0 - 132.4 (17.7)"
[1] "hr=" "1.3"
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1Q21.2) MUTATED         1       34       84        1        30
  AMP PEAK  1(1Q21.2) WILD-TYPE       1       53       67        1        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1Q21.2) MUTATED          49         2         35         12
  AMP PEAK  1(1Q21.2) WILD-TYPE        43         1         27          9
                               vv
clus                            STAGE IV
  AMP PEAK  1(1Q21.2) MUTATED          6
  AMP PEAK  1(1Q21.2) WILD-TYPE        1
D1V3, multiclass
            clus
vv           AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            34                            53
  STAGE IB                            84                            67
  STAGE II                             1                             1
  STAGE IIA                           30                            33
  STAGE IIB                           49                            43
  STAGE III                            2                             1
  STAGE IIIA                          35                            27
  STAGE IIIB                          12                             9
  STAGE IV                             6                             1
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  1(1Q21.2) MUTATED    45 156  37  16
  AMP PEAK  1(1Q21.2) WILD-TYPE  66 134  32   7
D1V4, multiclass
    clus
vv   AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  T1                          45                            66
  T2                         156                           134
  T3                          37                            32
  T4                          16                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  1(1Q21.2) MUTATED   157  68  25   1
  AMP PEAK  1(1Q21.2) WILD-TYPE 155  63  14   4
D1V5, multiclass
    clus
vv   AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  N0                         157                           155
  N1                          68                            63
  N2                          25                            14
  N3                           1                             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"
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.2) MUTATED   215   6
  AMP PEAK  1(1Q21.2) WILD-TYPE 189   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED    215    6
  AMP PEAK  1(1Q21.2) WILD-TYPE  189    1
   clus
vv  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  0                         215                           189
  1                           6                             1
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.2) MUTATED    58 196
  AMP PEAK  1(1Q21.2) WILD-TYPE  69 170
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED     58  196
  AMP PEAK  1(1Q21.2) WILD-TYPE   69  170
        clus
vv       AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  FEMALE                          58                            69
  MALE                           196                           170
[1] 2 2
[1] FALSE
D1V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(1Q21.2) MUTATED                                      13
  AMP PEAK  1(1Q21.2) WILD-TYPE                                     2
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(1Q21.2) MUTATED                                         0
  AMP PEAK  1(1Q21.2) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  1(1Q21.2) MUTATED                                        2
  AMP PEAK  1(1Q21.2) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  1(1Q21.2) MUTATED                                         1
  AMP PEAK  1(1Q21.2) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1Q21.2) MUTATED                                                           238
  AMP PEAK  1(1Q21.2) WILD-TYPE                                                         232
D1V9, multiclass
                                                             clus
vv                                                            AMP PEAK  1(1Q21.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         238
                                                             clus
vv                                                            AMP PEAK  1(1Q21.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   2
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           232
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.2) MUTATED     8 246
  AMP PEAK  1(1Q21.2) WILD-TYPE   5 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED      8  246
  AMP PEAK  1(1Q21.2) WILD-TYPE    5  234
     clus
vv    AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  NO                            8                             5
  YES                         246                           234
[1] 2 2
[1] FALSE
D1V11, continuous
D1V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1Q21.2) MUTATED   207   7   1  10
  AMP PEAK  1(1Q21.2) WILD-TYPE 187   5   3  12
D1V13, multiclass
    clus
vv   AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  R0                         207                           187
  R1                           7                             5
  R2                           1                             3
  RX                          10                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q21.2) MUTATED       4                        14   181
  AMP PEAK  1(1Q21.2) WILD-TYPE     5                        17   159
D1V14, multiclass
                           clus
vv                          AMP PEAK  1(1Q21.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          14
  WHITE                                             181
                           clus
vv                          AMP PEAK  1(1Q21.2) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            17
  WHITE                                               159
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.2) MUTATED     5 160
  AMP PEAK  1(1Q21.2) WILD-TYPE   3 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED      5  160
  AMP PEAK  1(1Q21.2) WILD-TYPE    3  149
                        clus
vv                       AMP PEAK  1(1Q21.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         160
                        clus
vv                       AMP PEAK  1(1Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           149
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(2P16.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(2P16.1) MUTATED   162  99
  AMP PEAK  2(2P16.1) WILD-TYPE 119  97
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                          261                           216 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                           99                            97 
$`AMP PEAK  2(2P16.1) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
        7.46        79.46       117.57        11.34        23.54        92.15 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-21-1071 TCGA-21-1072 
       31.99        36.07         1.64        86.96        46.88        99.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1081 TCGA-21-1083 TCGA-21-5783 
       60.89        34.78        31.73         9.34        43.23        88.11 
TCGA-21-5786 TCGA-21-A5DI TCGA-22-4591 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
       33.93        32.19        20.48        24.13        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 
       13.12        32.02        11.77        31.73        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 
       44.25         0.79        54.28        71.34        18.84        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4566 TCGA-33-4582 
       56.32        16.64        22.06         7.63       174.08       103.53 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 
       27.02         4.70       110.99       118.36         2.63        61.61 
TCGA-34-2604 TCGA-34-2605 TCGA-34-5231 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 
       31.50        28.96        65.23         9.07        12.00        16.93 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       18.15         1.12        27.19         4.04        26.43        20.91 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-37-4141 TCGA-39-5011 
        3.95         0.39         8.12         7.82         0.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5028 TCGA-39-5031 TCGA-39-5035 
       74.07        44.75        60.79         1.71        27.39        15.58 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       35.64        35.70        17.06        40.21        38.66        27.02 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-7658 
       33.11        18.38        27.91        12.36        24.89        66.51 
TCGA-43-8115 TCGA-43-8118 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
       13.38         2.93         9.99        10.65         0.39         0.39 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 
       29.95         5.46        30.35         8.75        28.96        18.25 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
        2.04         0.62         0.43         0.99         1.45         0.85 
TCGA-56-7730 TCGA-56-8304 TCGA-56-8308 TCGA-56-8503 TCGA-56-8504 TCGA-56-8628 
        6.51         3.48        17.00         1.35        16.77        20.25 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8387 
       15.81        19.23        13.32        17.85         0.26        13.25 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       71.24        16.47        34.36        56.65        35.24        29.92 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       10.22        96.82        80.45        41.42         9.01        35.34 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB 
       42.64        29.85        35.90        23.57        11.77       102.67 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR 
       66.61        58.65        59.97        45.57        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       78.28        16.37        25.41        36.16        53.88        34.59 
TCGA-66-2737 TCGA-66-2755 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 
        2.01         0.92        21.01         0.99         1.02         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 
        7.07        23.01        19.00         3.02         2.01         3.98 
TCGA-66-2787 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
       40.01         4.04         5.03        30.02        10.06        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-A59I 
        4.01        49.05         2.73         6.64         8.02        16.18 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 
       29.56        23.28        11.18        89.98        20.78         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 TCGA-77-8009 TCGA-77-8130 
       42.28        70.13       106.95        15.75        53.95        82.92 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 
       53.92        39.09       104.09        26.40         6.97         9.63 
TCGA-77-8150 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA 
       54.41         0.33       132.36       117.57        42.41        42.08 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
       27.62        38.86         9.67        11.97         6.41        36.53 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 
        1.15        29.95        24.13        31.56        16.87        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 TCGA-85-8664 
       10.09         0.76        22.45         5.29        32.71         0.10 
TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50M 
       15.62        19.33        17.72        14.96        19.73        12.56 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE 
       15.85        14.96         3.65         2.93        11.77        22.62 
TCGA-92-7341 TCGA-92-8064 TCGA-94-7557 TCGA-94-7943 TCGA-94-8490 TCGA-94-8491 
        3.48         5.26         0.16        11.70         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK 
       14.14        16.14        17.69        57.07        18.31        19.36 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53I 
        8.42        30.81        30.67        21.34        27.16        18.58 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HD 
       20.71        19.10        16.11        13.18        11.84         0.07 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN 
       51.78         1.22         4.21         2.89        39.85        37.22 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52N 
       24.00        14.73        29.75        83.57         0.43        33.07 
TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       43.89         8.58         0.20 

$`AMP PEAK  2(2P16.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3410 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       12.20        75.75         4.80         6.18         2.79       154.32 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1075 TCGA-21-1078 TCGA-21-1080 
       49.94        27.19       119.54        70.16        15.58       122.43 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
      119.80        31.63        41.69        10.82        21.99         7.33 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       14.93         4.31        64.21         1.74        14.10        27.02 
TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4607 TCGA-22-4609 
       48.82        35.08        48.33         0.56        19.30         9.57 
TCGA-22-5472 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-33-4533 TCGA-33-4538 
       64.93        79.20        11.74        30.12       133.74        98.01 
TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
       79.53       151.27        14.07        54.44         1.55        19.76 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-2608 
        0.30        36.62         6.94        44.19        27.16        32.88 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-34-5929 
       31.27        67.79        56.38        23.24        30.94         4.96 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 TCGA-37-5819 TCGA-39-5021 
        0.43         6.58         7.46         6.81         3.39        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5039 
       55.20        70.03        24.33         1.94        36.39        17.88 
TCGA-43-2578 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 
       22.49        21.47         5.46         3.81        19.59         7.76 
TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 
       11.77        11.61         9.73        14.20        12.03        13.91 
TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7580 TCGA-56-7731 
       28.34        27.45         0.10         0.99         1.32         0.10 
TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       17.49        26.89        14.07         1.81        22.75         1.18 
TCGA-56-8625 TCGA-56-8626 TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
       10.36         9.93        20.94        21.04        18.74         0.13 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J 
        2.76         0.03        13.55        29.95        34.78        85.12 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       21.11         3.58        12.23        37.94        92.71        21.93 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 
       49.48        66.54        56.91        50.33        48.49         3.19 
TCGA-60-2721 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-66-2727 
       32.32        26.83        70.62        14.99        11.34        16.96 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 
       43.10        21.07         0.99         1.02         2.01         0.99 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 TCGA-66-2778 TCGA-66-2780 
       43.99        25.05         2.01         2.01        19.00        12.03 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2790 
       12.00        24.95         1.97        25.97        22.98        22.98 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-7338 
        6.94        13.35        14.73        73.12        75.09         0.16 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 TCGA-77-8138 
       46.78         6.51        86.76        37.81        12.59        17.72 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G6 
       11.54        27.39        65.49        35.90       126.18        22.29 
TCGA-77-A5G7 TCGA-77-A5GB TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
        5.92        30.81        12.99        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8288 
        1.38        18.94        25.15        19.04        14.07        13.22 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
       16.77         3.09         2.01         0.72         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z 
       13.94        12.59        25.68        24.36        18.18        16.21 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED 
        0.79        12.39        24.92         9.50        14.07        20.22 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 
       10.59         2.70         4.01         2.30        21.04         4.01 
TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8020 TCGA-98-A539 TCGA-98-A53A 
       49.87        17.46        16.57         2.76         3.88        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A7SW 
        2.01        27.02        21.21        20.32        12.89        13.41 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HO TCGA-NC-A5HT 
       64.08         4.54        45.37        13.74        30.58        22.78 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB 
       65.49         3.65        16.80         3.72        12.72        11.18 

  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                       174.08                        154.32 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                        20.71                         17.80 
[1] "0.1 - 174.1 (20.7)" "0.0 - 154.3 (17.8)"
[1] "hr=" "1.3"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(2P16.1) MUTATED         2       41       75        2        38
  AMP PEAK  2(2P16.1) WILD-TYPE       0       46       76        0        25
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(2P16.1) MUTATED          56         0         35         14
  AMP PEAK  2(2P16.1) WILD-TYPE        36         3         27          7
                               vv
clus                            STAGE IV
  AMP PEAK  2(2P16.1) MUTATED          4
  AMP PEAK  2(2P16.1) WILD-TYPE        3
D2V3, multiclass
            clus
vv           AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                            41                            46
  STAGE IB                            75                            76
  STAGE II                             2                             0
  STAGE IIA                           38                            25
  STAGE IIB                           56                            36
  STAGE III                            0                             3
  STAGE IIIA                          35                            27
  STAGE IIIB                          14                             7
  STAGE IV                             4                             3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  2(2P16.1) MUTATED    54 157  41  17
  AMP PEAK  2(2P16.1) WILD-TYPE  57 133  28   6
D2V4, multiclass
    clus
vv   AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  T1                          54                            57
  T2                         157                           133
  T3                          41                            28
  T4                          17                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK  2(2P16.1) MUTATED   161  85  19   3
  AMP PEAK  2(2P16.1) WILD-TYPE 151  46  20   2
D2V5, multiclass
    clus
vv   AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  N0                         161                           151
  N1                          85                            46
  N2                          19                            20
  N3                           3                             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"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(2P16.1) MUTATED   228   4
  AMP PEAK  2(2P16.1) WILD-TYPE 176   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED    228    4
  AMP PEAK  2(2P16.1) WILD-TYPE  176    3
   clus
vv  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  0                         228                           176
  1                           4                             3
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(2P16.1) MUTATED    56 213
  AMP PEAK  2(2P16.1) WILD-TYPE  71 153
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED     56  213
  AMP PEAK  2(2P16.1) WILD-TYPE   71  153
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  FEMALE                          56                            71
  MALE                           213                           153
[1] 2 2
[1] FALSE
D2V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(2P16.1) MUTATED                                      12
  AMP PEAK  2(2P16.1) WILD-TYPE                                     3
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(2P16.1) MUTATED                                         1
  AMP PEAK  2(2P16.1) WILD-TYPE                                       0
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  2(2P16.1) MUTATED                                        1
  AMP PEAK  2(2P16.1) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  2(2P16.1) MUTATED                                         0
  AMP PEAK  2(2P16.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(2P16.1) MUTATED                                                           255
  AMP PEAK  2(2P16.1) WILD-TYPE                                                         215
D2V9, multiclass
                                                             clus
vv                                                            AMP PEAK  2(2P16.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         255
                                                             clus
vv                                                            AMP PEAK  2(2P16.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           215
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
                               cls
clus                              0   1
  AMP PEAK  2(2P16.1) MUTATED     8 261
  AMP PEAK  2(2P16.1) WILD-TYPE   5 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED      8  261
  AMP PEAK  2(2P16.1) WILD-TYPE    5  219
     clus
vv    AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  NO                            8                             5
  YES                         261                           219
[1] 2 2
[1] FALSE
D2V11, continuous
D2V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(2P16.1) MUTATED   221   6   1  10
  AMP PEAK  2(2P16.1) WILD-TYPE 173   6   3  12
D2V13, multiclass
    clus
vv   AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  R0                         221                           173
  R1                           6                             6
  R2                           1                             3
  RX                          10                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(2P16.1) MUTATED       5                        12   188
  AMP PEAK  2(2P16.1) WILD-TYPE     4                        19   152
D2V14, multiclass
                           clus
vv                          AMP PEAK  2(2P16.1) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             188
                           clus
vv                          AMP PEAK  2(2P16.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            19
  WHITE                                               152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, binary
                               cls
clus                              0   1
  AMP PEAK  2(2P16.1) MUTATED     1 164
  AMP PEAK  2(2P16.1) WILD-TYPE   7 145
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED      1  164
  AMP PEAK  2(2P16.1) WILD-TYPE    7  145
                        clus
vv                       AMP PEAK  2(2P16.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         164
                        clus
vv                       AMP PEAK  2(2P16.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           145
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(2Q31.2) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(2Q31.2) MUTATED    95  71
  AMP PEAK  3(2Q31.2) WILD-TYPE 186 125
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                          166                           311 
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                           71                           125 
$`AMP PEAK  3(2Q31.2) MUTATED`
TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
       79.46       117.57        11.34        92.15        31.99        36.07 
TCGA-18-3421 TCGA-18-4721 TCGA-21-1072 TCGA-21-1081 TCGA-21-1083 TCGA-21-A5DI 
       86.96       154.32        99.16         9.34        43.23        32.19 
TCGA-22-0944 TCGA-22-1012 TCGA-22-1017 TCGA-22-4594 TCGA-22-4601 TCGA-22-4605 
        7.33        14.10        48.82        48.33        34.75        32.02 
TCGA-22-4613 TCGA-22-5474 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 
       11.77        14.63        18.84        62.86        56.32         7.63 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-6737 
       98.01       174.08       103.53       151.27        54.44        19.76 
TCGA-33-6738 TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 
       27.02       110.99       118.36         2.63        61.61        28.96 
TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-7107 TCGA-34-8455 TCGA-34-A5IX 
        9.07        12.00        16.93         1.12         4.04        20.91 
TCGA-37-3792 TCGA-37-4130 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        0.39         8.12        47.80        74.07        44.75        68.58 
TCGA-39-5029 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 
       24.33        15.58        35.64        35.70        17.06        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-A474 
       27.02        33.11        18.38        27.91        12.36        11.61 
TCGA-46-3768 TCGA-46-6025 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 
        9.99        10.65        30.35         8.75        28.96         0.10 
TCGA-56-5898 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
       18.25         0.62         0.43         0.99         1.45         0.85 
TCGA-56-8504 TCGA-56-8629 TCGA-56-A5DS TCGA-58-8391 TCGA-58-A46K TCGA-58-A46N 
       16.77        15.81         0.26        71.24        34.36        29.92 
TCGA-60-2703 TCGA-60-2708 TCGA-60-2712 TCGA-60-2719 TCGA-60-2726 TCGA-63-A5MB 
       96.82        80.45         9.01        42.64        11.77       102.67 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MS TCGA-63-A5MU TCGA-63-A5MW TCGA-66-2727 
       58.65        59.97        78.28        25.41        53.88        16.96 
TCGA-66-2754 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2770 TCGA-66-2773 
        2.01        21.01        25.05         1.02        23.01         3.02 
TCGA-66-2785 TCGA-66-2791 TCGA-66-2792 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59J 
        1.97         5.03        30.02         2.73         6.64        14.73 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7140 TCGA-77-7142 TCGA-77-7338 TCGA-77-8009 
       29.56        23.28        20.78        42.28         0.16        53.95 
TCGA-77-8130 TCGA-77-8139 TCGA-77-8145 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 
       82.92       104.09         6.97        54.41        65.49         0.33 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
      132.36       117.57        42.08        38.86         9.67        11.97 
TCGA-85-6798 TCGA-85-7698 TCGA-85-7844 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 
        6.41        31.30        29.95        31.56        16.87        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 TCGA-85-8354 TCGA-85-8666 TCGA-85-A4CN 
       10.09         0.76         5.29        32.71        15.62        19.33 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7769 
       19.73        12.56        15.85        14.96         3.65        11.77 
TCGA-90-7964 TCGA-92-7341 TCGA-94-7557 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 
       14.07         3.48         0.16         5.03        26.63        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53I 
       57.07        19.36         2.76        27.16        18.15        18.58 
TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       20.71        16.11        13.18        11.84         0.07        64.08 
TCGA-NC-A5HG TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NK-A5CR 
       51.78         4.21         2.89        37.22        30.58        83.57 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52W 
        0.43        33.07        12.72         8.58 

$`AMP PEAK  3(2Q31.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3414 TCGA-18-3419 
       12.20         7.46        75.75         4.80        23.54         1.64 
TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
        6.18         2.79        49.94        27.19       119.54        46.88 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       70.16        60.89        34.78        15.58        31.73       122.43 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
      119.80        31.63        88.11        41.69        33.93        10.82 
TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
       21.99        14.93         4.31        64.21         1.74        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
       20.48        35.08        24.13         0.56        38.17        13.12 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 
       19.30         9.57        31.73        64.93        63.55        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 
        0.79        54.28        71.34        79.20        11.74        30.12 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4547 TCGA-33-4586 TCGA-33-4589 
       16.64        22.06       133.74        79.53        14.07         1.55 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL 
        4.70         0.30        36.62         6.94        44.19        27.16 
TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       31.50        32.88        31.27        65.23        67.79        56.38 
TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 
       23.24        30.94        18.15         4.96        27.19        26.43 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        3.95         0.43         6.58         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
        0.39         3.39        55.20        70.03        60.79         1.71 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 
        1.94        27.39        36.39        17.88        40.21        22.49 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 
       24.89        21.47         5.46         3.81        19.59         7.76 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U 
       66.51        13.38        11.77         2.93         9.73        14.20 
TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       12.03        13.91         0.39         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7812 TCGA-56-6545 TCGA-56-7221 TCGA-56-7580 TCGA-56-7730 
        5.46        27.45         2.04         0.99         1.32         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.10        17.49         3.48        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35         1.81        22.75         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
       20.25        20.94        19.23        13.32        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       18.74         0.13         2.76         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
       29.95        16.47        34.78        85.12        56.65        35.24 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 
       21.11         3.58        12.23        10.22        37.94        92.71 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
       21.93        49.48        66.54        41.42        56.91        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
       35.34        48.49         3.19        32.32        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5ML TCGA-63-A5MM 
       23.57        26.83        70.62        66.61        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MY 
       11.34        25.28        89.29        16.37        36.16        34.59 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 
       43.10         2.01        21.07         0.99         1.02         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 
        0.99        43.99         0.99         2.01         2.01         2.01 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        7.07        19.00         2.01        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
       12.00        24.95        25.97        40.01        22.98         4.04 
TCGA-66-2790 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 
       22.98        10.06        54.08         4.01        49.05         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 
        8.02        13.35        16.18        73.12        75.09        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 
       89.98         0.49        70.13       106.95        46.78        15.75 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        6.51        86.76        37.81        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8154 
       17.72        11.54        26.40        27.39         9.63        35.90 
TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GF 
      126.18        22.29         5.92        42.41        30.81        27.62 
TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       12.99        36.53        34.95        32.91         1.38         1.15 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8288 
       18.94        25.15        19.04        24.13        14.07        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       22.45        16.77         3.09         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JB 
       14.63        13.94        12.59         0.10        25.68        17.72 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A513 TCGA-85-A53L 
       14.96        24.36        18.18        16.21         0.79        12.39 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       24.92         9.50         2.93        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
        2.70         4.01         5.26         2.30        21.04        11.70 
TCGA-94-8035 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
        4.01        14.14        17.69        49.87        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 
       16.57         8.42        30.81        30.67        21.34         3.88 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH TCGA-L3-A4E7 
        2.01        27.02        21.21        20.32        19.10        12.89 
TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HM 
       13.41         4.54         1.22        45.37        13.74        39.85 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX 
       24.00        14.73        29.75        22.78        65.49         3.65 
TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       16.80         3.72        43.89        11.18         0.20 

  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                         0.07                          0.03 
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                       174.08                        133.74 
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                       20.745                        18.740 
[1] "0.1 - 174.1 (20.7)" "0.0 - 133.7 (18.7)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(2Q31.2) MUTATED         2       22       56        1        20
  AMP PEAK  3(2Q31.2) WILD-TYPE       0       65       95        1        43
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(2Q31.2) MUTATED          33         1         27          4
  AMP PEAK  3(2Q31.2) WILD-TYPE        59         2         35         17
                               vv
clus                            STAGE IV
  AMP PEAK  3(2Q31.2) MUTATED          2
  AMP PEAK  3(2Q31.2) WILD-TYPE        5
D3V3, multiclass
            clus
vv           AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                            22                            65
  STAGE IB                            56                            95
  STAGE II                             1                             1
  STAGE IIA                           20                            43
  STAGE IIB                           33                            59
  STAGE III                            1                             2
  STAGE IIIA                          27                            35
  STAGE IIIB                           4                            17
  STAGE IV                             2                             5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  3(2Q31.2) MUTATED    33 106  23   8
  AMP PEAK  3(2Q31.2) WILD-TYPE  78 184  46  15
D3V4, multiclass
    clus
vv   AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  T1                          33                            78
  T2                         106                           184
  T3                          23                            46
  T4                           8                            15
[1] 4 2
[1] TRUE
[1] "dimension of 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(2Q31.2) MUTATED   104  48  17   1
  AMP PEAK  3(2Q31.2) WILD-TYPE 208  83  22   4
D3V5, multiclass
    clus
vv   AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  N0                         104                           208
  N1                          48                            83
  N2                          17                            22
  N3                           1                             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"
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(2Q31.2) MUTATED   143   2
  AMP PEAK  3(2Q31.2) WILD-TYPE 261   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q31.2) MUTATED    143    2
  AMP PEAK  3(2Q31.2) WILD-TYPE  261    5
   clus
vv  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  0                         143                           261
  1                           2                             5
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(2Q31.2) MUTATED    34 136
  AMP PEAK  3(2Q31.2) WILD-TYPE  93 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q31.2) MUTATED     34  136
  AMP PEAK  3(2Q31.2) WILD-TYPE   93  230
        clus
vv       AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  FEMALE                          34                            93
  MALE                           136                           230
[1] 2 2
[1] FALSE
D3V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(2Q31.2) MUTATED                                       7
  AMP PEAK  3(2Q31.2) WILD-TYPE                                     8
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(2Q31.2) MUTATED                                         0
  AMP PEAK  3(2Q31.2) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  3(2Q31.2) MUTATED                                        1
  AMP PEAK  3(2Q31.2) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  3(2Q31.2) MUTATED                                         1
  AMP PEAK  3(2Q31.2) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(2Q31.2) MUTATED                                                           161
  AMP PEAK  3(2Q31.2) WILD-TYPE                                                         309
D3V9, multiclass
                                                             clus
vv                                                            AMP PEAK  3(2Q31.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         161
                                                             clus
vv                                                            AMP PEAK  3(2Q31.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           309
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                               cls
clus                              0   1
  AMP PEAK  3(2Q31.2) MUTATED     3 167
  AMP PEAK  3(2Q31.2) WILD-TYPE  10 313
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q31.2) MUTATED      3  167
  AMP PEAK  3(2Q31.2) WILD-TYPE   10  313
     clus
vv    AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  NO                            3                            10
  YES                         167                           313
[1] 2 2
[1] FALSE
D3V11, continuous
D3V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(2Q31.2) MUTATED   136   4   0   5
  AMP PEAK  3(2Q31.2) WILD-TYPE 258   8   4  17
D3V13, multiclass
    clus
vv   AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  R0                         136                           258
  R1                           4                             8
  R2                           0                             4
  RX                           5                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(2Q31.2) MUTATED       2                         9   123
  AMP PEAK  3(2Q31.2) WILD-TYPE     7                        22   217
D3V14, multiclass
                           clus
vv                          AMP PEAK  3(2Q31.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             123
                           clus
vv                          AMP PEAK  3(2Q31.2) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            22
  WHITE                                               217
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                               cls
clus                              0   1
  AMP PEAK  3(2Q31.2) MUTATED     3 109
  AMP PEAK  3(2Q31.2) WILD-TYPE   5 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q31.2) MUTATED      3  109
  AMP PEAK  3(2Q31.2) WILD-TYPE    5  200
                        clus
vv                       AMP PEAK  3(2Q31.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         109
                        clus
vv                       AMP PEAK  3(2Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           200
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(3Q26.33) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  4(3Q26.33) MUTATED   261 169
  AMP PEAK  4(3Q26.33) WILD-TYPE  20  27
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           430                             47 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           169                             27 
$`AMP PEAK  4(3Q26.33) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
       11.34        23.54        92.15        31.99        36.07         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
       86.96         6.18         2.79       154.32        49.94        27.19 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
      119.54        46.88        99.16        70.16        60.89        34.78 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       31.73       122.43         9.34       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
       88.11        41.69        33.93        10.82        32.19        21.99 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
        7.33        14.93         4.31        14.10        27.02        20.48 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       35.08        24.13        38.17        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 
       14.63        44.25        54.28        71.34        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 
       30.12        62.86        56.32        16.64         7.63       133.74 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       98.01        79.53       174.08       103.53       151.27        14.07 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       54.44         1.55        27.02         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 
        6.94       110.99        44.19       118.36        27.16         2.63 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
       61.61        31.50        28.96        32.88        31.27        65.23 
TCGA-34-5232 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       67.79         9.07        12.00        16.93        30.94        18.15 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
        4.96         1.12        27.19         4.04        26.43        20.91 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        3.95         0.43         0.39         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        6.81         0.39         3.39        74.07        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        70.03        60.79         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
       27.39        15.58        35.64        35.70        17.06        40.21 
TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       22.49        27.02        33.11        27.91        12.36        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       21.47         5.46        19.59         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
       11.77         2.93        11.61         9.73        14.20        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        9.99        10.65        13.91         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 
       28.34         5.46        30.35         8.75        28.96         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       18.25         2.04         0.99         0.43         0.99         1.45 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        1.32         0.85         6.51         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
       26.89        17.00        14.07         1.35        16.77         1.81 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.18        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
       19.23        13.32        17.85        21.04        18.74         0.13 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
        0.26         2.76         0.03        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       71.24        16.47        34.78        85.12        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       35.24        29.92        21.11        10.22        96.82        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       92.71        21.93        80.45        49.48        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2719 TCGA-60-2721 
        9.01        56.91        50.33        35.34        42.64        32.32 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB 
       29.85        35.90        23.57        26.83        11.77       102.67 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR 
       66.61        58.65        59.97        45.57        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       78.28        16.37        25.41        36.16        53.88        34.59 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       16.96        43.10         2.01        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        2.01         0.92         0.99        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
        0.99         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
       23.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
        3.98        12.00        24.95        25.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        4.04        22.98         5.03        30.02        10.06        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
        4.01        49.05         2.73         6.64         6.94         8.02 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       13.35        16.18        14.73        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
       23.28        11.18        89.98        20.78         0.49        42.28 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 
       70.13       106.95         0.16        46.78        15.75        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       53.95        37.81        82.92        53.92        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
      104.09        11.54        26.40        27.39         6.97         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 
       54.41        65.49        35.90         0.33       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
       22.29         5.92        42.41        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       38.86         9.67        11.97        12.99         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
       34.95        31.30        32.91         1.38         1.15        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       18.94        25.15        19.04        24.13        31.56        14.07 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       16.87        34.52        10.09         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       16.77         5.29         3.09        32.71         2.01         0.72 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
        7.76        14.63        13.94         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z 
       19.33        17.72        14.96        18.18        19.73        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
       15.85        14.96        12.39         3.65         9.50         2.93 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
       11.77        14.07        22.62        10.59         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        4.01         5.26         2.30        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
        4.01         5.03        26.63        14.14        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-7454 
       49.87        57.07        18.31        17.46        19.36         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        2.76        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       18.15         2.01        18.58        20.71        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       16.11        13.18        13.41        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
        4.54        51.78         1.22        45.37        13.74         4.21 
TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
        2.89        39.85        37.22        30.58        24.00        14.73 
TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N 
       29.75        83.57         3.65        16.80         0.43        33.07 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       12.72        43.89         8.58         0.20 

$`AMP PEAK  4(3Q26.33) WILD-TYPE`
TCGA-21-1078 TCGA-22-1005 TCGA-22-1011 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 
       15.58        64.21         1.74        48.82        48.33         0.56 
TCGA-22-5478 TCGA-22-5481 TCGA-22-A5C4 TCGA-33-6737 TCGA-34-5234 TCGA-34-5239 
        0.79        79.20        22.06        19.76        56.38        23.24 
TCGA-37-4129 TCGA-39-5011 TCGA-39-5034 TCGA-39-5039 TCGA-43-2581 TCGA-43-5668 
        6.58        47.80        36.39        17.88        38.66        18.38 
TCGA-43-6773 TCGA-52-7812 TCGA-56-6546 TCGA-56-8623 TCGA-60-2696 TCGA-60-2697 
        3.81        27.45         0.62        22.75         3.58        12.23 
TCGA-60-2716 TCGA-60-2720 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-66-2785 
       48.49         3.19        70.62        14.99        11.34         1.97 
TCGA-77-8007 TCGA-77-8131 TCGA-77-A5FZ TCGA-85-8584 TCGA-85-A4PA TCGA-85-A50M 
        6.51        12.59       126.18        12.59        24.36        12.56 
TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED TCGA-96-A4JL TCGA-98-A53C TCGA-98-A53D 
        0.79        24.92        20.22        16.57        27.02        21.21 
TCGA-98-A53H TCGA-NC-A5HT TCGA-NK-A5CT TCGA-O2-A52Q TCGA-O2-A5IB 
       20.32        22.78        65.49         3.72        11.18 

  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                          0.03                           0.56 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                        174.08                         126.18 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                         19.07                          19.76 
[1] "0.0 - 174.1 (19.1)" "0.6 - 126.2 (19.8)"
[1] "hr=" "1.6"
D4V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(3Q26.33) MUTATED         2       79      138        2        52
  AMP PEAK  4(3Q26.33) WILD-TYPE       0        8       13        0        11
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(3Q26.33) MUTATED          83         1         58         19
  AMP PEAK  4(3Q26.33) WILD-TYPE         9         2          4          2
                                vv
clus                             STAGE IV
  AMP PEAK  4(3Q26.33) MUTATED          7
  AMP PEAK  4(3Q26.33) WILD-TYPE        0
D4V3, multiclass
            clus
vv           AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             79                              8
  STAGE IB                            138                             13
  STAGE II                              2                              0
  STAGE IIA                            52                             11
  STAGE IIB                            83                              9
  STAGE III                             1                              2
  STAGE IIIA                           58                              4
  STAGE IIIB                           19                              2
  STAGE IV                              7                              0
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  4(3Q26.33) MUTATED   100 263  60  21
  AMP PEAK  4(3Q26.33) WILD-TYPE  11  27   9   2
D4V4, multiclass
    clus
vv   AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  T1                          100                             11
  T2                          263                             27
  T3                           60                              9
  T4                           21                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  4(3Q26.33) MUTATED   281 119  35   5
  AMP PEAK  4(3Q26.33) WILD-TYPE  31  12   4   0
D4V5, multiclass
    clus
vv   AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  N0                          281                             31
  N1                          119                             12
  N2                           35                              4
  N3                            5                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED   363   7
  AMP PEAK  4(3Q26.33) WILD-TYPE  41   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED    363    7
  AMP PEAK  4(3Q26.33) WILD-TYPE   41    0
   clus
vv  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  0                          363                             41
  1                            7                              0
[1] 2 2
[1] FALSE
D4V7, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED   108 336
  AMP PEAK  4(3Q26.33) WILD-TYPE  19  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED    108  336
  AMP PEAK  4(3Q26.33) WILD-TYPE   19   30
        clus
vv       AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  FEMALE                          108                             19
  MALE                            336                             30
[1] 2 2
[1] FALSE
D4V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(3Q26.33) MUTATED                                      15
  AMP PEAK  4(3Q26.33) WILD-TYPE                                     0
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(3Q26.33) MUTATED                                         1
  AMP PEAK  4(3Q26.33) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  4(3Q26.33) MUTATED                                        3
  AMP PEAK  4(3Q26.33) WILD-TYPE                                      3
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  4(3Q26.33) MUTATED                                         1
  AMP PEAK  4(3Q26.33) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(3Q26.33) MUTATED                                                           424
  AMP PEAK  4(3Q26.33) WILD-TYPE                                                          46
D4V9, multiclass
                                                             clus
vv                                                            AMP PEAK  4(3Q26.33) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 15
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          424
                                                             clus
vv                                                            AMP PEAK  4(3Q26.33) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    0
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED    13 431
  AMP PEAK  4(3Q26.33) WILD-TYPE   0  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED     13  431
  AMP PEAK  4(3Q26.33) WILD-TYPE    0   49
     clus
vv    AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  NO                            13                              0
  YES                          431                             49
[1] 2 2
[1] FALSE
D4V11, continuous
D4V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  4(3Q26.33) MUTATED   358  11   4  19
  AMP PEAK  4(3Q26.33) WILD-TYPE  36   1   0   3
D4V13, multiclass
    clus
vv   AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  R0                          358                             36
  R1                           11                              1
  R2                            4                              0
  RX                           19                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3Q26.33) MUTATED       6                        29   307
  AMP PEAK  4(3Q26.33) WILD-TYPE     3                         2    33
D4V14, multiclass
                           clus
vv                          AMP PEAK  4(3Q26.33) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           29
  WHITE                                              307
                           clus
vv                          AMP PEAK  4(3Q26.33) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED     7 278
  AMP PEAK  4(3Q26.33) WILD-TYPE   1  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED      7  278
  AMP PEAK  4(3Q26.33) WILD-TYPE    1   31
                        clus
vv                       AMP PEAK  4(3Q26.33) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          278
                        clus
vv                       AMP PEAK  4(3Q26.33) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             31
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(4Q12) MUTATION ANALYSIS
D5V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  5(4Q12) MUTATED    69  44
  AMP PEAK  5(4Q12) WILD-TYPE 212 152
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                        113                         364 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         44                         152 
$`AMP PEAK  5(4Q12) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3416 
        7.46        79.46         4.80       117.57        11.34        31.99 
TCGA-21-1075 TCGA-21-1082 TCGA-21-5782 TCGA-21-5786 TCGA-22-1017 TCGA-22-4591 
       70.16       119.80        31.63        33.93        48.82        20.48 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 TCGA-22-5478 TCGA-22-5481 
       35.08        24.13        34.75        13.12         0.79        79.20 
TCGA-22-A5C4 TCGA-33-4566 TCGA-33-4582 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASB 
       22.06       174.08       103.53        27.02         4.70         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 
      110.99        44.19       118.36         2.63        28.96        31.27 
TCGA-34-5236 TCGA-34-5241 TCGA-34-5928 TCGA-34-8456 TCGA-37-3789 TCGA-37-4130 
        9.07        16.93        18.15        26.43         0.43         8.12 
TCGA-37-4135 TCGA-39-5016 TCGA-39-5019 TCGA-39-5031 TCGA-43-2576 TCGA-43-2578 
        6.81        74.07        44.75        27.39        40.21        22.49 
TCGA-43-3920 TCGA-43-6647 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A56U 
       33.11        24.89         7.76        66.51         2.93        14.20 
TCGA-43-A56V TCGA-46-6025 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-7579 
       12.03        10.65         5.46        30.35        28.96         1.45 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZJ TCGA-58-8387 TCGA-58-8392 TCGA-58-A46L 
       15.81        20.94        21.04        13.25        16.47        56.65 
TCGA-58-A46M TCGA-60-2703 TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-60-2722 
       35.24        96.82        41.42        35.34        32.32        29.85 
TCGA-60-2726 TCGA-63-A5MH TCGA-63-A5MP TCGA-63-A5MV TCGA-66-2737 TCGA-66-2744 
       11.77        66.61        25.28        36.16         2.01         0.99 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2769 TCGA-66-2778 TCGA-66-2781 TCGA-66-2786 
       21.01         0.99         7.07        19.00         3.98        25.97 
TCGA-66-2787 TCGA-66-2793 TCGA-66-2800 TCGA-68-A59I TCGA-77-7140 TCGA-77-7465 
       40.01        10.06        49.05        16.18        20.78        15.75 
TCGA-77-8007 TCGA-77-8009 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-85-6561 
        6.51        53.95       117.57        22.29         5.92        12.99 
TCGA-85-7843 TCGA-85-8072 TCGA-85-8287 TCGA-85-8351 TCGA-85-8354 TCGA-85-8580 
        1.15        16.87         0.76        16.77        32.71        14.63 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
       17.72        14.96        12.39         3.65         2.93        11.77 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-8035 TCGA-94-A4VJ TCGA-96-7545 
        2.70         3.48         5.26         4.01        14.14        57.07 
TCGA-98-8020 TCGA-98-A538 TCGA-J1-A4AH TCGA-NC-A5HH TCGA-O2-A52V 
        2.76        27.16        19.10         1.22        43.89 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
       12.20        75.75        23.54        92.15        36.07         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
       86.96         6.18         2.79       154.32        49.94        27.19 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
      119.54        46.88        99.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 
       31.73       122.43         9.34        43.23        88.11        41.69 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       10.82        32.19        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 TCGA-22-4596 
       64.21         1.74        14.10        27.02        48.33         0.56 
TCGA-22-4599 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 
       38.17        32.02        19.30         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 
       64.93        63.55        14.63        44.25        54.28        71.34 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       11.74        18.84        30.12        62.86        56.32        16.64 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 
        7.63       133.74        98.01        79.53       151.27        14.07 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASL 
       54.44         1.55        19.76         0.30        36.62        27.16 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       61.61        31.50        32.88        65.23        67.79        56.38 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       23.24        12.00        30.94         4.96         1.12        27.19 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
        4.04        20.91         3.95         0.39         6.58         7.46 
TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 
        7.82         0.39         3.39        47.80        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 
       70.03        60.79         1.71        24.33         1.94        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2581 
       15.58        35.64        35.70        17.88        17.06        38.66 
TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 
       27.02        18.38        27.91        12.36        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 
        3.81        19.59        13.38        11.77        11.61         9.73 
TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        9.99        13.91         0.39         0.39        29.95        28.34 
TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        8.75        27.45         0.10        18.25         2.04         0.62 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
        0.99         0.43         0.99         1.32         0.85         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.10        17.49         3.48        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK 
        9.93        20.25        19.23        13.32        17.85        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 
        0.13         0.26         2.76         0.03        13.55        29.95 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46N TCGA-60-2695 
       71.24        34.78        85.12        34.36        29.92        21.11 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
        3.58        12.23        10.22        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
       80.45        49.48        66.54         9.01        56.91        50.33 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       48.49        42.64         3.19        35.90        23.57        26.83 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MW 
       11.34        89.29        78.28        16.37        25.41        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 
       34.59        16.96        43.10        21.07         1.02         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
        0.92         0.99        43.99        25.05         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         2.01        23.01        19.00         3.02         2.01 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 
       12.03        12.00        24.95         1.97        22.98         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 
       22.98         5.03        30.02        54.08         4.01         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 
        6.64         6.94         8.02        13.35        14.73        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
       73.12        75.09        23.28        11.18        89.98         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 
       42.28        70.13       106.95         0.16        46.78        86.76 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       37.81        82.92        12.59        53.92        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
      104.09        11.54        26.40        27.39         6.97         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       54.41        65.49        35.90         0.33       126.18       132.36 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       42.41        42.08        30.81        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       11.97         6.41        36.53        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
        1.38        29.95        18.94        25.15        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 
       31.56        14.07        34.52        10.09        13.22        22.45 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 
        5.29         3.09         2.01         0.72         7.76        13.94 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4PA 
       12.59         0.10        15.62        25.68        19.33        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       18.18        19.73        12.56        16.21        15.85        14.96 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
        0.79        24.92         9.50        14.07        20.22        22.62 
TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       10.59         4.01         2.30        21.04         0.16        11.70 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        5.03        26.63        16.14        17.69        49.87        18.31 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       17.46        19.36        16.57         8.42        30.81        30.67 
TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D 
       21.34         3.88        18.15         2.01        27.02        21.21 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       20.32        18.58        20.71        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       13.41        11.84         0.07        64.08         4.54        51.78 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN 
       45.37        13.74         4.21         2.89        39.85        37.22 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
       30.58        24.00        14.73        29.75        22.78        83.57 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       65.49         3.65        16.80         0.43        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72         8.58        11.18         0.20 

  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                       0.43                        0.03 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                     174.08                      154.32 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                      20.48                       19.02 
[1] "0.4 - 174.1 (20.5)" "0.0 - 154.3 (19.0)"
[1] "hr=" "1.2"
D5V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(4Q12) MUTATED         0       22       29        1        16
  AMP PEAK  5(4Q12) WILD-TYPE       2       65      122        1        47
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(4Q12) MUTATED          28         0         14          6
  AMP PEAK  5(4Q12) WILD-TYPE        64         3         48         15
                             vv
clus                          STAGE IV
  AMP PEAK  5(4Q12) MUTATED          0
  AMP PEAK  5(4Q12) WILD-TYPE        7
D5V3, multiclass
            clus
vv           AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                          22                          65
  STAGE IB                          29                         122
  STAGE II                           1                           1
  STAGE IIA                         16                          47
  STAGE IIB                         28                          64
  STAGE III                          0                           3
  STAGE IIIA                        14                          48
  STAGE IIIB                         6                          15
  STAGE IV                           0                           7
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  5(4Q12) MUTATED    25  75  11   6
  AMP PEAK  5(4Q12) WILD-TYPE  86 215  58  17
D5V4, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  T1                        25                          86
  T2                        75                         215
  T3                        11                          58
  T4                         6                          17
[1] 4 2
[1] TRUE
[1] "dimension of 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(4Q12) MUTATED    71  34  10   1
  AMP PEAK  5(4Q12) WILD-TYPE 241  97  29   4
D5V5, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  N0                        71                         241
  N1                        34                          97
  N2                        10                          29
  N3                         1                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    94   0
  AMP PEAK  5(4Q12) WILD-TYPE 310   7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     94    0
  AMP PEAK  5(4Q12) WILD-TYPE  310    7
   clus
vv  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  0                        94                         310
  1                         0                           7
[1] 2 2
[1] FALSE
D5V7, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    30  87
  AMP PEAK  5(4Q12) WILD-TYPE  97 279
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     30   87
  AMP PEAK  5(4Q12) WILD-TYPE   97  279
        clus
vv       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  FEMALE                        30                          97
  MALE                          87                         279
[1] 2 2
[1] FALSE
D5V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(4Q12) MUTATED                                       5
  AMP PEAK  5(4Q12) WILD-TYPE                                    10
                             vv
clus                          LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(4Q12) MUTATED                                         1
  AMP PEAK  5(4Q12) WILD-TYPE                                       0
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  5(4Q12) MUTATED                                        0
  AMP PEAK  5(4Q12) WILD-TYPE                                      6
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(4Q12) MUTATED                                         0
  AMP PEAK  5(4Q12) WILD-TYPE                                       1
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(4Q12) MUTATED                                                           111
  AMP PEAK  5(4Q12) WILD-TYPE                                                         359
D5V9, multiclass
                                                             clus
vv                                                            AMP PEAK  5(4Q12) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                             1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       111
                                                             clus
vv                                                            AMP PEAK  5(4Q12) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         359
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     3 114
  AMP PEAK  5(4Q12) WILD-TYPE  10 366
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      3  114
  AMP PEAK  5(4Q12) WILD-TYPE   10  366
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                          3                          10
  YES                       114                         366
[1] 2 2
[1] FALSE
D5V11, continuous
D5V12, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  5(4Q12) MUTATED    95   3   1   5
  AMP PEAK  5(4Q12) WILD-TYPE 299   9   3  17
D5V13, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  R0                        95                         299
  R1                         3                           9
  R2                         1                           3
  RX                         5                          17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(4Q12) MUTATED       2                        10    79
  AMP PEAK  5(4Q12) WILD-TYPE     7                        21   261
D5V14, multiclass
                           clus
vv                          AMP PEAK  5(4Q12) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                        10
  WHITE                                            79
                           clus
vv                          AMP PEAK  5(4Q12) WILD-TYPE
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          21
  WHITE                                             261
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     0  78
  AMP PEAK  5(4Q12) WILD-TYPE   8 231
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      0   78
  AMP PEAK  5(4Q12) WILD-TYPE    8  231
                        clus
vv                       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             0                           8
  NOT HISPANIC OR LATINO                        78                         231
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(5P15.33) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(5P15.33) MUTATED   217 153
  AMP PEAK  6(5P15.33) WILD-TYPE  64  43
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           370                            107 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           153                             43 
$`AMP PEAK  6(5P15.33) MUTATED`
TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
        4.80       117.57        11.34        23.54        92.15        36.07 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       86.96         6.18         2.79        49.94       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       99.16        70.16        34.78        31.73       122.43         9.34 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
      119.80        31.63        88.11        41.69        33.93        10.82 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
       32.19        21.99         7.33         4.31         1.74        14.10 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
       27.02        48.82        20.48        35.08        48.33        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 
        0.56        38.17        34.75        32.02         9.57        11.77 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       31.73        64.93        63.55        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       54.28        71.34        79.20        11.74        18.84        30.12 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       16.64        22.06         7.63        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
      103.53        14.07        54.44        19.76        27.02         4.70 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 
       36.62         6.94        44.19       118.36         2.63        61.61 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5236 TCGA-34-5239 
       31.50        28.96        32.88        31.27         9.07        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8455 
       12.00        16.93        18.15         4.96         1.12         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 
       26.43        20.91         3.95         0.39         8.12         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 
        6.81         0.39         3.39        47.80        74.07        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       55.20        70.03        60.79        24.33         1.94        27.39 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 
       36.39        15.58        35.64        17.88        40.21        22.49 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
       38.66        27.02        33.11        18.38        27.91        12.36 
TCGA-43-6647 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 
       24.89        19.59         7.76        66.51        11.77         2.93 
TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       11.61        14.20        12.03         9.99        10.65        13.91 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
        0.39        29.95        28.34         5.46        30.35         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
       27.45        28.96        18.25         2.04         0.62         0.99 
TCGA-56-7222 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        0.43         1.32         0.85         0.10        17.49         3.48 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 
       17.00        14.07         1.35        16.77         1.81         1.18 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
       10.36         9.93        20.25        15.81        20.94        19.23 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
       13.32        17.85        21.04        18.74         0.13         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        2.76         0.03        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       16.47        85.12        34.36        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2710 TCGA-60-2711 
       12.23        96.82        37.94        21.93        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 
        9.01        56.91        50.33        35.34        42.64         3.19 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB 
       32.32        35.90        23.57        26.83        11.77       102.67 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP 
       66.61        58.65        59.97        45.57        11.34        25.28 
TCGA-63-A5MS TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       78.28        25.41        36.16        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       43.10         2.01        21.07         0.99         1.02         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        0.92         0.99        43.99        21.01        25.05         0.99 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
        1.02         2.01         7.07        23.01        19.00         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 
        2.01        19.00        12.03         3.98        12.00         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 
       25.97        40.01        22.98         4.04        22.98        30.02 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       54.08        49.05         6.64         6.94         8.02        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       16.18        14.73        29.56        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       89.98         0.49        42.28        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
       46.78        15.75         6.51        86.76        53.95        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       82.92        53.92        39.09        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       26.40         6.97         9.63        54.41        65.49        35.90 
TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
        0.33       132.36        22.29         5.92        42.41        42.08 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
       27.62        38.86         9.67        11.97         6.41        36.53 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
       31.30        32.91         1.38         1.15        29.95        18.94 
TCGA-85-8048 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       25.15        31.56        14.07        16.87        34.52        10.09 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8479 
        0.76        13.22        22.45        16.77         5.29         0.72 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        7.76        14.63        13.94        12.59         0.10        15.62 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       19.33        17.72        14.96        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
       16.21        15.85        14.96         9.50         2.93        11.77 
TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
       14.07        22.62        10.59         2.70         3.48         5.26 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8491 
        2.30        21.04         0.16        11.70         4.01        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
       14.14        17.69        49.87        57.07        18.31        17.46 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
       19.36         2.76        30.67        21.34        27.16         3.88 
TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
        2.01        18.58        20.71        19.10        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG 
       13.18        13.41        11.84         0.07         4.54        51.78 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN 
        1.22        45.37        13.74         4.21        39.85        37.22 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE 
       14.73        22.78        83.57        65.49         3.65         0.43 
TCGA-O2-A52N TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       33.07        43.89         8.58         0.20 

$`AMP PEAK  6(5P15.33) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3416 TCGA-18-3419 
       12.20         7.46        75.75        79.46        31.99         1.64 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1076 TCGA-21-1078 TCGA-21-1083 TCGA-22-1000 
      154.32        27.19        60.89        15.58        43.23        14.93 
TCGA-22-1005 TCGA-22-4604 TCGA-22-4607 TCGA-22-5489 TCGA-22-5491 TCGA-33-4533 
       64.21        13.12        19.30        62.86        56.32       133.74 
TCGA-33-4583 TCGA-33-4589 TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASL TCGA-34-5231 
      151.27         1.55         0.30       110.99        27.16        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 
       67.79        56.38        30.94        27.19         0.43         6.58 
TCGA-37-4132 TCGA-39-5019 TCGA-39-5028 TCGA-39-5037 TCGA-39-5040 TCGA-43-6770 
        7.46        44.75         1.71        35.70        17.06        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-A475 TCGA-51-4080 TCGA-56-5897 
        5.46         3.81        13.38         9.73         0.39         0.10 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 TCGA-56-8307 TCGA-56-8623 TCGA-58-8393 
        0.99         1.45         6.51        26.89        22.75        34.78 
TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
       56.65         3.58        10.22        92.71        80.45        49.48 
TCGA-60-2716 TCGA-60-2722 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MT 
       48.49        29.85        70.62        14.99        89.29        16.37 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2783 TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 
        2.01         2.01        24.95         5.03        10.06         4.01 
TCGA-68-7755 TCGA-77-6843 TCGA-77-7140 TCGA-77-8131 TCGA-77-8144 TCGA-77-A5FZ 
        2.73        73.12        20.78        12.59        27.39       126.18 
TCGA-77-A5G3 TCGA-77-A5GB TCGA-85-6561 TCGA-85-7697 TCGA-85-8049 TCGA-85-8052 
      117.57        30.81        12.99        34.95        19.04        24.13 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A513 
        3.09        32.71         2.01        25.68        24.36         0.79 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-A4ED TCGA-92-8063 TCGA-94-8490 
       12.39         3.65        24.92        20.22         4.01         5.03 
TCGA-94-A5I4 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-A53A TCGA-98-A53C 
       16.14        16.57         8.42        30.81        18.15        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-NC-A5HE TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP 
       21.21        20.32        64.08         2.89        30.58        24.00 
TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB 
       29.75        16.80         3.72        12.72        11.18 

  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                          0.03                           0.10 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                        174.08                         154.32 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                         18.97                          20.32 
[1] "0.0 - 174.1 (19.0)" "0.1 - 154.3 (20.3)"
[1] "hr=" "1.1"
D6V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(5P15.33) MUTATED         2       65      122        2        46
  AMP PEAK  6(5P15.33) WILD-TYPE       0       22       29        0        17
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(5P15.33) MUTATED          72         0         52         14
  AMP PEAK  6(5P15.33) WILD-TYPE        20         3         10          7
                                vv
clus                             STAGE IV
  AMP PEAK  6(5P15.33) MUTATED          5
  AMP PEAK  6(5P15.33) WILD-TYPE        2
D6V3, multiclass
            clus
vv           AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             65                             22
  STAGE IB                            122                             29
  STAGE II                              2                              0
  STAGE IIA                            46                             17
  STAGE IIB                            72                             20
  STAGE III                             0                              3
  STAGE IIIA                           52                             10
  STAGE IIIB                           14                              7
  STAGE IV                              5                              2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  6(5P15.33) MUTATED    80 232  53  17
  AMP PEAK  6(5P15.33) WILD-TYPE  31  58  16   6
D6V4, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  T1                           80                             31
  T2                          232                             58
  T3                           53                             16
  T4                           17                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK  6(5P15.33) MUTATED   249  94  35   2
  AMP PEAK  6(5P15.33) WILD-TYPE  63  37   4   3
D6V5, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  N0                          249                             63
  N1                           94                             37
  N2                           35                              4
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED   315   5
  AMP PEAK  6(5P15.33) WILD-TYPE  89   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED    315    5
  AMP PEAK  6(5P15.33) WILD-TYPE   89    2
   clus
vv  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  0                          315                             89
  1                            5                              2
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    95 287
  AMP PEAK  6(5P15.33) WILD-TYPE  32  79
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     95  287
  AMP PEAK  6(5P15.33) WILD-TYPE   32   79
        clus
vv       AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  FEMALE                           95                             32
  MALE                            287                             79
[1] 2 2
[1] FALSE
D6V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                                      10
  AMP PEAK  6(5P15.33) WILD-TYPE                                     5
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                                         1
  AMP PEAK  6(5P15.33) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  6(5P15.33) MUTATED                                        4
  AMP PEAK  6(5P15.33) WILD-TYPE                                      2
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  6(5P15.33) MUTATED                                         1
  AMP PEAK  6(5P15.33) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P15.33) MUTATED                                                           366
  AMP PEAK  6(5P15.33) WILD-TYPE                                                         104
D6V9, multiclass
                                                             clus
vv                                                            AMP PEAK  6(5P15.33) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          366
                                                             clus
vv                                                            AMP PEAK  6(5P15.33) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            104
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED     9 373
  AMP PEAK  6(5P15.33) WILD-TYPE   4 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED      9  373
  AMP PEAK  6(5P15.33) WILD-TYPE    4  107
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  NO                             9                              4
  YES                          373                            107
[1] 2 2
[1] FALSE
D6V11, continuous
D6V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  6(5P15.33) MUTATED   307   9   3  16
  AMP PEAK  6(5P15.33) WILD-TYPE  87   3   1   6
D6V13, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  R0                          307                             87
  R1                            9                              3
  R2                            3                              1
  RX                           16                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(5P15.33) MUTATED       5                        22   265
  AMP PEAK  6(5P15.33) WILD-TYPE     4                         9    75
D6V14, multiclass
                           clus
vv                          AMP PEAK  6(5P15.33) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           22
  WHITE                                              265
                           clus
vv                          AMP PEAK  6(5P15.33) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                 75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED     7 236
  AMP PEAK  6(5P15.33) WILD-TYPE   1  73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED      7  236
  AMP PEAK  6(5P15.33) WILD-TYPE    1   73
                        clus
vv                       AMP PEAK  6(5P15.33) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          236
                        clus
vv                       AMP PEAK  6(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             73
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(5P12) MUTATION ANALYSIS
D7V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  7(5P12) MUTATED   199 140
  AMP PEAK  7(5P12) WILD-TYPE  82  56
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                        339                         138 
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                        140                          56 
$`AMP PEAK  7(5P12) MUTATED`
TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
        4.80       117.57        11.34        23.54        92.15        36.07 
TCGA-18-3421 TCGA-18-4083 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 
       86.96         6.18        49.94       119.54        46.88        70.16 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
       34.78        31.73       122.43         9.34       119.80        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
       31.63        88.11        41.69        33.93        10.82        32.19 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       21.99         7.33         4.31         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
       20.48        35.08        48.33        24.13         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 
       34.75        13.12        32.02         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5481 
       64.93        63.55        14.63        44.25         0.79        79.20 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
       11.74        18.84        30.12        16.64        22.06         7.63 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
      133.74        98.01        79.53       174.08       103.53       151.27 
TCGA-33-4586 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB 
       14.07        19.76        27.02         4.70        36.62         6.94 
TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
       44.19       118.36         2.63        61.61        31.50        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       32.88        31.27         9.07        23.24        12.00        16.93 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       18.15         4.96         1.12         4.04        26.43        20.91 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        3.95         0.39         8.12         7.82         6.81         0.39 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        3.39        47.80        74.07        68.58        55.20        70.03 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 
       24.33         1.94        27.39        15.58        35.64        17.88 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       40.21        38.66        27.02        33.11        27.91        12.36 
TCGA-43-6647 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 
       24.89         3.81        19.59         7.76        66.51        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
        2.93        11.61        12.03         9.99        10.65        13.91 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 
       29.95        28.34         5.46        30.35         8.75        28.96 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7580 
       18.25         2.04         0.62         0.99         0.43         1.32 
TCGA-56-7582 TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 
        0.85        17.49         3.48        17.00        14.07         1.35 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       16.77         1.81         1.18         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
       20.94        19.23        13.32        17.85        21.04         0.13 
TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        0.26         0.03        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       16.47        85.12        34.36        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 
       12.23        96.82        37.94        92.71        21.93        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
       66.54        41.42         9.01        56.91        50.33        42.64 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MH 
        3.19        32.32        35.90        26.83        11.77        66.61 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS 
       58.65        59.97        45.57        11.34        25.28        78.28 
TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       25.41        36.16        53.88        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
        2.01        21.07         0.99         1.02         2.01         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 
        0.99        43.99        25.05         1.02         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
       23.01        19.00         2.01        19.00        12.03        12.00 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
        1.97        25.97        40.01        22.98         4.04         5.03 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 
       30.02        54.08         4.01        49.05         6.64         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 
        8.02        13.35        14.73        29.56        75.09        11.18 
TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 
       89.98        20.78         0.49        42.28       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
       46.78        15.75         6.51        86.76        53.95        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       82.92        53.92        39.09        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       26.40         6.97         9.63        54.41        65.49        35.90 
TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        0.33       132.36       117.57        22.29         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 
       42.08        27.62        38.86         9.67        11.97         6.41 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
       36.53        31.30        32.91         1.38         1.15        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       18.94        25.15        14.07        16.87        34.52        10.09 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8481 
        0.76        13.22        22.45        16.77         5.29         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JC 
       14.63        13.94         0.10        15.62        19.33        14.96 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 
       18.18        19.73        12.56        15.85        14.96         3.65 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-92-7340 TCGA-92-7341 
        9.50         2.93        11.77        14.07         2.70         3.48 
TCGA-92-8064 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8491 TCGA-94-A5I6 
        5.26         0.16        11.70         4.01        26.63        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-98-8020 TCGA-98-8021 
       49.87        57.07        18.31        17.46         2.76        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J 
       30.67        21.34         3.88         2.01        18.58        20.71 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       19.10        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HM 
        0.07         4.54        51.78         1.22        13.74        39.85 
TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX 
       37.22        14.73        22.78        83.57        65.49         3.65 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-XC-AA0X 
        0.43         8.58         0.20 

$`AMP PEAK  7(5P12) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3416 TCGA-18-3419 
       12.20         7.46        75.75        79.46        31.99         1.64 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 
        2.79       154.32        27.19        99.16        60.89        15.58 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1017 TCGA-22-4607 TCGA-22-5479 TCGA-22-5480 
       14.93        64.21        48.82        19.30        54.28        71.34 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4587 TCGA-33-4589 TCGA-33-A5GW TCGA-33-AASD 
       62.86        56.32        54.44         1.55         0.30       110.99 
TCGA-33-AASL TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 TCGA-34-8454 
       27.16        65.23        67.79        56.38        30.94        27.19 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-39-5019 TCGA-39-5027 TCGA-39-5028 
        0.43         6.58         7.46        44.75        60.79         1.71 
TCGA-39-5034 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 TCGA-43-5668 TCGA-43-6770 
       36.39        35.70        17.06        22.49        18.38        21.47 
TCGA-43-6771 TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 TCGA-51-4080 
        5.46        13.38         9.73        14.20         0.39         0.39 
TCGA-52-7812 TCGA-56-5897 TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 
       27.45         0.10         0.99         1.45         6.51         0.10 
TCGA-56-8307 TCGA-56-8623 TCGA-56-8625 TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8393 
       26.89        22.75        10.36        18.74         2.76        34.78 
TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2708 TCGA-60-2715 TCGA-60-2716 
       56.65         3.58        10.22        80.45        35.34        48.49 
TCGA-60-2722 TCGA-60-2724 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MR 
       29.85        23.57       102.67        70.62        14.99        89.29 
TCGA-63-A5MT TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2773 
       16.37        21.01         0.99         2.01         2.01         3.02 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2790 TCGA-66-2793 TCGA-68-7755 TCGA-68-A59I 
        3.98        24.95        22.98        10.06         2.73        16.18 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7335 TCGA-77-8131 TCGA-77-8144 TCGA-77-A5FZ 
       73.12        23.28        70.13        12.59        27.39       126.18 
TCGA-77-A5GB TCGA-85-6561 TCGA-85-7697 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       30.81        12.99        34.95        19.04        24.13        31.56 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8584 TCGA-85-A4CL 
        3.09        32.71         2.01         0.72        12.59        25.68 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       17.72        24.36        16.21         0.79        12.39        24.92 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 
       20.22        22.62        10.59         4.01         2.30        21.04 
TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
        5.03        14.14        16.14        19.36        16.57         8.42 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-NC-A5HE 
       27.16        18.15        27.02        21.21        20.32        64.08 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR 
       45.37         4.21         2.89        30.58        24.00        29.75 
TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       16.80        33.07         3.72        12.72        43.89        11.18 

  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                       0.03                        0.10 
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                     174.08                      154.32 
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                      18.94                       20.27 
[1] "0.0 - 174.1 (18.9)" "0.1 - 154.3 (20.3)"
[1] "hr=" "1"  
D7V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(5P12) MUTATED         1       62      108        1        39
  AMP PEAK  7(5P12) WILD-TYPE       1       25       43        1        24
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(5P12) MUTATED          68         0         48         15
  AMP PEAK  7(5P12) WILD-TYPE        24         3         14          6
                             vv
clus                          STAGE IV
  AMP PEAK  7(5P12) MUTATED          5
  AMP PEAK  7(5P12) WILD-TYPE        2
D7V3, multiclass
            clus
vv           AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  STAGE I                            1                           1
  STAGE IA                          62                          25
  STAGE IB                         108                          43
  STAGE II                           1                           1
  STAGE IIA                         39                          24
  STAGE IIB                         68                          24
  STAGE III                          0                           3
  STAGE IIIA                        48                          14
  STAGE IIIB                        15                           6
  STAGE IV                           5                           2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  7(5P12) MUTATED    76 214  42  17
  AMP PEAK  7(5P12) WILD-TYPE  35  76  27   6
D7V4, multiclass
    clus
vv   AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  T1                        76                          35
  T2                       214                          76
  T3                        42                          27
  T4                        17                           6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK  7(5P12) MUTATED   222  89  33   3
  AMP PEAK  7(5P12) WILD-TYPE  90  42   6   2
D7V5, multiclass
    clus
vv   AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  N0                       222                          90
  N1                        89                          42
  N2                        33                           6
  N3                         3                           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"
D7V6, binary
                             cls
clus                            0   1
  AMP PEAK  7(5P12) MUTATED   292   5
  AMP PEAK  7(5P12) WILD-TYPE 112   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(5P12) MUTATED    292    5
  AMP PEAK  7(5P12) WILD-TYPE  112    2
   clus
vv  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  0                       292                         112
  1                         5                           2
[1] 2 2
[1] FALSE
D7V7, binary
                             cls
clus                            0   1
  AMP PEAK  7(5P12) MUTATED    79 270
  AMP PEAK  7(5P12) WILD-TYPE  48  96
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(5P12) MUTATED     79  270
  AMP PEAK  7(5P12) WILD-TYPE   48   96
        clus
vv       AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  FEMALE                        79                          48
  MALE                         270                          96
[1] 2 2
[1] FALSE
D7V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(5P12) MUTATED                                      10
  AMP PEAK  7(5P12) WILD-TYPE                                     5
                             vv
clus                          LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(5P12) MUTATED                                         1
  AMP PEAK  7(5P12) WILD-TYPE                                       0
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  7(5P12) MUTATED                                        2
  AMP PEAK  7(5P12) WILD-TYPE                                      4
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(5P12) MUTATED                                         0
  AMP PEAK  7(5P12) WILD-TYPE                                       1
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(5P12) MUTATED                                                           336
  AMP PEAK  7(5P12) WILD-TYPE                                                         134
D7V9, multiclass
                                                             clus
vv                                                            AMP PEAK  7(5P12) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                              10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                             1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       336
                                                             clus
vv                                                            AMP PEAK  7(5P12) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         134
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                             cls
clus                            0   1
  AMP PEAK  7(5P12) MUTATED     9 340
  AMP PEAK  7(5P12) WILD-TYPE   4 140
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(5P12) MUTATED      9  340
  AMP PEAK  7(5P12) WILD-TYPE    4  140
     clus
vv    AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  NO                          9                           4
  YES                       340                         140
[1] 2 2
[1] FALSE
D7V11, continuous
D7V12, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  7(5P12) MUTATED   284   8   3  12
  AMP PEAK  7(5P12) WILD-TYPE 110   4   1  10
D7V13, multiclass
    clus
vv   AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  R0                       284                         110
  R1                         8                           4
  R2                         3                           1
  RX                        12                          10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(5P12) MUTATED       4                        20   239
  AMP PEAK  7(5P12) WILD-TYPE     5                        11   101
D7V14, multiclass
                           clus
vv                          AMP PEAK  7(5P12) MUTATED
  ASIAN                                             4
  BLACK OR AFRICAN AMERICAN                        20
  WHITE                                           239
                           clus
vv                          AMP PEAK  7(5P12) WILD-TYPE
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V15, binary
                             cls
clus                            0   1
  AMP PEAK  7(5P12) MUTATED     6 210
  AMP PEAK  7(5P12) WILD-TYPE   2  99
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(5P12) MUTATED      6  210
  AMP PEAK  7(5P12) WILD-TYPE    2   99
                        clus
vv                       AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  HISPANIC OR LATINO                             6                           2
  NOT HISPANIC OR LATINO                       210                          99
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(6P12.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(6P12.1) MUTATED    96  64
  AMP PEAK  8(6P12.1) WILD-TYPE 185 132
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                          160                           317 
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                           64                           132 
$`AMP PEAK  8(6P12.1) MUTATED`
TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3421 TCGA-21-1070 TCGA-21-1072 
       79.46       117.57        11.34        86.96       119.54        99.16 
TCGA-21-1076 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
       60.89        31.73       119.80        43.23        33.93        10.82 
TCGA-22-1002 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
        4.31        14.10        48.82        20.48        48.33        24.13 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 TCGA-22-5482 
       34.75        13.12        32.02        19.30        31.73        11.74 
TCGA-22-5483 TCGA-33-4533 TCGA-33-4587 TCGA-33-AAS8 TCGA-33-AASI TCGA-34-2605 
       18.84       133.74        54.44        36.62        44.19        28.96 
TCGA-34-2609 TCGA-34-5928 TCGA-34-7107 TCGA-34-8456 TCGA-37-4133 TCGA-37-4141 
       31.27        18.15         1.12        26.43         7.82         0.39 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5037 TCGA-43-2578 
       44.75        68.58        55.20        60.79        35.70        22.49 
TCGA-43-3394 TCGA-43-5670 TCGA-43-6770 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       27.02        27.91        21.47         9.99        10.65        13.91 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 
        5.46        30.35         8.75        28.96        18.25         2.04 
TCGA-56-6546 TCGA-56-7582 TCGA-56-7730 TCGA-56-8308 TCGA-56-8503 TCGA-56-8629 
        0.62         0.85         6.51        17.00         1.35        15.81 
TCGA-56-A49D TCGA-58-8386 TCGA-58-8387 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
       20.94         0.03        13.25        71.24        34.78        85.12 
TCGA-58-A46K TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 
       34.36        29.92        21.11        10.22        96.82        92.71 
TCGA-60-2711 TCGA-60-2714 TCGA-60-2715 TCGA-60-2719 TCGA-60-2722 TCGA-60-2726 
       41.42        50.33        35.34        42.64        29.85        11.77 
TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW 
      102.67        66.61        58.65        78.28        16.37        53.88 
TCGA-66-2734 TCGA-66-2744 TCGA-66-2754 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 
       43.10         0.99         2.01        43.99         2.01         1.02 
TCGA-66-2769 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2791 TCGA-66-2793 
        7.07         3.98         1.97        25.97         5.03        10.06 
TCGA-66-2795 TCGA-66-2800 TCGA-68-8251 TCGA-68-A59J TCGA-77-7138 TCGA-77-7141 
        4.01        49.05        13.35        14.73        11.18         0.49 
TCGA-77-7142 TCGA-77-7465 TCGA-77-8007 TCGA-77-8130 TCGA-77-8143 TCGA-77-8156 
       42.28        15.75         6.51        82.92        26.40         0.33 
TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6798 TCGA-85-7699 TCGA-85-7843 
      117.57        27.62         9.67         6.41        32.91         1.15 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8352 
       24.13        31.56        16.87        34.52         0.76         5.29 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
        3.09        32.71         2.01        13.94        12.59         0.10 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE 
       19.33        17.72        19.73         3.65        11.77        22.62 
TCGA-90-A59Q TCGA-92-8064 TCGA-94-7943 TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 
       10.59         5.26        11.70         8.42         2.76        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A524 
       21.34        27.16         2.01        18.58        19.10        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG 
       13.18        13.41        11.84         0.07        64.08        51.78 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HR TCGA-NC-A5HT 
        4.21         2.89        39.85        37.22        29.75        22.78 
TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52W TCGA-O2-A5IB 
       83.57         0.43         8.58        11.18 

$`AMP PEAK  8(6P12.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
       12.20         7.46        75.75         4.80        23.54        92.15 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       31.99        36.07         1.64         6.18         2.79       154.32 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 
       49.94        27.19        46.88        70.16        34.78        15.58 
TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI 
      122.43         9.34        31.63        88.11        41.69        32.19 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
       21.99         7.33        14.93        64.21         1.74        27.02 
TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 
       35.08         0.56        38.17         9.57        11.77        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       63.55        14.63        44.25         0.79        54.28        71.34 
TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       79.20        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        7.63        98.01        79.53       174.08       103.53       151.27 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       14.07         1.55        19.76        27.02         4.70         0.30 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
        6.94       110.99       118.36        27.16         2.63        61.61 
TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       31.50        32.88        65.23        67.79        56.38         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 
       23.24        12.00        16.93        30.94         4.96        27.19 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
        4.04        20.91         3.95         0.43         0.39         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
        8.12         7.46         6.81         3.39        47.80        74.07 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       70.03         1.71        24.33         1.94        27.39        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
       15.58        35.64        17.88        17.06        40.21        38.66 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 
       33.11        18.38        12.36        24.89         5.46         3.81 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
       19.59         7.76        66.51        13.38        11.77         2.93 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-51-4079 TCGA-51-4080 
       11.61         9.73        14.20        12.03         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7222 
       29.95        28.34        27.45         0.10         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        0.99         1.45         1.32         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       26.89        14.07        16.77         1.81        22.75         1.18 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
       10.36         9.93        20.25        19.23        13.32        17.85 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8388 
       21.04        18.74         0.13         0.26         2.76        13.55 
TCGA-58-8390 TCGA-58-8392 TCGA-58-A46L TCGA-58-A46M TCGA-60-2696 TCGA-60-2697 
       29.95        16.47        56.65        35.24         3.58        12.23 
TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
       37.94        21.93        80.45        49.48        66.54         9.01 
TCGA-60-2713 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
       56.91        48.49         3.19        32.32        35.90        23.57 
TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
       26.83        70.62        59.97        45.57        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 
       25.28        89.29        25.41        36.16        34.59        16.96 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 
        2.01        21.07         1.02         0.92         0.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 
       25.05         0.99         2.01         2.01        23.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
        3.02         2.01        19.00        12.03        12.00        24.95 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 
       40.01        22.98         4.04        22.98        30.02        54.08 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-77-6842 
        2.73         6.64         6.94         8.02        16.18        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7335 
       73.12        75.09        23.28        89.98        20.78        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
      106.95         0.16        46.78        86.76        53.95        37.81 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       12.59        53.92        39.09        17.72       104.09        11.54 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       27.39         6.97         9.63        54.41        65.49        35.90 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
      126.18       132.36        22.29         5.92        42.41        42.08 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 
       30.81        38.86        11.97        12.99        36.53        34.95 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
       31.30         1.38        29.95        18.94        25.15        19.04 
TCGA-85-8071 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8479 
       14.07        10.09        13.22        22.45        16.77         0.72 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA 
        7.76        14.63        15.62        25.68        14.96        24.36 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       18.18        12.56        16.21        15.85        14.96         0.79 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED 
       12.39        24.92         9.50         2.93        14.07        20.22 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
        2.70         3.48         4.01         2.30        21.04         0.16 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
        4.01         5.03        26.63        14.14        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       49.87        57.07        18.31        17.46        19.36        16.57 
TCGA-98-8021 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       30.81         3.88        18.15        27.02        21.21        20.32 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
       20.71        12.89         4.54         1.22        45.37        13.74 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       30.58        24.00        14.73        65.49         3.65        16.80 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       33.07         3.72        12.72        43.89         0.20 

  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                       133.74                        174.08 
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                        19.53                         19.00 
[1] "0.0 - 133.7 (19.5)" "0.1 - 174.1 (19.0)"
[1] "hr=" "1.1"
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(6P12.1) MUTATED         1       20       51        1        24
  AMP PEAK  8(6P12.1) WILD-TYPE       1       67      100        1        39
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(6P12.1) MUTATED          30         1         25          8
  AMP PEAK  8(6P12.1) WILD-TYPE        62         2         37         13
                               vv
clus                            STAGE IV
  AMP PEAK  8(6P12.1) MUTATED          1
  AMP PEAK  8(6P12.1) WILD-TYPE        6
D8V3, multiclass
            clus
vv           AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            20                            67
  STAGE IB                            51                           100
  STAGE II                             1                             1
  STAGE IIA                           24                            39
  STAGE IIB                           30                            62
  STAGE III                            1                             2
  STAGE IIIA                          25                            37
  STAGE IIIB                           8                            13
  STAGE IV                             1                             6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  8(6P12.1) MUTATED    25 102  26  10
  AMP PEAK  8(6P12.1) WILD-TYPE  86 188  43  13
D8V4, multiclass
    clus
vv   AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  T1                          25                            86
  T2                         102                           188
  T3                          26                            43
  T4                          10                            13
[1] 4 2
[1] TRUE
[1] "dimension of 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(6P12.1) MUTATED   101  44  15   1
  AMP PEAK  8(6P12.1) WILD-TYPE 211  87  24   4
D8V5, multiclass
    clus
vv   AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  N0                         101                           211
  N1                          44                            87
  N2                          15                            24
  N3                           1                             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(6P12.1) MUTATED   140   1
  AMP PEAK  8(6P12.1) WILD-TYPE 264   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P12.1) MUTATED    140    1
  AMP PEAK  8(6P12.1) WILD-TYPE  264    6
   clus
vv  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  0                         140                           264
  1                           1                             6
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P12.1) MUTATED    38 125
  AMP PEAK  8(6P12.1) WILD-TYPE  89 241
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P12.1) MUTATED     38  125
  AMP PEAK  8(6P12.1) WILD-TYPE   89  241
        clus
vv       AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  FEMALE                          38                            89
  MALE                           125                           241
[1] 2 2
[1] FALSE
D8V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(6P12.1) MUTATED                                       7
  AMP PEAK  8(6P12.1) WILD-TYPE                                     8
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(6P12.1) MUTATED                                         0
  AMP PEAK  8(6P12.1) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  8(6P12.1) MUTATED                                        2
  AMP PEAK  8(6P12.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  8(6P12.1) MUTATED                                         1
  AMP PEAK  8(6P12.1) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(6P12.1) MUTATED                                                           153
  AMP PEAK  8(6P12.1) WILD-TYPE                                                         317
D8V9, multiclass
                                                             clus
vv                                                            AMP PEAK  8(6P12.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         153
                                                             clus
vv                                                            AMP PEAK  8(6P12.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           317
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P12.1) MUTATED     5 158
  AMP PEAK  8(6P12.1) WILD-TYPE   8 322
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P12.1) MUTATED      5  158
  AMP PEAK  8(6P12.1) WILD-TYPE    8  322
     clus
vv    AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  NO                            5                             8
  YES                         158                           322
[1] 2 2
[1] FALSE
D8V11, continuous
D8V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(6P12.1) MUTATED   137   5   2   6
  AMP PEAK  8(6P12.1) WILD-TYPE 257   7   2  16
D8V13, multiclass
    clus
vv   AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  R0                         137                           257
  R1                           5                             7
  R2                           2                             2
  RX                           6                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(6P12.1) MUTATED       1                        12   116
  AMP PEAK  8(6P12.1) WILD-TYPE     8                        19   224
D8V14, multiclass
                           clus
vv                          AMP PEAK  8(6P12.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             116
                           clus
vv                          AMP PEAK  8(6P12.1) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            19
  WHITE                                               224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P12.1) MUTATED     2 104
  AMP PEAK  8(6P12.1) WILD-TYPE   6 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P12.1) MUTATED      2  104
  AMP PEAK  8(6P12.1) WILD-TYPE    6  205
                        clus
vv                       AMP PEAK  8(6P12.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         104
                        clus
vv                       AMP PEAK  8(6P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           205
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(6Q12) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  9(6Q12) MUTATED    90  57
  AMP PEAK  9(6Q12) WILD-TYPE 191 139
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                        147                         330 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         57                         139 
$`AMP PEAK  9(6Q12) MUTATED`
TCGA-18-3409 TCGA-18-3412 TCGA-18-3421 TCGA-18-4721 TCGA-21-1076 TCGA-21-1079 
       79.46        11.34        86.96       154.32        60.89        31.73 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-1012 
      119.80        43.23        33.93        10.82         4.31        14.10 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4595 TCGA-22-4601 TCGA-22-4605 TCGA-22-5471 
       48.82        48.33        24.13        34.75        32.02        31.73 
TCGA-22-5477 TCGA-22-5482 TCGA-22-5483 TCGA-33-4533 TCGA-33-4547 TCGA-33-4582 
       44.25        11.74        18.84       133.74        79.53       103.53 
TCGA-33-4587 TCGA-33-AAS8 TCGA-34-2605 TCGA-34-2609 TCGA-34-7107 TCGA-37-4133 
       54.44        36.62        28.96        31.27         1.12         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5037 
        6.81         0.39        44.75        68.58        55.20        35.70 
TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-6770 TCGA-46-3768 TCGA-46-6025 
       22.49        27.02        33.11        21.47         9.99        10.65 
TCGA-46-6026 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 
       13.91        30.35         8.75        28.96        18.25         2.04 
TCGA-56-6546 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-8308 TCGA-56-8629 
        0.62         0.85         6.51        17.49        17.00        15.81 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46N 
        0.03        13.25        34.78        85.12        34.36        29.92 
TCGA-60-2703 TCGA-60-2711 TCGA-60-2714 TCGA-60-2719 TCGA-60-2723 TCGA-63-A5MH 
       96.82        41.42        50.33        42.64        35.90        66.61 
TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MS TCGA-63-A5MT TCGA-66-2734 TCGA-66-2744 
       58.65        45.57        78.28        16.37        43.10         0.99 
TCGA-66-2754 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2769 
        2.01        43.99        25.05         2.01         1.02         7.07 
TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 
        3.98         1.97        25.97         4.04         5.03        30.02 
TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-8251 TCGA-68-A59J TCGA-77-7142 
       10.06         4.01        49.05        13.35        14.73        42.28 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8130 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6175 
       15.75        53.95        82.92       117.57        27.62         9.67 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 TCGA-85-8052 
       11.97         6.41        32.91         1.15        18.94        24.13 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       16.87        34.52         0.76         5.29         3.09        32.71 
TCGA-85-8355 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
        2.01        13.94         0.10        15.62        19.33        17.72 
TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8064 
        3.65        11.77        22.62        10.59         3.48         5.26 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-7454 
        0.16        11.70        14.14        16.14        19.36         8.42 
TCGA-98-8020 TCGA-98-8022 TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH 
        2.76        30.67         2.01        18.58        20.71        19.10 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HH 
       13.18        13.41        11.84         0.07        64.08         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
       13.74         2.89        39.85        29.75        22.78        83.57 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-O2-A5IB 
        0.43         8.58        11.18 

$`AMP PEAK  9(6Q12) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
       12.20         7.46        75.75         4.80       117.57        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 
       92.15        31.99        36.07         1.64         6.18         2.79 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
       49.94        27.19       119.54        46.88        99.16        70.16 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 
       34.78        15.58       122.43         9.34        31.63        88.11 
TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 
       41.69        32.19        21.99         7.33        14.93        64.21 
TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 
        1.74        27.02        20.48        35.08         0.56        38.17 
TCGA-22-4604 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 
       13.12        19.30         9.57        11.77        64.93        63.55 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 
       14.63         0.79        54.28        71.34        79.20        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 
       62.86        56.32        16.64        22.06         7.63        98.01 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
      174.08       151.27        14.07         1.55        19.76        27.02 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        4.70         0.30         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 
       27.16         2.63        61.61        31.50        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       67.79        56.38         9.07        23.24        12.00        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       30.94        18.15         4.96        27.19         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       20.91         3.95         0.43         0.39         6.58         8.12 
TCGA-37-4132 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5024 TCGA-39-5027 
        7.46         3.39        47.80        74.07        70.03        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1.71        24.33         1.94        27.39        36.39        15.58 
TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-5668 
       35.64        17.88        17.06        40.21        38.66        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.91        12.36        24.89         5.46         3.81        19.59 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
        7.76        66.51        13.38        11.77         2.93        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        9.73        14.20        12.03         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7222 
       28.34         5.46        27.45         0.10         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 
        0.99         1.45         1.32         0.10         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       14.07         1.35        16.77         1.81        22.75         1.18 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
       10.36         9.93        20.25        20.94        19.23        13.32 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T 
       17.85        21.04        18.74         0.13         0.26         2.76 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46L TCGA-58-A46M 
       13.55        29.95        71.24        16.47        56.65        35.24 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 
       21.11         3.58        12.23        10.22        37.94        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 
       21.93        80.45        49.48        66.54         9.01        56.91 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 
       35.34        48.49         3.19        32.32        29.85        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5MM 
       26.83        11.77       102.67        70.62        59.97        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       11.34        25.28        89.29        25.41        36.16        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 
       34.59        16.96         2.01        21.07         1.02         0.92 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 
        0.99        21.01         0.99         2.01         2.01        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
       19.00         3.02         2.01        19.00        12.03        12.00 
TCGA-66-2783 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 TCGA-66-2794 TCGA-68-7755 
       24.95        40.01        22.98        22.98        54.08         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 
        6.64         6.94         8.02        16.18        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 
       75.09        23.28        11.18        89.98        20.78         0.49 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 
       70.13       106.95         0.16        46.78         6.51        86.76 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       37.81        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       11.54        26.40        27.39         6.97         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
       65.49        35.90         0.33       126.18       132.36        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6561 
        5.92        42.41        42.08        30.81        38.86        12.99 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 
       36.53        34.95        31.30         1.38        29.95        25.15 
TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 
       19.04        31.56        14.07        10.09        13.22        22.45 
TCGA-85-8351 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8584 TCGA-85-A4CL 
       16.77         0.72         7.76        14.63        12.59        25.68 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       14.96        24.36        18.18        19.73        12.56        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 
       15.85        14.96         0.79        12.39        24.92         9.50 
TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 
        2.93        14.07        20.22         2.70         4.01         2.30 
TCGA-94-7033 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 
       21.04         4.01         5.03        26.63        17.69        49.87 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 TCGA-98-8023 
       57.07        18.31        17.46        16.57        30.81        21.34 
TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       27.16         3.88        18.15        27.02        21.21        20.32 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK 
       12.89        16.11         4.54        51.78        45.37         4.21 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CT TCGA-NK-A5CX 
       37.22        30.58        24.00        14.73        65.49         3.65 
TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       16.80        33.07         3.72        12.72        43.89         0.20 

  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                       0.03                        0.10 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                     154.32                      174.08 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                      18.58                       19.66 
[1] "0.0 - 154.3 (18.6)" "0.1 - 174.1 (19.7)"
[1] "hr=" "1.1"
D9V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(6Q12) MUTATED         1       23       49        1        21
  AMP PEAK  9(6Q12) WILD-TYPE       1       64      102        1        42
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(6Q12) MUTATED          24         1         18         10
  AMP PEAK  9(6Q12) WILD-TYPE        68         2         44         11
                             vv
clus                          STAGE IV
  AMP PEAK  9(6Q12) MUTATED          1
  AMP PEAK  9(6Q12) WILD-TYPE        6
D9V3, multiclass
            clus
vv           AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  STAGE I                            1                           1
  STAGE IA                          23                          64
  STAGE IB                          49                         102
  STAGE II                           1                           1
  STAGE IIA                         21                          42
  STAGE IIB                         24                          68
  STAGE III                          1                           2
  STAGE IIIA                        18                          44
  STAGE IIIB                        10                          11
  STAGE IV                           1                           6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  9(6Q12) MUTATED    30  91  20   9
  AMP PEAK  9(6Q12) WILD-TYPE  81 199  49  14
D9V4, multiclass
    clus
vv   AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  T1                        30                          81
  T2                        91                         199
  T3                        20                          49
  T4                         9                          14
[1] 4 2
[1] TRUE
[1] "dimension of 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(6Q12) MUTATED    97  39  10   2
  AMP PEAK  9(6Q12) WILD-TYPE 215  92  29   3
D9V5, multiclass
    clus
vv   AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  N0                        97                         215
  N1                        39                          92
  N2                        10                          29
  N3                         2                           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(6Q12) MUTATED   126   1
  AMP PEAK  9(6Q12) WILD-TYPE 278   6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED    126    1
  AMP PEAK  9(6Q12) WILD-TYPE  278    6
   clus
vv  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  0                       126                         278
  1                         1                           6
[1] 2 2
[1] FALSE
D9V7, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED    31 119
  AMP PEAK  9(6Q12) WILD-TYPE  96 247
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     31  119
  AMP PEAK  9(6Q12) WILD-TYPE   96  247
        clus
vv       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  FEMALE                        31                          96
  MALE                         119                         247
[1] 2 2
[1] FALSE
D9V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(6Q12) MUTATED                                       5
  AMP PEAK  9(6Q12) WILD-TYPE                                    10
                             vv
clus                          LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(6Q12) MUTATED                                         0
  AMP PEAK  9(6Q12) WILD-TYPE                                       1
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK  9(6Q12) MUTATED                                        1
  AMP PEAK  9(6Q12) WILD-TYPE                                      5
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(6Q12) MUTATED                                         1
  AMP PEAK  9(6Q12) WILD-TYPE                                       0
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(6Q12) MUTATED                                                           143
  AMP PEAK  9(6Q12) WILD-TYPE                                                         327
D9V9, multiclass
                                                             clus
vv                                                            AMP PEAK  9(6Q12) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       143
                                                             clus
vv                                                            AMP PEAK  9(6Q12) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         327
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED     5 145
  AMP PEAK  9(6Q12) WILD-TYPE   8 335
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED      5  145
  AMP PEAK  9(6Q12) WILD-TYPE    8  335
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  NO                          5                           8
  YES                       145                         335
[1] 2 2
[1] FALSE
D9V11, continuous
D9V12, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  9(6Q12) MUTATED   126   4   2   6
  AMP PEAK  9(6Q12) WILD-TYPE 268   8   2  16
D9V13, multiclass
    clus
vv   AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  R0                       126                         268
  R1                         4                           8
  R2                         2                           2
  RX                         6                          16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6Q12) MUTATED       1                        13   104
  AMP PEAK  9(6Q12) WILD-TYPE     8                        18   236
D9V14, multiclass
                           clus
vv                          AMP PEAK  9(6Q12) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                        13
  WHITE                                           104
                           clus
vv                          AMP PEAK  9(6Q12) WILD-TYPE
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          18
  WHITE                                             236
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V15, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED     2  99
  AMP PEAK  9(6Q12) WILD-TYPE   6 210
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED      2   99
  AMP PEAK  9(6Q12) WILD-TYPE    6  210
                        clus
vv                       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             2                           6
  NOT HISPANIC OR LATINO                        99                         210
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7P11.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7P11.2) MUTATED   154  87
  AMP PEAK 10(7P11.2) WILD-TYPE 127 109
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          241                           236 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                           87                           109 
$`AMP PEAK 10(7P11.2) MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        7.46        75.75        79.46       117.57        11.34        23.54 
TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       36.07        86.96         6.18       154.32        49.94       119.54 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 
       99.16        70.16        60.89        31.73         9.34       119.80 
TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 
       88.11        41.69        32.19         7.33         1.74        14.10 
TCGA-22-1017 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
       48.82        35.08        24.13         0.56        38.17        13.12 
TCGA-22-4605 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
       32.02        31.73        64.93        63.55        44.25         0.79 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 
       54.28        11.74        56.32        22.06       133.74        98.01 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN 
      174.08       103.53        14.07         1.55        27.02         4.70 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 
      110.99        44.19        27.16         2.63        28.96        31.27 
TCGA-34-5231 TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 TCGA-34-5928 TCGA-34-8456 
       65.23        56.38         9.07        12.00        18.15        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4141 TCGA-37-5819 
       20.91         3.95         0.43         8.12         0.39         3.39 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 
       74.07        44.75        60.79        27.39        15.58        35.70 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 
       40.21        38.66        27.02        18.38        27.91        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-A475 TCGA-43-A56V TCGA-46-3768 
        5.46         3.81         7.76         9.73        12.03         9.99 
TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
       10.65         0.39         0.39        29.95         5.46        30.35 
TCGA-56-6545 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-8304 
        2.04         0.99         0.99         1.45         0.85         3.48 
TCGA-56-8504 TCGA-56-8624 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DR 
       16.77         1.18        20.94        19.23        13.32         0.13 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46L 
        2.76         0.03        71.24        16.47        34.78        56.65 
TCGA-58-A46N TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 
       29.92        10.22        96.82        37.94        92.71        80.45 
TCGA-60-2709 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
       49.48        41.42         9.01        56.91        50.33        42.64 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH 
       29.85        35.90        11.77       102.67        70.62        66.61 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       58.65        59.97        45.57        89.29        78.28        16.37 
TCGA-63-A5MU TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       25.41        53.88        43.10         2.01        21.07         0.99 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2763 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 
        2.01         0.92         0.99         2.01        23.01        19.00 
TCGA-66-2777 TCGA-66-2782 TCGA-66-2785 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
        2.01        12.00         1.97         5.03        30.02        10.06 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-8250 TCGA-68-A59J TCGA-77-6845 
        4.01        49.05         2.73         8.02        14.73        23.28 
TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       11.18        20.78         0.49         0.16        46.78        15.75 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 
        6.51        86.76        53.95        37.81        82.92        53.92 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 
       39.09       104.09        26.40        27.39         9.63        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
       65.49         0.33       117.57        22.29         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 
       42.08        30.81        27.62         9.67        12.99         6.41 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 
       36.53        34.95        29.95        18.94        19.04        24.13 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8351 TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 
       34.52         0.76        16.77        32.71         0.10        15.62 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 
       19.33        17.72        18.18        19.73        12.56        15.85 
TCGA-85-A513 TCGA-85-A53L TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        0.79        12.39        11.77        20.22        22.62        10.59 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7557 TCGA-94-A4VJ TCGA-94-A5I6 
        3.48         4.01         5.26         0.16        14.14        17.69 
TCGA-96-7545 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8020 TCGA-98-8023 TCGA-98-A539 
       57.07        19.36        16.57         2.76        21.34         3.88 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HE 
       18.58        20.71        12.89        13.41        11.84        64.08 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP 
       51.78        45.37         2.89        39.85        37.22        24.00 
TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       29.75        83.57         0.43        33.07         3.72        12.72 
TCGA-O2-A52W 
        8.58 

$`AMP PEAK 10(7P11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4086 
       12.20         4.80        92.15        31.99         1.64         2.79 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1083 
       27.19        46.88        34.78        15.58       122.43        43.23 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 
       31.63        33.93        10.82        21.99        14.93         4.31 
TCGA-22-1005 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4601 TCGA-22-4607 
       64.21        27.02        20.48        48.33        34.75        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 
        9.57        11.77        14.63        71.34        79.20        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4532 TCGA-33-4547 TCGA-33-4583 
       30.12        62.86        16.64         7.63        79.53       151.27 
TCGA-33-4587 TCGA-33-6737 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ 
       54.44        19.76         0.30        36.62         6.94       118.36 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 TCGA-34-5239 TCGA-34-5241 
       61.61        31.50        32.88        67.79        23.24        16.93 
TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-37-3792 
       30.94         4.96         1.12        27.19         4.04         0.39 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-39-5011 TCGA-39-5021 
        6.58         7.46         7.82         6.81        47.80        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 
       55.20        70.03         1.71        24.33         1.94        36.39 
TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2578 TCGA-43-3920 TCGA-43-6143 
       35.64        17.88        17.06        22.49        33.11        12.36 
TCGA-43-6770 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
       21.47        19.59        66.51        13.38        11.77         2.93 
TCGA-43-A474 TCGA-43-A56U TCGA-46-6026 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 
       11.61        14.20        13.91        28.34         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7222 TCGA-56-7580 
       28.96         0.10        18.25         0.62         0.43         1.32 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        6.51         0.10        17.49        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.35         1.81        22.75        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8387 
       15.81        17.85        21.04        18.74         0.26        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 
       13.55        29.95        85.12        34.36        35.24        21.11 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2707 TCGA-60-2710 TCGA-60-2715 TCGA-60-2716 
        3.58        12.23        21.93        66.54        35.34        48.49 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MM TCGA-63-A5MN 
        3.19        32.32        23.57        26.83        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2753 TCGA-66-2756 
       25.28        36.16        34.59        16.96         1.02         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
       43.99        21.01        25.05         2.01         1.02         2.01 
TCGA-66-2769 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 
        7.07         3.02        19.00        12.03         3.98        24.95 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 
       25.97        40.01        22.98         4.04        22.98        54.08 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 
        6.64         6.94        13.35        16.18        29.56        73.12 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8131 
       75.09        89.98        42.28        70.13       106.95        12.59 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8145 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
       17.72        11.54         6.97        35.90       126.18       132.36 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       38.86        11.97        31.30        32.91         1.38         1.15 
TCGA-85-8048 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8288 
       25.15        31.56        14.07        16.87        10.09        13.22 
TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       22.45         5.29         3.09         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA 
       14.63        13.94        12.59        25.68        14.96        24.36 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
       16.21        14.96         3.65        24.92         9.50         2.93 
TCGA-90-7964 TCGA-92-7340 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-8035 
       14.07         2.70         2.30        21.04        11.70         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
        5.03        26.63        16.14        49.87        18.31        17.46 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B 
        8.42        30.81        30.67        27.16        18.15         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 
       27.02        21.21        20.32        19.10        16.11        13.18 
TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HO 
        0.07         4.54         1.22        13.74         4.21        30.58 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52V 
       14.73        22.78        65.49         3.65        16.80        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                       174.08                        151.27 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                       21.070                        17.605 
[1] "0.0 - 174.1 (21.1)" "0.1 - 151.3 (17.6)"
[1] "hr=" "1.6"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(7P11.2) MUTATED         2       29       86        0        30
  AMP PEAK 10(7P11.2) WILD-TYPE       0       58       65        2        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(7P11.2) MUTATED          56         2         32          8
  AMP PEAK 10(7P11.2) WILD-TYPE        36         1         30         13
                               vv
clus                            STAGE IV
  AMP PEAK 10(7P11.2) MUTATED          5
  AMP PEAK 10(7P11.2) WILD-TYPE        2
D10V3, multiclass
            clus
vv           AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                            29                            58
  STAGE IB                            86                            65
  STAGE II                             0                             2
  STAGE IIA                           30                            33
  STAGE IIB                           56                            36
  STAGE III                            2                             1
  STAGE IIIA                          32                            30
  STAGE IIIB                           8                            13
  STAGE IV                             5                             2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 10(7P11.2) MUTATED    39 169  35   9
  AMP PEAK 10(7P11.2) WILD-TYPE  72 121  34  14
D10V4, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  T1                          39                            72
  T2                         169                           121
  T3                          35                            34
  T4                           9                            14
[1] 4 2
[1] TRUE
[1] "dimension of 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(7P11.2) MUTATED   148  76  22   2
  AMP PEAK 10(7P11.2) WILD-TYPE 164  55  17   3
D10V5, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  N0                         148                           164
  N1                          76                            55
  N2                          22                            17
  N3                           2                             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"
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED   206   5
  AMP PEAK 10(7P11.2) WILD-TYPE 198   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED    206    5
  AMP PEAK 10(7P11.2) WILD-TYPE  198    2
   clus
vv  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  0                         206                           198
  1                           5                             2
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED    59 193
  AMP PEAK 10(7P11.2) WILD-TYPE  68 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED     59  193
  AMP PEAK 10(7P11.2) WILD-TYPE   68  173
        clus
vv       AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  FEMALE                          59                            68
  MALE                           193                           173
[1] 2 2
[1] FALSE
D10V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                                       9
  AMP PEAK 10(7P11.2) WILD-TYPE                                     6
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                                         0
  AMP PEAK 10(7P11.2) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 10(7P11.2) MUTATED                                        1
  AMP PEAK 10(7P11.2) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                                         0
  AMP PEAK 10(7P11.2) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7P11.2) MUTATED                                                           242
  AMP PEAK 10(7P11.2) WILD-TYPE                                                         228
D10V9, multiclass
                                                             clus
vv                                                            AMP PEAK 10(7P11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         242
                                                             clus
vv                                                            AMP PEAK 10(7P11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           228
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED     6 246
  AMP PEAK 10(7P11.2) WILD-TYPE   7 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED      6  246
  AMP PEAK 10(7P11.2) WILD-TYPE    7  234
     clus
vv    AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  NO                            6                             7
  YES                         246                           234
[1] 2 2
[1] FALSE
D10V11, continuous
D10V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(7P11.2) MUTATED   204   5   1  12
  AMP PEAK 10(7P11.2) WILD-TYPE 190   7   3  10
D10V13, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  R0                         204                           190
  R1                           5                             7
  R2                           1                             3
  RX                          12                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7P11.2) MUTATED       8                        19   159
  AMP PEAK 10(7P11.2) WILD-TYPE     1                        12   181
D10V14, multiclass
                           clus
vv                          AMP PEAK 10(7P11.2) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          19
  WHITE                                             159
                           clus
vv                          AMP PEAK 10(7P11.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED     2 152
  AMP PEAK 10(7P11.2) WILD-TYPE   6 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED      2  152
  AMP PEAK 10(7P11.2) WILD-TYPE    6  157
                        clus
vv                       AMP PEAK 10(7P11.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         152
                        clus
vv                       AMP PEAK 10(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           157
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(7Q21.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(7Q21.2) MUTATED   155  94
  AMP PEAK 11(7Q21.2) WILD-TYPE 126 102
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                          249                           228 
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                           94                           102 
$`AMP PEAK 11(7Q21.2) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       12.20         7.46        79.46       117.57        11.34        23.54 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 
       31.99        36.07         1.64        86.96         6.18       154.32 
TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1081 
      119.54        99.16        70.16        60.89        34.78         9.34 
TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 
       43.23        88.11        33.93        10.82        32.19         7.33 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
       64.21         1.74        14.10        20.48        35.08        48.33 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 TCGA-22-5472 
        0.56        38.17        13.12        32.02        31.73        64.93 
TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 
       63.55        44.25         0.79        54.28        11.74        18.84 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
       56.32        16.64        22.06       133.74        98.01        79.53 
TCGA-33-4566 TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI 
      174.08        14.07         1.55        27.02       110.99        44.19 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 
       27.16         2.63        61.61        28.96        31.27        65.23 
TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 
        9.07        12.00        16.93        30.94        18.15         1.12 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 
       26.43        20.91         3.95         0.43         7.82         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5029 
        0.39        47.80        74.07        44.75        60.79        24.33 
TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-43-3394 TCGA-43-3920 TCGA-43-6647 
       27.39        15.58        35.64        27.02        33.11        24.89 
TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V 
        3.81         7.76        66.51        11.61         9.73        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
        9.99        10.65         0.39        29.95         5.46        30.35 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7223 
       28.96        18.25         2.04         0.62         0.99         0.99 
TCGA-56-7579 TCGA-56-7582 TCGA-56-8304 TCGA-56-8308 TCGA-56-8504 TCGA-56-A49D 
        1.45         0.85         3.48        17.00        16.77        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-8391 
       19.23        13.32         0.13         2.76         0.03        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2698 
       16.47        34.78        34.36        35.24        29.92        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2711 
       96.82        37.94        92.71        80.45        49.48        41.42 
TCGA-60-2712 TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 
        9.01        50.33        42.64        29.85        35.90        11.77 
TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MU 
      102.67        59.97        45.57        89.29        78.28        25.41 
TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       36.16        53.88        43.10         2.01        21.07         0.99 
TCGA-66-2755 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 
        0.92        21.01         0.99         1.02         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 
       23.01        19.00        12.03         3.98        12.00         1.97 
TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       40.01         5.03        30.02        10.06        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-8250 TCGA-77-6843 TCGA-77-6845 TCGA-77-7140 
       49.05         2.73         8.02        73.12        23.28        20.78 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
        0.49        42.28         0.16        46.78        15.75         6.51 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8143 TCGA-77-8148 
       53.95        37.81        82.92        53.92        26.40         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 
       54.41        65.49         0.33       117.57        22.29        42.41 
TCGA-77-A5GA TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 
       42.08        38.86        12.99         6.41        36.53        32.91 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
        1.15        18.94        19.04        24.13        31.56        16.87 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 TCGA-85-8354 TCGA-85-8666 
       34.52        10.09         0.76         5.29        32.71        15.62 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A53L 
       19.33        17.72        18.18        19.73        12.56        12.39 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        3.65         2.93        11.77        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
        2.70         3.48         4.01        14.14        16.14        17.69 
TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8023 TCGA-98-A538 
       57.07        18.31        19.36        16.57        21.34        27.16 
TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
        2.01        18.58        20.71        19.10        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG 
       13.18        13.41        11.84         0.07        64.08        51.78 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR 
       45.37         2.89        39.85        24.00        14.73        29.75 
TCGA-NK-A5CR TCGA-O2-A52Q TCGA-O2-A52W 
       83.57         3.72         8.58 

$`AMP PEAK 11(7Q21.2) WILD-TYPE`
TCGA-18-3408 TCGA-18-3410 TCGA-18-3415 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 
       75.75         4.80        92.15         2.79        49.94        27.19 
TCGA-21-1071 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 
       46.88        15.58        31.73       122.43       119.80        31.63 
TCGA-21-5784 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1016 TCGA-22-1017 
       41.69        21.99        14.93         4.31        27.02        48.82 
TCGA-22-4595 TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 
       24.13        34.75        19.30         9.57        11.77        14.63 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-33-4532 TCGA-33-4582 
       71.34        79.20        30.12        62.86         7.63       103.53 
TCGA-33-4583 TCGA-33-4587 TCGA-33-6737 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      151.27        54.44        19.76         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASJ TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 
        6.94       118.36        31.50        32.88        67.79        56.38 
TCGA-34-5239 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-37-3792 TCGA-37-4129 
       23.24         4.96        27.19         4.04         0.39         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        8.12         7.46         3.39        68.58        55.20        70.03 
TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
        1.71         1.94        36.39        35.70        17.88        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
       40.21        22.49        38.66        18.38        27.91        12.36 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
       21.47         5.46        19.59        13.38        11.77         2.93 
TCGA-43-A56U TCGA-46-6026 TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 
       14.20        13.91         0.39        28.34         8.75        27.45 
TCGA-56-5897 TCGA-56-7222 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
        0.10         0.43         1.32         6.51         0.10        17.49 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       26.89        14.07         1.35         1.81        22.75         1.18 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BY TCGA-56-A4ZJ 
       10.36         9.93        20.25        15.81        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J 
       18.74         0.26        13.25        13.55        29.95        85.12 
TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2707 TCGA-60-2710 
       56.65        21.11         3.58        12.23        21.93        66.54 
TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
       56.91        35.34        48.49         3.19        32.32        23.57 
TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN 
       26.83        70.62        66.61        58.65        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 
       25.28        16.37        34.59        16.96         1.02         2.01 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 TCGA-66-2773 
        0.99        43.99        25.05         2.01         2.01         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 
        2.01        19.00        24.95        25.97        22.98         4.04 
TCGA-66-2790 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
       22.98         6.64         6.94        13.35        16.18        14.73 
TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7335 TCGA-77-7337 
       29.56        75.09        11.18        89.98        70.13       106.95 
TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       86.76        12.59        39.09        17.72       104.09        11.54 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 
       27.39         6.97        35.90       126.18       132.36         5.92 
TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 
       30.81        27.62         9.67        11.97        34.95        31.30 
TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8071 TCGA-85-8288 TCGA-85-8350 
        1.38        29.95        25.15        14.07        13.22        22.45 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
       16.77         3.09         2.01         0.72         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA 
       13.94        12.59         0.10        25.68        14.96        24.36 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 
       16.21        15.85        14.96         0.79        24.92         9.50 
TCGA-90-7964 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       14.07         5.26         2.30        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-8170 TCGA-98-7454 
        4.01         5.03        26.63        49.87        17.46         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C 
        2.76        30.81        30.67         3.88        18.15        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK 
       21.21        20.32         4.54         1.22        13.74         4.21 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       37.22        30.58        22.78        65.49         3.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
        0.43        33.07        12.72        43.89        11.18         0.20 

  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                         0.03                          0.10 
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                       174.08                        151.27 
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                       20.480                        17.785 
[1] "0.0 - 174.1 (20.5)" "0.1 - 151.3 (17.8)"
[1] "hr=" "1.3"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(7Q21.2) MUTATED         1       35       82        1        34
  AMP PEAK 11(7Q21.2) WILD-TYPE       1       52       69        1        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(7Q21.2) MUTATED          55         1         34         10
  AMP PEAK 11(7Q21.2) WILD-TYPE        37         2         28         11
                               vv
clus                            STAGE IV
  AMP PEAK 11(7Q21.2) MUTATED          5
  AMP PEAK 11(7Q21.2) WILD-TYPE        2
D11V3, multiclass
            clus
vv           AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            35                            52
  STAGE IB                            82                            69
  STAGE II                             1                             1
  STAGE IIA                           34                            29
  STAGE IIB                           55                            37
  STAGE III                            1                             2
  STAGE IIIA                          34                            28
  STAGE IIIB                          10                            11
  STAGE IV                             5                             2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 11(7Q21.2) MUTATED    46 170  34  10
  AMP PEAK 11(7Q21.2) WILD-TYPE  65 120  35  13
D11V4, multiclass
    clus
vv   AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  T1                          46                            65
  T2                         170                           120
  T3                          34                            35
  T4                          10                            13
[1] 4 2
[1] TRUE
[1] "dimension of 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(7Q21.2) MUTATED   155  79  22   2
  AMP PEAK 11(7Q21.2) WILD-TYPE 157  52  17   3
D11V5, multiclass
    clus
vv   AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  N0                         155                           157
  N1                          79                            52
  N2                          22                            17
  N3                           2                             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"
D11V6, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q21.2) MUTATED   216   5
  AMP PEAK 11(7Q21.2) WILD-TYPE 188   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q21.2) MUTATED    216    5
  AMP PEAK 11(7Q21.2) WILD-TYPE  188    2
   clus
vv  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  0                         216                           188
  1                           5                             2
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q21.2) MUTATED    56 204
  AMP PEAK 11(7Q21.2) WILD-TYPE  71 162
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q21.2) MUTATED     56  204
  AMP PEAK 11(7Q21.2) WILD-TYPE   71  162
        clus
vv       AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  FEMALE                          56                            71
  MALE                           204                           162
[1] 2 2
[1] FALSE
D11V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(7Q21.2) MUTATED                                       8
  AMP PEAK 11(7Q21.2) WILD-TYPE                                     7
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(7Q21.2) MUTATED                                         1
  AMP PEAK 11(7Q21.2) WILD-TYPE                                       0
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 11(7Q21.2) MUTATED                                        1
  AMP PEAK 11(7Q21.2) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 11(7Q21.2) MUTATED                                         0
  AMP PEAK 11(7Q21.2) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(7Q21.2) MUTATED                                                           250
  AMP PEAK 11(7Q21.2) WILD-TYPE                                                         220
D11V9, multiclass
                                                             clus
vv                                                            AMP PEAK 11(7Q21.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         250
                                                             clus
vv                                                            AMP PEAK 11(7Q21.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           220
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q21.2) MUTATED     5 255
  AMP PEAK 11(7Q21.2) WILD-TYPE   8 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q21.2) MUTATED      5  255
  AMP PEAK 11(7Q21.2) WILD-TYPE    8  225
     clus
vv    AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  NO                            5                             8
  YES                         255                           225
[1] 2 2
[1] FALSE
D11V11, continuous
D11V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(7Q21.2) MUTATED   210   8   1  11
  AMP PEAK 11(7Q21.2) WILD-TYPE 184   4   3  11
D11V13, multiclass
    clus
vv   AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  R0                         210                           184
  R1                           8                             4
  R2                           1                             3
  RX                          11                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7Q21.2) MUTATED       7                        16   173
  AMP PEAK 11(7Q21.2) WILD-TYPE     2                        15   167
D11V14, multiclass
                           clus
vv                          AMP PEAK 11(7Q21.2) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          16
  WHITE                                             173
                           clus
vv                          AMP PEAK 11(7Q21.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V15, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q21.2) MUTATED     3 155
  AMP PEAK 11(7Q21.2) WILD-TYPE   5 154
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q21.2) MUTATED      3  155
  AMP PEAK 11(7Q21.2) WILD-TYPE    5  154
                        clus
vv                       AMP PEAK 11(7Q21.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         155
                        clus
vv                       AMP PEAK 11(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           154
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8P11.23) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8P11.23) MUTATED   135  93
  AMP PEAK 12(8P11.23) WILD-TYPE 146 103
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                           228                            249 
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                            93                            103 
$`AMP PEAK 12(8P11.23) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        7.46        79.46         4.80       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 
       92.15        31.99         1.64        86.96         6.18       154.32 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 
       27.19       119.54        99.16        70.16        34.78        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI 
      122.43         9.34       119.80        88.11        41.69        32.19 
TCGA-22-1002 TCGA-22-1011 TCGA-22-1017 TCGA-22-4591 TCGA-22-4595 TCGA-22-4596 
        4.31         1.74        48.82        20.48        24.13         0.56 
TCGA-22-4601 TCGA-22-4604 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       34.75        13.12        64.93        63.55        14.63        44.25 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 
       54.28        71.34        11.74        18.84        62.86        56.32 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       22.06       133.74        79.53       103.53       151.27        14.07 
TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASD 
       54.44        19.76        27.02         4.70         6.94       110.99 
TCGA-33-AASI TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 
       44.19         2.63        31.50        28.96        31.27        65.23 
TCGA-34-5232 TCGA-34-5239 TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 
       67.79        23.24        16.93        18.15         1.12        27.19 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3789 TCGA-37-4132 TCGA-39-5016 TCGA-39-5019 
        4.04        20.91         0.43         7.46        74.07        44.75 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 
       70.03         1.71        24.33        15.58        35.70        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       17.06        40.21        22.49        27.02        33.11        27.91 
TCGA-43-6647 TCGA-43-6770 TCGA-43-8116 TCGA-43-8118 TCGA-43-A56V TCGA-52-7810 
       24.89        21.47        11.77         2.93        12.03        30.35 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7579 
        8.75        28.96         0.10        18.25         0.62         1.45 
TCGA-56-7730 TCGA-56-8304 TCGA-56-8308 TCGA-56-8622 TCGA-56-8628 TCGA-56-A49D 
        6.51         3.48        17.00         1.81        20.25        20.94 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8390 TCGA-58-8392 
        0.13         0.26         2.76        13.25        29.95        16.47 
TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
       34.36        35.24        21.11        92.71        80.45        49.48 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG 
        3.19        32.32        29.85        23.57        26.83        70.62 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MU 
       66.61        58.65        59.97        25.28        89.29        25.41 
TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2753 
       36.16        34.59        16.96        43.10        21.07         1.02 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 
        0.92         0.99        43.99        25.05         0.99         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        7.07        23.01         3.02        12.03         3.98        12.00 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 
       22.98         4.04        30.02        10.06        49.05         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 
        6.64         6.94         8.02        73.12        75.09        89.98 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 TCGA-77-8128 
       70.13       106.95         0.16        46.78        86.76        37.81 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8148 
       39.09        17.72       104.09        11.54        26.40         9.63 
TCGA-77-8150 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
       54.41        35.90       117.57         5.92        42.41        42.08 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 
       38.86        11.97        36.53        32.91         1.15        25.15 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
       24.13        31.56        34.52        14.63        13.94        12.59 
TCGA-85-8664 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 
        0.10        17.72        14.96        19.73        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE 
       14.96         0.79        12.39         2.93        11.77        22.62 
TCGA-92-7340 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7544 
        2.70        21.04         0.16        11.70        16.14        49.87 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
       57.07        19.36        30.81        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HD 
       18.15         2.01        19.10        12.89        13.18         0.07 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
       51.78         1.22        45.37         4.21         2.89        39.85 
TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52W TCGA-XC-AA0X 
       29.75        22.78        83.57         3.65         8.58         0.20 

$`AMP PEAK 12(8P11.23) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3417 TCGA-18-4086 TCGA-18-5592 TCGA-21-1071 
       12.20        75.75        36.07         2.79        49.94        46.88 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 
       60.89        15.58        43.23        31.63        33.93        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 
       21.99         7.33        14.93        64.21        14.10        27.02 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       35.08        48.33        38.17        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5478 TCGA-22-5481 TCGA-22-5485 TCGA-22-5492 
       11.77        31.73         0.79        79.20        30.12        16.64 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4566 TCGA-33-4589 TCGA-33-A5GW TCGA-33-AAS8 
        7.63        98.01       174.08         1.55         0.30        36.62 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5234 TCGA-34-5236 
      118.36        27.16        61.61        32.88        56.38         9.07 
TCGA-34-5240 TCGA-34-5927 TCGA-34-5929 TCGA-34-8456 TCGA-37-3783 TCGA-37-3792 
       12.00        30.94         4.96        26.43         3.95         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        6.58         8.12         7.82         6.81         0.39         3.39 
TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5030 TCGA-39-5031 
       47.80        68.58        55.20        60.79         1.94        27.39 
TCGA-39-5034 TCGA-39-5036 TCGA-43-2581 TCGA-43-5668 TCGA-43-6143 TCGA-43-6771 
       36.39        35.64        38.66        18.38        12.36         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-A474 
        3.81        19.59         7.76        66.51        13.38        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
        9.73        14.20         9.99        10.65        13.91         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-6545 
        0.39        29.95        28.34         5.46        27.45         2.04 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 
        0.99         0.43         0.99         1.32         0.85         0.10 
TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8623 
       17.49        26.89        14.07         1.35        16.77        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
        1.18        10.36         9.93        15.81        19.23        13.32 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-58-8386 TCGA-58-8388 TCGA-58-8391 
       17.85        21.04        18.74         0.03        13.55        71.24 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 
       34.78        85.12        56.65        29.92         3.58        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2710 TCGA-60-2711 
       10.22        96.82        37.94        21.93        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
        9.01        56.91        50.33        35.34        48.49        42.64 
TCGA-60-2723 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
       35.90        11.77       102.67        45.57        14.99        11.34 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2737 TCGA-66-2744 TCGA-66-2754 
       78.28        16.37        53.88         2.01         0.99         2.01 
TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 TCGA-66-2777 
       21.01         2.01         1.02         2.01        19.00         2.01 
TCGA-66-2778 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 
       19.00        24.95         1.97        25.97        40.01        22.98 
TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        5.03        54.08         4.01        13.35        16.18        14.73 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
       29.56        23.28        11.18        20.78         0.49        42.28 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
       15.75         6.51        53.95        82.92        12.59        53.92 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       27.39         6.97        65.49         0.33       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 
       22.29        30.81        27.62         9.67        12.99         6.41 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
       34.95        31.30         1.38        29.95        18.94        19.04 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       14.07        16.87        10.09         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       16.77         5.29         3.09        32.71         2.01         0.72 
TCGA-85-8481 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A4QQ 
        7.76        15.62        25.68        19.33        24.36        18.18 
TCGA-85-A50M TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED 
       12.56         3.65        24.92         9.50        14.07        20.22 
TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 
       10.59         3.48         4.01         5.26         2.30         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 
        5.03        26.63        14.14        17.69        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 TCGA-98-A53C TCGA-98-A53D 
       16.57         8.42         2.76        30.67        27.02        21.21 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 
       20.32        18.58        20.71        16.11        13.41        11.84 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HJ TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       64.08         4.54        13.74        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       14.73        65.49        16.80         0.43        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       12.72        43.89        11.18 

  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                        154.32                         174.08 
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                         22.70                          16.77 
[1] "0.1 - 154.3 (22.7)" "0.0 - 174.1 (16.8)"
[1] "hr=" "1.3"
D12V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(8P11.23) MUTATED         1       41       70        1        32
  AMP PEAK 12(8P11.23) WILD-TYPE       1       46       81        1        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(8P11.23) MUTATED          42         0         34          9
  AMP PEAK 12(8P11.23) WILD-TYPE        50         3         28         12
                                vv
clus                             STAGE IV
  AMP PEAK 12(8P11.23) MUTATED          4
  AMP PEAK 12(8P11.23) WILD-TYPE        3
D12V3, multiclass
            clus
vv           AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             41                             46
  STAGE IB                             70                             81
  STAGE II                              1                              1
  STAGE IIA                            32                             31
  STAGE IIB                            42                             50
  STAGE III                             0                              3
  STAGE IIIA                           34                             28
  STAGE IIIB                            9                             12
  STAGE IV                              4                              3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 12(8P11.23) MUTATED    54 141  27  13
  AMP PEAK 12(8P11.23) WILD-TYPE  57 149  42  10
D12V4, multiclass
    clus
vv   AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  T1                           54                             57
  T2                          141                            149
  T3                           27                             42
  T4                           13                             10
[1] 4 2
[1] TRUE
[1] "dimension of 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(8P11.23) MUTATED   150  62  19   2
  AMP PEAK 12(8P11.23) WILD-TYPE 162  69  20   3
D12V5, multiclass
    clus
vv   AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  N0                          150                            162
  N1                           62                             69
  N2                           19                             20
  N3                            2                              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"
D12V6, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.23) MUTATED   193   4
  AMP PEAK 12(8P11.23) WILD-TYPE 211   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.23) MUTATED    193    4
  AMP PEAK 12(8P11.23) WILD-TYPE  211    3
   clus
vv  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  0                          193                            211
  1                            4                              3
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.23) MUTATED    47 188
  AMP PEAK 12(8P11.23) WILD-TYPE  80 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.23) MUTATED     47  188
  AMP PEAK 12(8P11.23) WILD-TYPE   80  178
        clus
vv       AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  FEMALE                           47                             80
  MALE                            188                            178
[1] 2 2
[1] FALSE
D12V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(8P11.23) MUTATED                                       7
  AMP PEAK 12(8P11.23) WILD-TYPE                                     8
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(8P11.23) MUTATED                                         1
  AMP PEAK 12(8P11.23) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 12(8P11.23) MUTATED                                        1
  AMP PEAK 12(8P11.23) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 12(8P11.23) MUTATED                                         1
  AMP PEAK 12(8P11.23) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(8P11.23) MUTATED                                                           225
  AMP PEAK 12(8P11.23) WILD-TYPE                                                         245
D12V9, multiclass
                                                             clus
vv                                                            AMP PEAK 12(8P11.23) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          225
                                                             clus
vv                                                            AMP PEAK 12(8P11.23) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            245
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.23) MUTATED     7 228
  AMP PEAK 12(8P11.23) WILD-TYPE   6 252
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.23) MUTATED      7  228
  AMP PEAK 12(8P11.23) WILD-TYPE    6  252
     clus
vv    AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  NO                             7                              6
  YES                          228                            252
[1] 2 2
[1] FALSE
D12V11, continuous
D12V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 12(8P11.23) MUTATED   195   6   0   5
  AMP PEAK 12(8P11.23) WILD-TYPE 199   6   4  17
D12V13, multiclass
    clus
vv   AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  R0                          195                            199
  R1                            6                              6
  R2                            0                              4
  RX                            5                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8P11.23) MUTATED       4                        18   155
  AMP PEAK 12(8P11.23) WILD-TYPE     5                        13   185
D12V14, multiclass
                           clus
vv                          AMP PEAK 12(8P11.23) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           18
  WHITE                                              155
                           clus
vv                          AMP PEAK 12(8P11.23) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                185
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.23) MUTATED     2 142
  AMP PEAK 12(8P11.23) WILD-TYPE   6 167
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.23) MUTATED      2  142
  AMP PEAK 12(8P11.23) WILD-TYPE    6  167
                        clus
vv                       AMP PEAK 12(8P11.23) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          142
                        clus
vv                       AMP PEAK 12(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            167
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(8Q24.21) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(8Q24.21) MUTATED   192 144
  AMP PEAK 13(8Q24.21) WILD-TYPE  89  52
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           336                            141 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           144                             52 
$`AMP PEAK 13(8Q24.21) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        7.46        79.46         4.80       117.57        11.34        23.54 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       31.99        36.07         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
      154.32        27.19       119.54        99.16        70.16        60.89 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
       34.78        31.73       122.43         9.34       119.80        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
       31.63        88.11        41.69        33.93        10.82        32.19 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 
        1.74        14.10        27.02        48.82        20.48        48.33 
TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 
        0.56        34.75        13.12        32.02         9.57        11.77 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       31.73        64.93        63.55        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
       54.28        79.20        11.74        18.84        30.12        62.86 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       22.06         7.63       174.08       151.27        14.07        54.44 
TCGA-33-4589 TCGA-33-6737 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        1.55        19.76         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
       27.16        31.50        28.96        31.27        65.23        67.79 
TCGA-34-5239 TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX 
       23.24        16.93        18.15        27.19         4.04        20.91 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 
        3.95         0.43         7.46         7.82         6.81         3.39 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
       47.80        74.07        44.75        55.20        70.03         1.71 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 
       24.33        27.39        36.39        15.58        35.70        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
       40.21        22.49        38.66        27.02        33.11        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7657 TCGA-43-7658 
       27.91        12.36        24.89        21.47         7.76        66.51 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-3768 
       11.77         2.93        11.61         9.73        12.03         9.99 
TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
       10.65         0.39        28.34         5.46        30.35         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
       27.45        28.96         0.10        18.25         2.04         0.62 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 
        0.43         1.45         1.32         0.85         0.10        17.49 
TCGA-56-8304 TCGA-56-8308 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8626 
        3.48        17.00         1.35        16.77         1.81         9.93 
TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK 
       20.25        20.94        19.23        13.32        17.85        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8392 
        0.13         0.26         2.76         0.03        13.25        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       34.78        85.12        34.36        56.65        35.24        29.92 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       21.11        10.22        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
       80.45        66.54         9.01        56.91        50.33        42.64 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
        3.19        29.85        35.90        23.57        26.83        11.77 
TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR 
       70.62        66.61        58.65        59.97        45.57        89.29 
TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 
       16.37        25.41        53.88        34.59        43.10         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
       21.07         0.99         1.02         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 
       21.01         0.99         1.02         2.01         7.07        23.01 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 
        3.02         2.01        12.03        12.00         1.97        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        4.04        22.98         5.03        30.02        10.06        54.08 
TCGA-66-2800 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 
       49.05         6.64         8.02        13.35        16.18        29.56 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 
       75.09        23.28        11.18        89.98        20.78         0.49 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       70.13       106.95         0.16        46.78        15.75         6.51 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       53.95        37.81        82.92        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
       17.72       104.09        11.54        26.40        27.39         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
        9.63        54.41        65.49       117.57        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       42.41        42.08        27.62        38.86         9.67        11.97 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 
       12.99         6.41        31.30        32.91         1.15        29.95 
TCGA-85-7950 TCGA-85-8052 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
       18.94        24.13        34.52        10.09         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8481 TCGA-85-8580 
       22.45        16.77         5.29         3.09         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
       13.94        12.59         0.10        15.62        19.33        17.72 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       14.96        18.18        19.73        15.85        14.96         0.79 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q 
       12.39         3.65         2.93        11.77        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
        2.70         3.48         5.26         2.30        21.04         0.16 
TCGA-94-7943 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 
       11.70        26.63        14.14        16.14        17.69        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8020 TCGA-98-8022 TCGA-98-8023 
       18.31        17.46        19.36         2.76        30.67        21.34 
TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-J1-A4AH TCGA-L3-A4E7 
       27.16         3.88        18.15         2.01        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF 
       16.11        13.18        13.41        11.84         0.07         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN 
       51.78         1.22        13.74         4.21        39.85        37.22 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
       24.00        14.73        29.75        22.78        83.57         3.65 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52W TCGA-XC-AA0X 
        0.43        33.07         3.72        12.72         8.58         0.20 

$`AMP PEAK 13(8Q24.21) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3415 TCGA-18-5592 TCGA-21-1071 TCGA-21-1078 
       12.20        75.75        92.15        49.94        46.88        15.58 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-4593 
       21.99         7.33        14.93         4.31        64.21        35.08 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4607 TCGA-22-5480 TCGA-22-5491 TCGA-22-5492 
       24.13        38.17        19.30        71.34        56.32        16.64 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-6738 TCGA-33-A4WN 
      133.74        98.01        79.53       103.53        27.02         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5234 
        0.30        36.62         2.63        61.61        32.88        56.38 
TCGA-34-5236 TCGA-34-5240 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 
        9.07        12.00        30.94         4.96         1.12        26.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4141 TCGA-39-5021 TCGA-39-5027 
        0.39         6.58         8.12         0.39        68.58        60.79 
TCGA-39-5030 TCGA-39-5036 TCGA-39-5039 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
        1.94        35.64        17.88         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-A56U TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-56-7221 
       13.38        14.20        13.91         0.39        29.95         0.99 
TCGA-56-7223 TCGA-56-7730 TCGA-56-8307 TCGA-56-8309 TCGA-56-8623 TCGA-56-8624 
        0.99         6.51        26.89        14.07        22.75         1.18 
TCGA-56-8625 TCGA-56-8629 TCGA-56-A4ZJ TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
       10.36        15.81        21.04        13.55        29.95        71.24 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2709 TCGA-60-2711 TCGA-60-2715 TCGA-60-2716 
        3.58        12.23        49.48        41.42        35.34        48.49 
TCGA-60-2721 TCGA-63-A5MB TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS 
       32.32       102.67        14.99        11.34        25.28        78.28 
TCGA-63-A5MV TCGA-66-2727 TCGA-66-2754 TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 
       36.16        16.96         2.01        25.05         2.01         2.01 
TCGA-66-2771 TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 
       19.00        19.00         3.98        24.95        25.97        40.01 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59J TCGA-77-6843 TCGA-77-7142 
        4.01         2.73         6.94        14.73        73.12        42.28 
TCGA-77-8008 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5GB 
       86.76        35.90         0.33       126.18       132.36        30.81 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-8048 TCGA-85-8049 TCGA-85-8070 
       36.53        34.95         1.38        25.15        19.04        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-A4CL 
       14.07        16.87        32.71         2.01         0.72        25.68 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 
       24.36        12.56        16.21        24.92         9.50        14.07 
TCGA-90-A4ED TCGA-92-8063 TCGA-94-8035 TCGA-94-8490 TCGA-96-7544 TCGA-96-A4JL 
       20.22         4.01         4.01         5.03        49.87        16.57 
TCGA-98-7454 TCGA-98-8021 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I 
        8.42        30.81        27.02        21.21        20.32        18.58 
TCGA-98-A53J TCGA-NC-A5HE TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NK-A5CT 
       20.71        64.08        45.37         2.89        30.58        65.49 
TCGA-NK-A5D1 TCGA-O2-A52V TCGA-O2-A5IB 
       16.80        43.89        11.18 

  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                          0.03                           0.30 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                        174.08                         133.74 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                         18.79                          20.22 
[1] "0.0 - 174.1 (18.8)" "0.3 - 133.7 (20.2)"
[1] "hr=" "1.2"
D13V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(8Q24.21) MUTATED         2       52      106        0        42
  AMP PEAK 13(8Q24.21) WILD-TYPE       0       35       45        2        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(8Q24.21) MUTATED          70         2         49         17
  AMP PEAK 13(8Q24.21) WILD-TYPE        22         1         13          4
                                vv
clus                             STAGE IV
  AMP PEAK 13(8Q24.21) MUTATED          7
  AMP PEAK 13(8Q24.21) WILD-TYPE        0
D13V3, multiclass
            clus
vv           AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             52                             35
  STAGE IB                            106                             45
  STAGE II                              0                              2
  STAGE IIA                            42                             21
  STAGE IIB                            70                             22
  STAGE III                             2                              1
  STAGE IIIA                           49                             13
  STAGE IIIB                           17                              4
  STAGE IV                              7                              0
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 13(8Q24.21) MUTATED    68 208  52  21
  AMP PEAK 13(8Q24.21) WILD-TYPE  43  82  17   2
D13V4, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  T1                           68                             43
  T2                          208                             82
  T3                           52                             17
  T4                           21                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 13(8Q24.21) MUTATED   210 102  29   3
  AMP PEAK 13(8Q24.21) WILD-TYPE 102  29  10   2
D13V5, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  N0                          210                            102
  N1                          102                             29
  N2                           29                             10
  N3                            3                              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"
D13V6, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED   290   7
  AMP PEAK 13(8Q24.21) WILD-TYPE 114   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED    290    7
  AMP PEAK 13(8Q24.21) WILD-TYPE  114    0
   clus
vv  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  0                          290                            114
  1                            7                              0
[1] 2 2
[1] FALSE
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED    83 266
  AMP PEAK 13(8Q24.21) WILD-TYPE  44 100
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED     83  266
  AMP PEAK 13(8Q24.21) WILD-TYPE   44  100
        clus
vv       AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  FEMALE                           83                             44
  MALE                            266                            100
[1] 2 2
[1] FALSE
D13V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                                      12
  AMP PEAK 13(8Q24.21) WILD-TYPE                                     3
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                                         0
  AMP PEAK 13(8Q24.21) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 13(8Q24.21) MUTATED                                        3
  AMP PEAK 13(8Q24.21) WILD-TYPE                                      3
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                                         1
  AMP PEAK 13(8Q24.21) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(8Q24.21) MUTATED                                                           333
  AMP PEAK 13(8Q24.21) WILD-TYPE                                                         137
D13V9, multiclass
                                                             clus
vv                                                            AMP PEAK 13(8Q24.21) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          333
                                                             clus
vv                                                            AMP PEAK 13(8Q24.21) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            137
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED    10 339
  AMP PEAK 13(8Q24.21) WILD-TYPE   3 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED     10  339
  AMP PEAK 13(8Q24.21) WILD-TYPE    3  141
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  NO                            10                              3
  YES                          339                            141
[1] 2 2
[1] FALSE
D13V11, continuous
D13V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(8Q24.21) MUTATED   281  10   1  15
  AMP PEAK 13(8Q24.21) WILD-TYPE 113   2   3   7
D13V13, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  R0                          281                            113
  R1                           10                              2
  R2                            1                              3
  RX                           15                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(8Q24.21) MUTATED       6                        25   235
  AMP PEAK 13(8Q24.21) WILD-TYPE     3                         6   105
D13V14, multiclass
                           clus
vv                          AMP PEAK 13(8Q24.21) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           25
  WHITE                                              235
                           clus
vv                          AMP PEAK 13(8Q24.21) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED     7 214
  AMP PEAK 13(8Q24.21) WILD-TYPE   1  95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED      7  214
  AMP PEAK 13(8Q24.21) WILD-TYPE    1   95
                        clus
vv                       AMP PEAK 13(8Q24.21) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          214
                        clus
vv                       AMP PEAK 13(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             95
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(9P13.3) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 14(9P13.3) MUTATED    76  52
  AMP PEAK 14(9P13.3) WILD-TYPE 205 144
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          128                           349 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                           52                           144 
$`AMP PEAK 14(9P13.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3417 TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 
       12.20         7.46        36.07         6.18       154.32       119.54 
TCGA-21-1075 TCGA-22-0944 TCGA-22-4591 TCGA-22-4595 TCGA-22-4604 TCGA-22-4609 
       70.16         7.33        20.48        24.13        13.12         9.57 
TCGA-22-4613 TCGA-22-5474 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5489 
       11.77        14.63        54.28        79.20        11.74        62.86 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
        7.63       133.74       174.08       103.53       151.27        14.07 
TCGA-33-4587 TCGA-33-4589 TCGA-33-AAS8 TCGA-34-2600 TCGA-34-5239 TCGA-34-5240 
       54.44         1.55        36.62        61.61        23.24        12.00 
TCGA-34-7107 TCGA-37-3792 TCGA-37-4133 TCGA-39-5011 TCGA-39-5021 TCGA-39-5024 
        1.12         0.39         7.82        47.80        68.58        70.03 
TCGA-39-5031 TCGA-43-6143 TCGA-43-7658 TCGA-43-A475 TCGA-43-A56V TCGA-46-3768 
       27.39        12.36        66.51         9.73        12.03         9.99 
TCGA-46-6025 TCGA-51-4079 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-7221 
       10.65         0.39        28.34         5.46        30.35         0.99 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8504 TCGA-56-8626 TCGA-56-A49D TCGA-58-8386 
        3.48        26.89        16.77         9.93        20.94         0.03 
TCGA-58-8387 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2704 
       13.25        85.12        56.65        35.24        21.11        37.94 
TCGA-60-2712 TCGA-60-2714 TCGA-60-2719 TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MT 
        9.01        50.33        42.64        59.97        45.57        16.37 
TCGA-63-A5MU TCGA-63-A5MV TCGA-66-2744 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
       25.41        36.16         0.99         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 
       25.05         0.99         2.01        54.08        49.05         2.73 
TCGA-68-8250 TCGA-68-A59J TCGA-77-6842 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
        8.02        14.73        29.56        11.18        89.98         0.49 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8136 TCGA-77-8150 TCGA-77-8156 
        6.51        53.95        37.81        39.09        54.41         0.33 
TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
      117.57        42.08        27.62        12.99         6.41        36.53 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       31.30        32.91         1.15        16.87        34.52        10.09 
TCGA-85-8352 TCGA-85-8353 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A511 TCGA-90-7767 
        5.29         3.09        25.68        17.72        14.96         2.93 
TCGA-92-8064 TCGA-94-8035 TCGA-94-8490 TCGA-96-7544 TCGA-96-A4JK TCGA-98-8022 
        5.26         4.01         5.03        49.87        19.36        30.67 
TCGA-98-A539 TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
        3.88        18.58        12.89        16.11        13.18        13.41 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HR 
       45.37         2.89        39.85        37.22        24.00        29.75 
TCGA-NC-A5HT TCGA-O2-A52S 
       22.78        12.72 

$`AMP PEAK 14(9P13.3) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       75.75        79.46         4.80       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 
       92.15        31.99         1.64        86.96         2.79        49.94 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       27.19        46.88        99.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       31.73       122.43         9.34       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
       88.11        41.69        33.93        10.82        32.19        21.99 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       14.93         4.31        64.21         1.74        14.10        27.02 
TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       48.82        35.08        48.33         0.56        38.17        34.75 
TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 
       32.02        19.30        31.73        64.93        63.55        44.25 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 
        0.79        71.34        18.84        30.12        56.32        16.64 
TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4547 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
       22.06        98.01        79.53        19.76        27.02         4.70 
TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
        0.30         6.94       110.99        44.19       118.36        27.16 
TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
        2.63        31.50        28.96        32.88        31.27        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       67.79        56.38         9.07        16.93        30.94        18.15 
TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        4.96        27.19         4.04        26.43        20.91         3.95 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 
        0.43         6.58         8.12         7.46         6.81         0.39 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 
        3.39        74.07        44.75        55.20        60.79         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
       24.33         1.94        36.39        15.58        35.64        35.70 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
       17.88        17.06        40.21        22.49        38.66        27.02 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       33.11        18.38        27.91        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
        3.81        19.59         7.76        13.38        11.77         2.93 
TCGA-43-A474 TCGA-43-A56U TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7811 
       11.61        14.20        13.91         0.39        29.95         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
       27.45        28.96         0.10        18.25         2.04         0.62 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
        0.43         0.99         1.45         1.32         0.85         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        0.10        17.49        17.00        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
       22.75         1.18        10.36        20.25        15.81        19.23 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
       13.32        17.85        21.04        18.74         0.13         0.26 
TCGA-56-A62T TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
        2.76        13.55        29.95        71.24        16.47        34.78 
TCGA-58-A46K TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       34.36        29.92         3.58        12.23        10.22        96.82 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       92.71        21.93        80.45        49.48        66.54        41.42 
TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
       56.91        35.34        48.49         3.19        32.32        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG 
       35.90        23.57        26.83        11.77       102.67        70.62 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       66.61        58.65        14.99        11.34        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
       78.28        53.88        34.59        16.96        43.10         2.01 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2766 TCGA-66-2767 
       21.07         1.02         2.01         0.92         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         7.07        23.01        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
       25.97        40.01        22.98         4.04        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
       30.02        10.06         4.01         6.64         6.94        13.35 
TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7140 TCGA-77-7142 
       16.18        73.12        75.09        23.28        20.78        42.28 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 
       70.13       106.95         0.16        46.78        15.75        86.76 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       82.92        12.59        53.92        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 
       26.40        27.39         6.97         9.63        65.49        35.90 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB 
      126.18       132.36        22.29         5.92        42.41        30.81 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 TCGA-85-7710 TCGA-85-7844 
       38.86         9.67        11.97        34.95         1.38        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       18.94        25.15        19.04        24.13        31.56        14.07 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 
        0.76        13.22        22.45        16.77        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
        0.72         7.76        14.63        13.94        12.59         0.10 
TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       15.62        19.33        14.96        24.36        18.18        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       12.56        16.21        15.85         0.79        12.39         3.65 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
       24.92         9.50        11.77        14.07        20.22        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 
       10.59         2.70         3.48         4.01         2.30        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
        0.16        11.70        26.63        14.14        16.14        17.69 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       57.07        18.31        17.46        16.57         8.42         2.76 
TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.81        21.34        27.16        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-J1-A4AH TCGA-MF-A522 TCGA-NC-A5HD 
       21.21        20.32        20.71        19.10        11.84         0.07 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK 
       64.08         4.54        51.78         1.22        13.74         4.21 
TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       30.58        14.73        83.57        65.49         3.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
        0.43        33.07         3.72        43.89         8.58        11.18 
TCGA-XC-AA0X 
        0.20 

  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                         0.03                          0.07 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                       174.08                        132.36 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                        19.92                         19.04 
[1] "0.0 - 174.1 (19.9)" "0.1 - 132.4 (19.0)"
[1] "hr=" "1.2"
D14V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(9P13.3) MUTATED         0       24       31        1        13
  AMP PEAK 14(9P13.3) WILD-TYPE       2       63      120        1        50
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(9P13.3) MUTATED          34         1         19          5
  AMP PEAK 14(9P13.3) WILD-TYPE        58         2         43         16
                               vv
clus                            STAGE IV
  AMP PEAK 14(9P13.3) MUTATED          3
  AMP PEAK 14(9P13.3) WILD-TYPE        4
D14V3, multiclass
            clus
vv           AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                            24                            63
  STAGE IB                            31                           120
  STAGE II                             1                             1
  STAGE IIA                           13                            50
  STAGE IIB                           34                            58
  STAGE III                            1                             2
  STAGE IIIA                          19                            43
  STAGE IIIB                           5                            16
  STAGE IV                             3                             4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 14(9P13.3) MUTATED    27  76  21   8
  AMP PEAK 14(9P13.3) WILD-TYPE  84 214  48  15
D14V4, multiclass
    clus
vv   AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  T1                          27                            84
  T2                          76                           214
  T3                          21                            48
  T4                           8                            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  AMP PEAK 14(9P13.3) MUTATED    77  42  11   0
  AMP PEAK 14(9P13.3) WILD-TYPE 235  89  28   5
D14V5, multiclass
    clus
vv   AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  N0                          77                           235
  N1                          42                            89
  N2                          11                            28
  N3                           0                             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"
D14V6, binary
                               cls
clus                              0   1
  AMP PEAK 14(9P13.3) MUTATED   111   3
  AMP PEAK 14(9P13.3) WILD-TYPE 293   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED    111    3
  AMP PEAK 14(9P13.3) WILD-TYPE  293    4
   clus
vv  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  0                         111                           293
  1                           3                             4
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(9P13.3) MUTATED    33  99
  AMP PEAK 14(9P13.3) WILD-TYPE  94 267
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED     33   99
  AMP PEAK 14(9P13.3) WILD-TYPE   94  267
        clus
vv       AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  FEMALE                          33                            94
  MALE                            99                           267
[1] 2 2
[1] FALSE
D14V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(9P13.3) MUTATED                                       6
  AMP PEAK 14(9P13.3) WILD-TYPE                                     9
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(9P13.3) MUTATED                                         1
  AMP PEAK 14(9P13.3) WILD-TYPE                                       0
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 14(9P13.3) MUTATED                                        0
  AMP PEAK 14(9P13.3) WILD-TYPE                                      6
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 14(9P13.3) MUTATED                                         1
  AMP PEAK 14(9P13.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(9P13.3) MUTATED                                                           124
  AMP PEAK 14(9P13.3) WILD-TYPE                                                         346
D14V9, multiclass
                                                             clus
vv                                                            AMP PEAK 14(9P13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         124
                                                             clus
vv                                                            AMP PEAK 14(9P13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           346
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, binary
                               cls
clus                              0   1
  AMP PEAK 14(9P13.3) MUTATED     3 129
  AMP PEAK 14(9P13.3) WILD-TYPE  10 351
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED      3  129
  AMP PEAK 14(9P13.3) WILD-TYPE   10  351
     clus
vv    AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  NO                            3                            10
  YES                         129                           351
[1] 2 2
[1] FALSE
D14V11, continuous
D14V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 14(9P13.3) MUTATED   115   2   0   2
  AMP PEAK 14(9P13.3) WILD-TYPE 279  10   4  20
D14V13, multiclass
    clus
vv   AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  R0                         115                           279
  R1                           2                            10
  R2                           0                             4
  RX                           2                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(9P13.3) MUTATED       1                         7    95
  AMP PEAK 14(9P13.3) WILD-TYPE     8                        24   245
D14V14, multiclass
                           clus
vv                          AMP PEAK 14(9P13.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              95
                           clus
vv                          AMP PEAK 14(9P13.3) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            24
  WHITE                                               245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, binary
                               cls
clus                              0   1
  AMP PEAK 14(9P13.3) MUTATED     2  77
  AMP PEAK 14(9P13.3) WILD-TYPE   6 232
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED      2   77
  AMP PEAK 14(9P13.3) WILD-TYPE    6  232
                        clus
vv                       AMP PEAK 14(9P13.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          77
                        clus
vv                       AMP PEAK 14(9P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           232
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(11Q13.3) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(11Q13.3) MUTATED   112  66
  AMP PEAK 15(11Q13.3) WILD-TYPE 169 130
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           178                            299 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            66                            130 
$`AMP PEAK 15(11Q13.3) MUTATED`
TCGA-18-3410 TCGA-18-3412 TCGA-18-3416 TCGA-21-1070 TCGA-21-1072 TCGA-21-1079 
        4.80        11.34        31.99       119.54        99.16        31.73 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
       43.23        31.63        33.93         4.31         1.74        14.10 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-5471 
       48.82        20.48        35.08        48.33        24.13        31.73 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4582 TCGA-33-4583 TCGA-33-4589 TCGA-33-6737 
       56.32        22.06       103.53       151.27         1.55        19.76 
TCGA-33-AASB TCGA-33-AASD TCGA-34-5231 TCGA-34-5232 TCGA-34-5239 TCGA-34-8455 
        6.94       110.99        65.23        67.79        23.24         4.04 
TCGA-34-8456 TCGA-37-3789 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
       26.43         0.43         7.46         6.81         0.39         3.39 
TCGA-39-5011 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 
       47.80        24.33        27.39        36.39        35.64        35.70 
TCGA-43-2578 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6771 TCGA-43-7657 
       22.49        18.38        27.91        12.36         5.46         7.76 
TCGA-43-7658 TCGA-43-8116 TCGA-46-6025 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 
       66.51        11.77        10.65         5.46        30.35        27.45 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7579 TCGA-56-7582 
       28.96        18.25         2.04         0.99         1.45         0.85 
TCGA-56-7822 TCGA-56-8308 TCGA-56-8503 TCGA-56-8504 TCGA-56-A49D TCGA-56-A4BX 
       17.49        17.00         1.35        16.77        20.94        13.32 
TCGA-56-A5DR TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-60-2698 
        0.13         0.03        13.25        29.95        71.24        10.22 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2725 
       50.33        35.34        42.64         3.19        29.85        26.83 
TCGA-60-2726 TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       11.77        58.65        59.97        78.28        16.37        25.41 
TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       36.16        53.88        43.10         2.01        21.07         0.99 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2777 
       25.05         0.99         2.01         2.01         2.01         2.01 
TCGA-66-2781 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 
        3.98        25.97         4.04        22.98         5.03        10.06 
TCGA-68-7755 TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 
        2.73        14.73        29.56        23.28        11.18         0.49 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 
       42.28       106.95        46.78        15.75         6.51        53.95 
TCGA-77-8133 TCGA-77-8139 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 
       53.92       104.09        26.40        27.39         9.63        65.49 
TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GB TCGA-85-7697 
       35.90       132.36       117.57         5.92        30.81        34.95 
TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 
       32.91         1.15        18.94        25.15        14.07        16.87 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 TCGA-85-8354 TCGA-85-8582 
       34.52        10.09         0.76         5.29        32.71        13.94 
TCGA-85-8664 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
        0.10        19.33        17.72        18.18        19.73        12.56 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
       15.85        14.96        12.39         3.65         9.50         2.93 
TCGA-90-7964 TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 TCGA-94-7943 
       14.07        22.62         3.48         5.26        21.04        11.70 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-98-8020 
       14.14        49.87        57.07        18.31        19.36         2.76 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A53B TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
       30.67        27.16         2.01        13.41        11.84         0.07 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HR 
       51.78         1.22        39.85        30.58        14.73        29.75 
TCGA-NC-A5HT TCGA-NK-A5D1 TCGA-O2-A52S TCGA-XC-AA0X 
       22.78        16.80        12.72         0.20 

$`AMP PEAK 15(11Q13.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 
       12.20         7.46        75.75        79.46       117.57        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       92.15        36.07         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 
      154.32        49.94        27.19        46.88        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5783 
       34.78        15.58       122.43         9.34       119.80        88.11 
TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
       41.69        10.82        32.19        21.99         7.33        14.93 
TCGA-22-1005 TCGA-22-1016 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       64.21        27.02         0.56        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 
       32.02        19.30         9.57        11.77        64.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       14.63        44.25         0.79        54.28        71.34        79.20 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4532 
       11.74        18.84        30.12        62.86        16.64         7.63 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 
      133.74        98.01        79.53       174.08        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASI TCGA-33-AASJ 
       27.02         4.70         0.30        36.62        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       27.16         2.63        61.61        31.50        28.96        32.88 
TCGA-34-2609 TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       31.27        56.38         9.07        12.00        16.93        30.94 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 
       18.15         4.96         1.12        27.19        20.91         3.95 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 TCGA-39-5016 TCGA-39-5019 
        0.39         6.58         8.12         7.82        74.07        44.75 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
       68.58        55.20        70.03        60.79         1.71         1.94 
TCGA-39-5035 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       15.58        17.88        17.06        40.21        38.66        27.02 
TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       33.11        24.89        21.47         3.81        19.59        13.38 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
        2.93        11.61         9.73        14.20        12.03         9.99 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 
       13.91         0.39         0.39        29.95        28.34         8.75 
TCGA-56-5897 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 
        0.10         0.62         0.43         0.99         1.32         6.51 
TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 
        0.10         3.48        26.89        14.07         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
        1.18        10.36         9.93        20.25        15.81        19.23 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8388 
       17.85        21.04        18.74         0.26         2.76        13.55 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       16.47        34.78        85.12        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 
       29.92        21.11         3.58        12.23        96.82        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       92.71        21.93        80.45        49.48        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2716 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
        9.01        56.91        48.49        32.32        35.90        23.57 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
      102.67        70.62        66.61        45.57        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MY TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 
       25.28        89.29        34.59        16.96         1.02         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2766 TCGA-66-2769 
        0.92         0.99        43.99        21.01         1.02         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
       23.01        19.00         3.02        19.00        12.03        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2792 TCGA-66-2794 
       24.95         1.97        40.01        22.98        30.02        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
        4.01        49.05         6.64         6.94         8.02        13.35 
TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7140 TCGA-77-7335 
       16.18        73.12        75.09        89.98        20.78        70.13 
TCGA-77-7338 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 
        0.16        86.76        37.81        82.92        12.59        39.09 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8145 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ 
       17.72        11.54         6.97        54.41         0.33       126.18 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       22.29        42.41        42.08        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7710 
       11.97        12.99         6.41        36.53        31.30         1.38 
TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8288 TCGA-85-8350 
       29.95        19.04        24.13        31.56        13.22        22.45 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
       16.77         3.09         2.01         0.72         7.76        14.63 
TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50Z 
       12.59        15.62        25.68        14.96        24.36        16.21 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 
        0.79        24.92        11.77        20.22        10.59         2.70 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        4.01         2.30         0.16         4.01         5.03        26.63 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       16.14        17.69        17.46        16.57         8.42        30.81 
TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       21.34         3.88        18.15        27.02        21.21        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       18.58        20.71        19.10        12.89        16.11        13.18 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
       64.08         4.54        45.37        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE 
       37.22        24.00        83.57        65.49         3.65         0.43 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       33.07         3.72        43.89         8.58        11.18 

  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                          0.03                           0.10 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                        151.27                         174.08 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                         18.66                          19.23 
[1] "0.0 - 151.3 (18.7)" "0.1 - 174.1 (19.2)"
[1] "hr=" "1.1"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(11Q13.3) MUTATED         0       37       46        0        25
  AMP PEAK 15(11Q13.3) WILD-TYPE       2       50      105        2        38
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(11Q13.3) MUTATED          36         1         26          6
  AMP PEAK 15(11Q13.3) WILD-TYPE        56         2         36         15
                                vv
clus                             STAGE IV
  AMP PEAK 15(11Q13.3) MUTATED          4
  AMP PEAK 15(11Q13.3) WILD-TYPE        3
D15V3, multiclass
            clus
vv           AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                             37                             50
  STAGE IB                             46                            105
  STAGE II                              0                              2
  STAGE IIA                            25                             38
  STAGE IIB                            36                             56
  STAGE III                             1                              2
  STAGE IIIA                           26                             36
  STAGE IIIB                            6                             15
  STAGE IV                              4                              3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 15(11Q13.3) MUTATED    46 102  28   6
  AMP PEAK 15(11Q13.3) WILD-TYPE  65 188  41  17
D15V4, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  T1                           46                             65
  T2                          102                            188
  T3                           28                             41
  T4                            6                             17
[1] 4 2
[1] TRUE
[1] "dimension of 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(11Q13.3) MUTATED   111  49  16   3
  AMP PEAK 15(11Q13.3) WILD-TYPE 201  82  23   2
D15V5, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  N0                          111                            201
  N1                           49                             82
  N2                           16                             23
  N3                            3                              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"
D15V6, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED   152   4
  AMP PEAK 15(11Q13.3) WILD-TYPE 252   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED    152    4
  AMP PEAK 15(11Q13.3) WILD-TYPE  252    3
   clus
vv  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  0                          152                            252
  1                            4                              3
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED    40 142
  AMP PEAK 15(11Q13.3) WILD-TYPE  87 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED     40  142
  AMP PEAK 15(11Q13.3) WILD-TYPE   87  224
        clus
vv       AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  FEMALE                           40                             87
  MALE                            142                            224
[1] 2 2
[1] FALSE
D15V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                                       6
  AMP PEAK 15(11Q13.3) WILD-TYPE                                     9
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                                         1
  AMP PEAK 15(11Q13.3) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 15(11Q13.3) MUTATED                                        1
  AMP PEAK 15(11Q13.3) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                                         0
  AMP PEAK 15(11Q13.3) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(11Q13.3) MUTATED                                                           174
  AMP PEAK 15(11Q13.3) WILD-TYPE                                                         296
D15V9, multiclass
                                                             clus
vv                                                            AMP PEAK 15(11Q13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          174
                                                             clus
vv                                                            AMP PEAK 15(11Q13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            296
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED     2 180
  AMP PEAK 15(11Q13.3) WILD-TYPE  11 300
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      2  180
  AMP PEAK 15(11Q13.3) WILD-TYPE   11  300
     clus
vv    AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  NO                             2                             11
  YES                          180                            300
[1] 2 2
[1] FALSE
D15V11, continuous
D15V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(11Q13.3) MUTATED   149   3   1   7
  AMP PEAK 15(11Q13.3) WILD-TYPE 245   9   3  15
D15V13, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  R0                          149                            245
  R1                            3                              9
  R2                            1                              3
  RX                            7                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(11Q13.3) MUTATED       3                         8   128
  AMP PEAK 15(11Q13.3) WILD-TYPE     6                        23   212
D15V14, multiclass
                           clus
vv                          AMP PEAK 15(11Q13.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              128
                           clus
vv                          AMP PEAK 15(11Q13.3) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             23
  WHITE                                                212
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V15, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED     3 107
  AMP PEAK 15(11Q13.3) WILD-TYPE   5 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      3  107
  AMP PEAK 15(11Q13.3) WILD-TYPE    5  202
                        clus
vv                       AMP PEAK 15(11Q13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          107
                        clus
vv                       AMP PEAK 15(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            202
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(12P13.33) MUTATION ANALYSIS
D16V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 16(12P13.33) MUTATED   140 100
  AMP PEAK 16(12P13.33) WILD-TYPE 141  96
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                            240                             237 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                            100                              96 
$`AMP PEAK 16(12P13.33) MUTATED`
TCGA-18-3410 TCGA-18-3412 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 
        4.80        11.34        31.99        36.07        86.96       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1077 TCGA-21-1079 
       49.94       119.54        46.88        99.16        34.78        31.73 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-A5DI TCGA-22-1012 TCGA-22-1016 
       43.23        31.63        33.93        32.19        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       20.48        35.08        24.13        38.17        34.75        13.12 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 
       11.77        63.55        14.63        44.25        54.28        71.34 
TCGA-22-5482 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4538 TCGA-33-4566 
       11.74        62.86        56.32         7.63        98.01       174.08 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 TCGA-33-AASD 
      103.53        14.07        54.44        19.76        27.02       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 
       44.19       118.36         2.63        28.96        31.27        65.23 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 
       23.24        12.00        16.93        18.15         1.12         4.04 
TCGA-34-8456 TCGA-37-3792 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 TCGA-39-5034 
       26.43         0.39         3.39        44.75        68.58        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 
       15.58        35.64        35.70        17.06        38.66        27.02 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6770 TCGA-43-6771 TCGA-43-7658 
       33.11        18.38        27.91        21.47         5.46        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V 
       13.38        11.77         2.93        11.61         9.73        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 
        9.99        10.65        13.91         0.39        29.95         5.46 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
        8.75        27.45        28.96        18.25         2.04         0.62 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-8304 
        0.43         0.99         0.85         6.51        17.49         3.48 
TCGA-56-8308 TCGA-56-8504 TCGA-56-8622 TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D 
       17.00        16.77         1.81        10.36        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DR TCGA-58-8387 TCGA-58-8391 TCGA-58-A46K 
       19.23        13.32         0.13        13.25        71.24        34.36 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
       29.92        21.11        10.22        96.82        37.94        92.71 
TCGA-60-2708 TCGA-60-2711 TCGA-60-2712 TCGA-60-2719 TCGA-60-2723 TCGA-60-2725 
       80.45        41.42         9.01        42.64        35.90        26.83 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML 
       11.77       102.67        66.61        58.65        59.97        45.57 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2727 TCGA-66-2737 
       89.29        78.28        16.37        53.88        16.96         2.01 
TCGA-66-2744 TCGA-66-2756 TCGA-66-2758 TCGA-66-2767 TCGA-66-2773 TCGA-66-2777 
        0.99         0.99        21.01         2.01         3.02         2.01 
TCGA-66-2781 TCGA-66-2785 TCGA-66-2787 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        3.98         1.97        40.01        30.02        10.06        54.08 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        2.73         6.64         8.02        13.35        16.18        14.73 
TCGA-77-6842 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       29.56        89.98        20.78         0.49        42.28        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
      106.95         0.16        46.78        15.75        53.95        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8143 TCGA-77-8148 TCGA-77-8156 
       82.92        53.92        17.72        26.40         9.63         0.33 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
      132.36       117.57        22.29         5.92        42.41        42.08 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 
       27.62        38.86        11.97        36.53        34.95        32.91 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       29.95        18.94        25.15        19.04        24.13        31.56 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 TCGA-85-8481 
       10.09         0.76        22.45         5.29        32.71         7.76 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QR 
       12.59         0.10        15.62        19.33        17.72        19.73 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
       15.85        14.96        12.39         2.93        11.77        14.07 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7557 
       22.62        10.59         2.70         3.48         5.26         0.16 
TCGA-94-7943 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
       11.70        14.14        16.14        17.69        49.87        57.07 
TCGA-96-A4JK TCGA-98-8023 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53J TCGA-J1-A4AH 
       19.36        21.34        27.16         2.01        20.71        19.10 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HH 
       16.11        13.18        13.41        11.84        51.78         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HR 
       13.74         4.21        39.85        30.58        14.73        29.75 
TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       83.57         0.43        33.07        43.89         8.58        11.18 

$`AMP PEAK 16(12P13.33) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 
       12.20         7.46        75.75        79.46       117.57        23.54 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-5595 TCGA-21-1075 
       92.15         1.64         6.18         2.79        27.19        70.16 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5783 
       60.89        15.58       122.43         9.34       119.80        88.11 
TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       41.69        10.82        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-22-4605 
       64.21         1.74        48.82        48.33         0.56        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 TCGA-22-5478 TCGA-22-5481 
       19.30         9.57        31.73        64.93         0.79        79.20 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4547 
       18.84        30.12        16.64        22.06       133.74        79.53 
TCGA-33-4583 TCGA-33-4589 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
      151.27         1.55         4.70         0.30        36.62         6.94 
TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 
       27.16        61.61        31.50        32.88        67.79        56.38 
TCGA-34-5236 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 
        9.07        30.94         4.96        27.19        20.91         3.95 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         6.58         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        0.39        47.80        74.07        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5039 TCGA-43-2576 
        1.71        24.33         1.94        27.39        17.88        40.21 
TCGA-43-2578 TCGA-43-6143 TCGA-43-6647 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 
       22.49        12.36        24.89         3.81        19.59         7.76 
TCGA-43-A56U TCGA-51-4080 TCGA-52-7622 TCGA-52-7810 TCGA-56-5897 TCGA-56-7221 
       14.20         0.39        28.34        30.35         0.10         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
        1.45         1.32         0.10        26.89        14.07         1.35 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BY TCGA-56-A4ZJ 
       22.75         1.18         9.93        20.25        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 
       18.74         0.26         2.76         0.03        13.55        29.95 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2696 
       16.47        34.78        85.12        56.65        35.24         3.58 
TCGA-60-2697 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       12.23        21.93        49.48        66.54        56.91        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 
       35.34        48.49         3.19        32.32        29.85        23.57 
TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MU TCGA-63-A5MV 
       70.62        14.99        11.34        25.28        25.41        36.16 
TCGA-63-A5MY TCGA-66-2734 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       34.59        43.10        21.07         1.02         2.01         0.92 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
       43.99        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
        7.07        23.01        19.00        19.00        12.03        12.00 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
       24.95        25.97        22.98         4.04        22.98         5.03 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
        4.01        49.05         6.94        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 
       11.18         6.51        86.76        12.59        39.09       104.09 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       11.54        27.39         6.97        54.41        65.49        35.90 
TCGA-77-A5FZ TCGA-77-A5GB TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 
      126.18        30.81         9.67        12.99         6.41        31.30 
TCGA-85-7710 TCGA-85-7843 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8288 
        1.38         1.15        14.07        16.87        34.52        13.22 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 
       16.77         3.09         2.01         0.72        14.63        13.94 
TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z 
       25.68        14.96        24.36        18.18        12.56        16.21 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-A4ED TCGA-92-8063 
        0.79         3.65        24.92         9.50        20.22         4.01 
TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-8169 
        2.30        21.04         4.01         5.03        26.63        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       17.46        16.57         8.42         2.76        30.81        30.67 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I 
        3.88        18.15        27.02        21.21        20.32        18.58 
TCGA-L3-A4E7 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HI TCGA-NC-A5HL 
       12.89         0.07        64.08         4.54        45.37         2.89 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       37.22        24.00        22.78        65.49         3.65        16.80 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-XC-AA0X 
        3.72        12.72         0.20 

  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                           0.10                            0.03 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                         174.08                          151.27 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                         19.745                          18.580 
[1] "0.1 - 174.1 (19.7)" "0.0 - 151.3 (18.6)"
[1] "hr=" "1.1"
D16V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(12P13.33) MUTATED         2       37       79        2        31
  AMP PEAK 16(12P13.33) WILD-TYPE       0       50       72        0        32
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(12P13.33) MUTATED          51         1         37          8
  AMP PEAK 16(12P13.33) WILD-TYPE        41         2         25         13
                                 vv
clus                              STAGE IV
  AMP PEAK 16(12P13.33) MUTATED          2
  AMP PEAK 16(12P13.33) WILD-TYPE        5
D16V3, multiclass
            clus
vv           AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  STAGE I                                2                               0
  STAGE IA                              37                              50
  STAGE IB                              79                              72
  STAGE II                               2                               0
  STAGE IIA                             31                              32
  STAGE IIB                             51                              41
  STAGE III                              1                               2
  STAGE IIIA                            37                              25
  STAGE IIIB                             8                              13
  STAGE IV                               2                               5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 16(12P13.33) MUTATED    45 157  37  12
  AMP PEAK 16(12P13.33) WILD-TYPE  66 133  32  11
D16V4, multiclass
    clus
vv   AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  T1                            45                              66
  T2                           157                             133
  T3                            37                              32
  T4                            12                              11
[1] 4 2
[1] TRUE
[1] "dimension of 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(12P13.33) MUTATED   154  73  22   1
  AMP PEAK 16(12P13.33) WILD-TYPE 158  58  17   4
D16V5, multiclass
    clus
vv   AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  N0                           154                             158
  N1                            73                              58
  N2                            22                              17
  N3                             1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                                 cls
clus                                0   1
  AMP PEAK 16(12P13.33) MUTATED   203   2
  AMP PEAK 16(12P13.33) WILD-TYPE 201   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(12P13.33) MUTATED    203    2
  AMP PEAK 16(12P13.33) WILD-TYPE  201    5
   clus
vv  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  0                           203                             201
  1                             2                               5
[1] 2 2
[1] FALSE
D16V7, binary
                                 cls
clus                                0   1
  AMP PEAK 16(12P13.33) MUTATED    54 197
  AMP PEAK 16(12P13.33) WILD-TYPE  73 169
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(12P13.33) MUTATED     54  197
  AMP PEAK 16(12P13.33) WILD-TYPE   73  169
        clus
vv       AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  FEMALE                            54                              73
  MALE                             197                             169
[1] 2 2
[1] FALSE
D16V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(12P13.33) MUTATED                                       8
  AMP PEAK 16(12P13.33) WILD-TYPE                                     7
                                 vv
clus                              LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(12P13.33) MUTATED                                         0
  AMP PEAK 16(12P13.33) WILD-TYPE                                       1
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 16(12P13.33) MUTATED                                        2
  AMP PEAK 16(12P13.33) WILD-TYPE                                      4
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 16(12P13.33) MUTATED                                         1
  AMP PEAK 16(12P13.33) WILD-TYPE                                       0
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(12P13.33) MUTATED                                                           240
  AMP PEAK 16(12P13.33) WILD-TYPE                                                         230
D16V9, multiclass
                                                             clus
vv                                                            AMP PEAK 16(12P13.33) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           240
                                                             clus
vv                                                            AMP PEAK 16(12P13.33) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             230
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, binary
                                 cls
clus                                0   1
  AMP PEAK 16(12P13.33) MUTATED     5 246
  AMP PEAK 16(12P13.33) WILD-TYPE   8 234
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(12P13.33) MUTATED      5  246
  AMP PEAK 16(12P13.33) WILD-TYPE    8  234
     clus
vv    AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  NO                              5                               8
  YES                           246                             234
[1] 2 2
[1] FALSE
D16V11, continuous
D16V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 16(12P13.33) MUTATED   196   6   1  12
  AMP PEAK 16(12P13.33) WILD-TYPE 198   6   3  10
D16V13, multiclass
    clus
vv   AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  R0                           196                             198
  R1                             6                               6
  R2                             1                               3
  RX                            12                              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(12P13.33) MUTATED       2                        18   182
  AMP PEAK 16(12P13.33) WILD-TYPE     7                        13   158
D16V14, multiclass
                           clus
vv                          AMP PEAK 16(12P13.33) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            18
  WHITE                                               182
                           clus
vv                          AMP PEAK 16(12P13.33) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              13
  WHITE                                                 158
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V15, binary
                                 cls
clus                                0   1
  AMP PEAK 16(12P13.33) MUTATED     4 159
  AMP PEAK 16(12P13.33) WILD-TYPE   4 150
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(12P13.33) MUTATED      4  159
  AMP PEAK 16(12P13.33) WILD-TYPE    4  150
                        clus
vv                       AMP PEAK 16(12P13.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           159
                        clus
vv                       AMP PEAK 16(12P13.33) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             150
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(12Q15) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 17(12Q15) MUTATED   100  72
  AMP PEAK 17(12Q15) WILD-TYPE 181 124
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                         172                          305 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                          72                          124 
$`AMP PEAK 17(12Q15) MUTATED`
TCGA-18-3410 TCGA-18-3412 TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 
        4.80        11.34        36.07        86.96       154.32       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1077 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 
       46.88        99.16        34.78       119.80        43.23        33.93 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 
       10.82        32.19        27.02        48.82        35.08        48.33 
TCGA-22-4601 TCGA-22-4604 TCGA-22-5471 TCGA-22-5473 TCGA-22-5477 TCGA-22-5479 
       34.75        13.12        31.73        63.55        44.25        54.28 
TCGA-22-5480 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 
       71.34        56.32        22.06         7.63        98.01       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-6737 TCGA-33-A5GW TCGA-34-2596 TCGA-34-2605 
      151.27        14.07        19.76         0.30         2.63        28.96 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-34-5241 TCGA-34-7107 TCGA-34-8455 
       31.27        65.23        23.24        16.93         1.12         4.04 
TCGA-34-8456 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-37-5819 TCGA-39-5011 
       26.43         0.39         8.12         7.82         3.39        47.80 
TCGA-39-5019 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-43-3394 TCGA-43-5668 
       44.75        36.39        15.58        35.64        27.02        18.38 
TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 
       21.47         5.46        13.38        11.77         2.93         9.73 
TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
        9.99        10.65         0.39         5.46         8.75        27.45 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7223 TCGA-56-7582 
       28.96        18.25         2.04         0.62         0.99         0.85 
TCGA-56-7730 TCGA-56-8304 TCGA-56-8308 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A5DR 
        6.51         3.48        17.00        20.94        13.32         0.13 
TCGA-58-A46K TCGA-60-2695 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 
       34.36        21.11        10.22        37.94        92.71        80.45 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2719 TCGA-60-2723 TCGA-60-2724 
       41.42         9.01        35.34        42.64        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML 
       26.83        11.77       102.67        66.61        59.97        45.57 
TCGA-63-A5MR TCGA-66-2744 TCGA-66-2754 TCGA-66-2756 TCGA-66-2758 TCGA-66-2766 
       89.29         0.99         2.01         0.99        21.01         1.02 
TCGA-66-2767 TCGA-66-2773 TCGA-66-2781 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
        2.01         3.02         3.98        10.06        54.08        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 
        2.73         6.64         8.02        13.35        16.18        29.56 
TCGA-77-7140 TCGA-77-7142 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
       20.78        42.28        46.78        15.75        53.95        37.81 
TCGA-77-8133 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 
       53.92        26.40        27.39         9.63        54.41        35.90 
TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 TCGA-85-7950 
      117.57         5.92        42.08        27.62         9.67        18.94 
TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 
       25.15        24.13        31.56        34.52        10.09        22.45 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CN 
        3.09        32.71         0.72        12.59         0.10        19.33 
TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A510 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-7767 
       14.96        19.73        15.85         0.79         3.65         2.93 
TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-94-7557 
       11.77        22.62        10.59         2.70         3.48         0.16 
TCGA-94-7943 TCGA-98-8020 TCGA-98-8023 TCGA-98-A53B TCGA-J1-A4AH TCGA-L3-A524 
       11.70         2.76        21.34         2.01        19.10        16.11 
TCGA-LA-A446 TCGA-NC-A5HD TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK 
       13.18         0.07        51.78         1.22        13.74         4.21 
TCGA-NC-A5HM TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-O2-A52Q 
       39.85        14.73        29.75         3.72 

$`AMP PEAK 17(12Q15) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 
       12.20         7.46        75.75        79.46       117.57        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 
       92.15        31.99         1.64         6.18         2.79        49.94 
TCGA-18-5595 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       27.19        70.16        60.89        15.58        31.73       122.43 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 
        9.34        31.63        88.11        41.69        21.99         7.33 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 
       14.93         4.31        64.21         1.74        14.10        20.48 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       24.13         0.56        38.17        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5472 TCGA-22-5474 TCGA-22-5478 TCGA-22-5481 TCGA-22-5482 
       11.77        64.93        14.63         0.79        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4533 TCGA-33-4547 
       18.84        30.12        62.86        16.64       133.74        79.53 
TCGA-33-4566 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 
      174.08        54.44         1.55        27.02         4.70        36.62 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 
        6.94       110.99        44.19       118.36        27.16        61.61 
TCGA-34-2604 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 
       31.50        32.88        67.79        56.38         9.07        12.00 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 
       30.94        18.15         4.96        27.19        20.91         3.95 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 
        0.43         6.58         7.46         6.81         0.39        74.07 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        70.03        60.79         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
        1.94        27.39        35.70        17.88        17.06        40.21 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       22.49        38.66        33.11        27.91        12.36        24.89 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56U 
        3.81        19.59         7.76        66.51        11.61        14.20 
TCGA-43-A56V TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 
       12.03        13.91         0.39        29.95        28.34        30.35 
TCGA-56-5897 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 
        0.10         0.99         0.43         1.45         1.32         0.10 
TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
       17.49        26.89        14.07         1.35        16.77         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75         1.18        10.36         9.93        20.25        15.81 
TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       19.23        17.85        21.04        18.74         0.26         2.76 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        0.03        13.25        13.55        29.95        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 
       34.78        85.12        56.65        35.24        29.92         3.58 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       12.23        96.82        21.93        49.48        66.54        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-63-A5MG 
       50.33        48.49         3.19        32.32        29.85        70.62 
TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT 
       58.65        14.99        11.34        25.28        78.28        16.37 
TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       25.41        36.16        53.88        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 
        2.01        21.07         1.02         0.92        43.99        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
        0.99         2.01         2.01         7.07        23.01        19.00 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
        2.01        19.00        12.03        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
       25.97        40.01        22.98         4.04        22.98         5.03 
TCGA-66-2792 TCGA-66-2795 TCGA-68-7757 TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 
       30.02         4.01         6.94        14.73        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       23.28        11.18        89.98         0.49        70.13       106.95 
TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 
        0.16         6.51        86.76        82.92        12.59        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 
       17.72       104.09        11.54         6.97        65.49         0.33 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH 
      126.18       132.36        22.29        42.41        30.81        38.86 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       11.97        12.99         6.41        36.53        34.95        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 TCGA-85-8071 
       32.91         1.38         1.15        29.95        19.04        14.07 
TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 
       16.87         0.76        13.22        16.77         5.29         2.01 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB 
        7.76        14.63        13.94        15.62        25.68        17.72 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A53L 
       24.36        18.18        12.56        16.21        14.96        12.39 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8064 
       24.92         9.50        14.07        20.22         4.01         5.26 
TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        2.30        21.04         4.01         5.03        26.63        14.14 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
       16.14        17.69        49.87        57.07        18.31        17.46 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 
       19.36        16.57         8.42        30.81        30.67        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I 
        3.88        18.15        27.02        21.21        20.32        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HF 
       20.71        12.89        13.41        11.84        64.08         4.54 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT 
       45.37         2.89        37.22        30.58        24.00        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N 
       83.57        65.49         3.65        16.80         0.43        33.07 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89         8.58        11.18         0.20 

  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                        0.07                         0.03 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                      154.32                       174.08 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                       19.53                        19.00 
[1] "0.1 - 154.3 (19.5)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1"  
D17V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(12Q15) MUTATED         0       31       49        1        25
  AMP PEAK 17(12Q15) WILD-TYPE       2       56      102        1        38
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(12Q15) MUTATED          28         1         28          8
  AMP PEAK 17(12Q15) WILD-TYPE        64         2         34         13
                              vv
clus                           STAGE IV
  AMP PEAK 17(12Q15) MUTATED          2
  AMP PEAK 17(12Q15) WILD-TYPE        5
D17V3, multiclass
            clus
vv           AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                           31                           56
  STAGE IB                           49                          102
  STAGE II                            1                            1
  STAGE IIA                          25                           38
  STAGE IIB                          28                           64
  STAGE III                           1                            2
  STAGE IIIA                         28                           34
  STAGE IIIB                          8                           13
  STAGE IV                            2                            5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 17(12Q15) MUTATED    38 100  25  10
  AMP PEAK 17(12Q15) WILD-TYPE  73 190  44  13
D17V4, multiclass
    clus
vv   AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  T1                         38                           73
  T2                        100                          190
  T3                         25                           44
  T4                         10                           13
[1] 4 2
[1] TRUE
[1] "dimension of 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(12Q15) MUTATED   104  49  17   1
  AMP PEAK 17(12Q15) WILD-TYPE 208  82  22   4
D17V5, multiclass
    clus
vv   AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  N0                        104                          208
  N1                         49                           82
  N2                         17                           22
  N3                          1                            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(12Q15) MUTATED   147   2
  AMP PEAK 17(12Q15) WILD-TYPE 257   5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED    147    2
  AMP PEAK 17(12Q15) WILD-TYPE  257    5
   clus
vv  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  0                        147                          257
  1                          2                            5
[1] 2 2
[1] FALSE
D17V7, binary
                              cls
clus                             0   1
  AMP PEAK 17(12Q15) MUTATED    37 136
  AMP PEAK 17(12Q15) WILD-TYPE  90 230
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED     37  136
  AMP PEAK 17(12Q15) WILD-TYPE   90  230
        clus
vv       AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  FEMALE                         37                           90
  MALE                          136                          230
[1] 2 2
[1] FALSE
D17V8, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(12Q15) MUTATED                                       6
  AMP PEAK 17(12Q15) WILD-TYPE                                     9
                              vv
clus                           LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(12Q15) MUTATED                                         0
  AMP PEAK 17(12Q15) WILD-TYPE                                       1
                              vv
clus                           LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 17(12Q15) MUTATED                                        3
  AMP PEAK 17(12Q15) WILD-TYPE                                      3
                              vv
clus                           LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(12Q15) MUTATED                                         0
  AMP PEAK 17(12Q15) WILD-TYPE                                       1
                              vv
clus                           LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(12Q15) MUTATED                                                           164
  AMP PEAK 17(12Q15) WILD-TYPE                                                         306
D17V9, multiclass
                                                             clus
vv                                                            AMP PEAK 17(12Q15) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        164
                                                             clus
vv                                                            AMP PEAK 17(12Q15) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          306
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                              cls
clus                             0   1
  AMP PEAK 17(12Q15) MUTATED     3 170
  AMP PEAK 17(12Q15) WILD-TYPE  10 310
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED      3  170
  AMP PEAK 17(12Q15) WILD-TYPE   10  310
     clus
vv    AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  NO                           3                           10
  YES                        170                          310
[1] 2 2
[1] FALSE
D17V11, continuous
D17V12, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 17(12Q15) MUTATED   142   4   1   7
  AMP PEAK 17(12Q15) WILD-TYPE 252   8   3  15
D17V13, multiclass
    clus
vv   AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  R0                        142                          252
  R1                          4                            8
  R2                          1                            3
  RX                          7                           15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(12Q15) MUTATED       2                        10   129
  AMP PEAK 17(12Q15) WILD-TYPE     7                        21   211
D17V14, multiclass
                           clus
vv                          AMP PEAK 17(12Q15) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                         10
  WHITE                                            129
                           clus
vv                          AMP PEAK 17(12Q15) WILD-TYPE
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                           21
  WHITE                                              211
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V15, binary
                              cls
clus                             0   1
  AMP PEAK 17(12Q15) MUTATED     4 111
  AMP PEAK 17(12Q15) WILD-TYPE   4 198
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED      4  111
  AMP PEAK 17(12Q15) WILD-TYPE    4  198
                        clus
vv                       AMP PEAK 17(12Q15) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        111
                        clus
vv                       AMP PEAK 17(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          198
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(13Q34) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 18(13Q34) MUTATED    52  33
  AMP PEAK 18(13Q34) WILD-TYPE 229 163
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          85                          392 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          33                          163 
$`AMP PEAK 18(13Q34) MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-21-1070 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 
        7.46       117.57       119.54        31.73         9.34       119.80 
TCGA-21-5782 TCGA-21-5786 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
       31.63        33.93        35.08        48.33        24.13        38.17 
TCGA-22-5479 TCGA-33-4538 TCGA-33-4587 TCGA-33-AASB TCGA-34-8455 TCGA-34-A5IX 
       54.28        98.01        54.44         6.94         4.04        20.91 
TCGA-37-4130 TCGA-37-5819 TCGA-39-5011 TCGA-39-5021 TCGA-39-5024 TCGA-39-5034 
        8.12         3.39        47.80        68.58        70.03        36.39 
TCGA-39-5035 TCGA-39-5037 TCGA-43-2576 TCGA-43-6143 TCGA-43-7657 TCGA-43-7658 
       15.58        35.70        40.21        12.36         7.76        66.51 
TCGA-43-8115 TCGA-43-8118 TCGA-43-A56V TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
       13.38         2.93        12.03        29.95         5.46        30.35 
TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 TCGA-56-7822 TCGA-56-8308 TCGA-56-8626 
        0.10        18.25         0.99        17.49        17.00         9.93 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 TCGA-60-2704 
       13.32        18.74        29.92        21.11        10.22        37.94 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2714 TCGA-63-A5MH TCGA-63-A5MS TCGA-63-A5MT 
       92.71        80.45        50.33        66.61        78.28        16.37 
TCGA-66-2737 TCGA-66-2763 TCGA-66-2766 TCGA-66-2791 TCGA-77-6845 TCGA-77-7138 
        2.01         0.99         1.02         5.03        23.28        11.18 
TCGA-77-7337 TCGA-77-8133 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5GH TCGA-85-6798 
      106.95        53.92         0.33       132.36        38.86         6.41 
TCGA-85-7696 TCGA-85-7843 TCGA-85-7950 TCGA-85-8072 TCGA-85-8277 TCGA-85-8353 
       36.53         1.15        18.94        16.87        10.09         3.09 
TCGA-85-8479 TCGA-85-A4JC TCGA-90-A59Q TCGA-92-8065 TCGA-94-7943 TCGA-98-8020 
        0.72        14.96        10.59         2.30        11.70         2.76 
TCGA-98-A53C TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HJ 
       27.02        12.89        13.41        11.84         1.22        13.74 
TCGA-NK-A7XE 
        0.43 

$`AMP PEAK 18(13Q34) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 
       12.20        75.75        79.46         4.80        11.34        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
       92.15        31.99        36.07         1.64        86.96         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 
        2.79       154.32        49.94        27.19        46.88        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1083 
       70.16        60.89        34.78        15.58       122.43        43.23 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
       88.11        41.69        10.82        32.19        21.99         7.33 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       14.93         4.31        64.21         1.74        14.10        27.02 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       48.82        20.48         0.56        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
       14.63        44.25         0.79        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       18.84        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        7.63       133.74        79.53       174.08       103.53       151.27 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       14.07         1.55        19.76        27.02         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 
       36.62       110.99        44.19       118.36        27.16         2.63 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
       61.61        31.50        28.96        32.88        31.27        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       67.79        56.38         9.07        23.24        12.00        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 
       30.94        18.15         4.96         1.12        27.19        26.43 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
        3.95         0.43         0.39         6.58         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5027 
        6.81         0.39        74.07        44.75        55.20        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5039 
        1.71        24.33         1.94        27.39        35.64        17.88 
TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
       17.06        22.49        38.66        27.02        33.11        18.38 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.91        24.89        21.47         5.46         3.81        19.59 
TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 TCGA-46-6025 
       11.77        11.61         9.73        14.20         9.99        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 
       13.91         0.39         0.39        28.34         8.75        27.45 
TCGA-56-1622 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 
       28.96         2.04         0.62         0.99         0.43         1.45 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 
        1.32         0.85         6.51         0.10         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       14.07         1.35        16.77         1.81        22.75         1.18 
TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY 
       10.36        20.25        15.81        20.94        19.23        17.85 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       21.04         0.13         0.26         2.76         0.03        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
       13.55        29.95        71.24        16.47        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 
       34.36        56.65        35.24         3.58        12.23        96.82 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
       21.93        49.48        66.54        41.42         9.01        56.91 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
       35.34        48.49        42.64         3.19        32.32        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG 
       35.90        23.57        26.83        11.77       102.67        70.62 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       58.65        59.97        45.57        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       89.29        25.41        36.16        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       43.10        21.07         0.99         1.02         2.01         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2767 
        0.99        43.99        21.01        25.05         2.01         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         7.07        23.01        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 
       25.97        40.01        22.98         4.04        22.98        30.02 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       10.06        54.08         4.01        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
        6.94         8.02        13.35        16.18        14.73        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
       73.12        75.09        89.98        20.78         0.49        42.28 
TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
       70.13         0.16        46.78        15.75         6.51        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 
       53.95        37.81        82.92        12.59        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
      104.09        11.54        26.40        27.39         6.97         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 
       54.41        65.49        35.90       126.18       117.57        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6175 
        5.92        42.41        42.08        30.81        27.62         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
       11.97        12.99        34.95        31.30        32.91         1.38 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       29.95        25.15        19.04        24.13        31.56        14.07 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       34.52         0.76        13.22        22.45        16.77         5.29 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
       32.71         2.01         7.76        14.63        13.94        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA 
        0.10        15.62        25.68        19.33        17.72        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       18.18        19.73        12.56        16.21        15.85        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        0.79        12.39         3.65        24.92         9.50         2.93 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 
       11.77        14.07        20.22        22.62         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 
        4.01         5.26        21.04         0.16         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
       26.63        14.14        16.14        17.69        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       18.31        17.46        19.36        16.57         8.42        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
       30.67        21.34        27.16         3.88        18.15         2.01 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 
       21.21        20.32        18.58        20.71        19.10        16.11 
TCGA-LA-A446 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       13.18         0.07        64.08         4.54        51.78        45.37 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
        4.21         2.89        39.85        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX 
       14.73        29.75        22.78        83.57        65.49         3.65 
TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W 
       16.80        33.07         3.72        12.72        43.89         8.58 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                        0.10                         0.03 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                      132.36                       174.08 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                      17.000                       19.475 
[1] "0.1 - 132.4 (17.0)" "0.0 - 174.1 (19.5)"
[1] "hr=" "1.1"
D18V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(13Q34) MUTATED         0       16       23        0         9
  AMP PEAK 18(13Q34) WILD-TYPE       2       71      128        2        54
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(13Q34) MUTATED          17         0         18          2
  AMP PEAK 18(13Q34) WILD-TYPE        75         3         44         19
                              vv
clus                           STAGE IV
  AMP PEAK 18(13Q34) MUTATED          1
  AMP PEAK 18(13Q34) WILD-TYPE        6
D18V3, multiclass
            clus
vv           AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  STAGE I                             0                            2
  STAGE IA                           16                           71
  STAGE IB                           23                          128
  STAGE II                            0                            2
  STAGE IIA                           9                           54
  STAGE IIB                          17                           75
  STAGE III                           0                            3
  STAGE IIIA                         18                           44
  STAGE IIIB                          2                           19
  STAGE IV                            1                            6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 18(13Q34) MUTATED    19  46  19   2
  AMP PEAK 18(13Q34) WILD-TYPE  92 244  50  21
D18V4, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  T1                         19                           92
  T2                         46                          244
  T3                         19                           50
  T4                          2                           21
[1] 4 2
[1] TRUE
[1] "dimension of 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(13Q34) MUTATED    53  20  11   1
  AMP PEAK 18(13Q34) WILD-TYPE 259 111  28   4
D18V5, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  N0                         53                          259
  N1                         20                          111
  N2                         11                           28
  N3                          1                            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(13Q34) MUTATED    70   1
  AMP PEAK 18(13Q34) WILD-TYPE 334   6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     70    1
  AMP PEAK 18(13Q34) WILD-TYPE  334    6
   clus
vv  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  0                         70                          334
  1                          1                            6
[1] 2 2
[1] FALSE
D18V7, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED    25  61
  AMP PEAK 18(13Q34) WILD-TYPE 102 305
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     25   61
  AMP PEAK 18(13Q34) WILD-TYPE  102  305
        clus
vv       AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  FEMALE                         25                          102
  MALE                           61                          305
[1] 2 2
[1] FALSE
D18V8, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(13Q34) MUTATED                                       5
  AMP PEAK 18(13Q34) WILD-TYPE                                    10
                              vv
clus                           LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(13Q34) MUTATED                                         0
  AMP PEAK 18(13Q34) WILD-TYPE                                       1
                              vv
clus                           LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 18(13Q34) MUTATED                                        2
  AMP PEAK 18(13Q34) WILD-TYPE                                      4
                              vv
clus                           LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(13Q34) MUTATED                                         1
  AMP PEAK 18(13Q34) WILD-TYPE                                       0
                              vv
clus                           LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(13Q34) MUTATED                                                            78
  AMP PEAK 18(13Q34) WILD-TYPE                                                         392
D18V9, multiclass
                                                             clus
vv                                                            AMP PEAK 18(13Q34) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         78
                                                             clus
vv                                                            AMP PEAK 18(13Q34) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          392
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED     2  84
  AMP PEAK 18(13Q34) WILD-TYPE  11 396
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      2   84
  AMP PEAK 18(13Q34) WILD-TYPE   11  396
     clus
vv    AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  NO                           2                           11
  YES                         84                          396
[1] 2 2
[1] FALSE
D18V11, continuous
D18V12, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 18(13Q34) MUTATED    67   3   0   6
  AMP PEAK 18(13Q34) WILD-TYPE 327   9   4  16
D18V13, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  R0                         67                          327
  R1                          3                            9
  R2                          0                            4
  RX                          6                           16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(13Q34) MUTATED       2                         7    62
  AMP PEAK 18(13Q34) WILD-TYPE     7                        24   278
D18V14, multiclass
                           clus
vv                          AMP PEAK 18(13Q34) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                          7
  WHITE                                             62
                           clus
vv                          AMP PEAK 18(13Q34) WILD-TYPE
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                           24
  WHITE                                              278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V15, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED     1  60
  AMP PEAK 18(13Q34) WILD-TYPE   7 249
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      1   60
  AMP PEAK 18(13Q34) WILD-TYPE    7  249
                        clus
vv                       AMP PEAK 18(13Q34) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         60
                        clus
vv                       AMP PEAK 18(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          249
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(14Q13.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(14Q13.3) MUTATED    94  56
  AMP PEAK 19(14Q13.3) WILD-TYPE 187 140
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                           150                            327 
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                            56                            140 
$`AMP PEAK 19(14Q13.3) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3421 TCGA-18-5592 
       75.75       117.57        11.34        92.15        86.96        49.94 
TCGA-21-1076 TCGA-21-1079 TCGA-21-1082 TCGA-21-5782 TCGA-21-5786 TCGA-22-1011 
       60.89        31.73       119.80        31.63        33.93         1.74 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4604 TCGA-22-4613 
       48.82        20.48        48.33        24.13        13.12        11.77 
TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 
       31.73        22.06         7.63       133.74        98.01       174.08 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-AASD 
      103.53        14.07         1.55        19.76        27.02       110.99 
TCGA-33-AASI TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3792 TCGA-37-5819 
       44.19         4.04        26.43         3.95         0.39         3.39 
TCGA-39-5011 TCGA-39-5019 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 TCGA-39-5039 
       47.80        44.75        24.33        27.39        35.70        17.88 
TCGA-43-2578 TCGA-43-6143 TCGA-43-6771 TCGA-43-8118 TCGA-43-A56V TCGA-46-6025 
       22.49        12.36         5.46         2.93        12.03        10.65 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 
       29.95        28.34         8.75        28.96        18.25         2.04 
TCGA-56-6546 TCGA-56-7580 TCGA-56-7730 TCGA-56-8304 TCGA-56-8504 TCGA-56-8624 
        0.62         1.32         6.51         3.48        16.77         1.18 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A62T TCGA-58-8387 TCGA-58-8393 TCGA-58-A46J 
       15.81        20.94         2.76        13.25        34.78        85.12 
TCGA-58-A46N TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 
       29.92        10.22        92.71        21.93        80.45        50.33 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MI 
       42.64        29.85        23.57        11.77        70.62        58.65 
TCGA-63-A5ML TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MY TCGA-66-2744 TCGA-66-2756 
       45.57        16.37        25.41        34.59         0.99         0.99 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2771 TCGA-66-2782 TCGA-66-2788 TCGA-66-2791 
        0.99         2.01        19.00        12.00        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-77-6845 
       30.02        10.06         4.01        49.05         2.73        23.28 
TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 
       11.18         0.49        42.28       106.95        46.78         6.51 
TCGA-77-8130 TCGA-77-8136 TCGA-77-8139 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 
       82.92        39.09       104.09        26.40         9.63        54.41 
TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       65.49       117.57        42.41         9.67        11.97        12.99 
TCGA-85-7698 TCGA-85-7843 TCGA-85-8276 TCGA-85-8353 TCGA-85-8355 TCGA-85-A4JB 
       31.30         1.15        34.52         3.09         2.01        17.72 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7766 TCGA-92-7340 
       18.18        12.56        15.85         3.65         9.50         2.70 
TCGA-92-7341 TCGA-92-8064 TCGA-94-A4VJ TCGA-96-A4JK TCGA-98-8020 TCGA-98-A538 
        3.48         5.26        14.14        19.36         2.76        27.16 
TCGA-98-A539 TCGA-98-A53I TCGA-L3-A4E7 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI 
        3.88        18.58        12.89        11.84        51.78        45.37 
TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CX 
       39.85        30.58        24.00        14.73        29.75         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       33.07         3.72        12.72        43.89         8.58         0.20 

$`AMP PEAK 19(14Q13.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
       12.20         7.46        79.46         4.80        23.54        31.99 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
       36.07         1.64         6.18         2.79       154.32        27.19 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 
      119.54        46.88        99.16        70.16        34.78        15.58 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 
      122.43         9.34        43.23        88.11        41.69        10.82 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       32.19        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       14.10        27.02        35.08         0.56        38.17        34.75 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
       32.02        19.30         9.57        64.93        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 
       44.25         0.79        54.28        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 
       18.84        30.12        62.86        56.32        16.64        79.53 
TCGA-33-4583 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
      151.27        54.44         4.70         0.30        36.62         6.94 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
      118.36        27.16         2.63        61.61        31.50        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       32.88        31.27        65.23        67.79        56.38         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       23.24        12.00        16.93        30.94        18.15         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 
        1.12        27.19        20.91         0.43         6.58         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 TCGA-39-5021 
        7.46         7.82         6.81         0.39        74.07        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 
       55.20        70.03        60.79         1.71         1.94        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       15.58        35.64        17.06        40.21        38.66        27.02 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 
       33.11        18.38        27.91        24.89        21.47         3.81 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 
       19.59         7.76        66.51        13.38        11.77        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
        9.73        14.20         9.99        13.91         0.39         0.39 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7222 
        5.46        30.35        27.45         0.10         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 
        0.99         1.45         0.85         0.10        17.49        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 
       17.00        14.07         1.35         1.81        22.75        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
        9.93        20.25        19.23        13.32        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 
       18.74         0.13         0.26         0.03        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 
       71.24        16.47        34.36        56.65        35.24        21.11 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 
        3.58        12.23        96.82        37.94        49.48        66.54 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 
       41.42         9.01        56.91        35.34        48.49         3.19 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ 
       32.32        35.90        26.83       102.67        66.61        59.97 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV 
       14.99        11.34        25.28        89.29        78.28        36.16 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
       53.88        16.96        43.10         2.01        21.07         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 
        2.01         0.92        43.99        21.01        25.05         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
        2.01         2.01         7.07        23.01         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       19.00        12.03         3.98        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 TCGA-68-7756 TCGA-68-7757 
       40.01         4.04        22.98        54.08         6.64         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
        8.02        13.35        16.18        14.73        29.56        73.12 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7140 TCGA-77-7335 TCGA-77-7338 TCGA-77-7465 
       75.09        89.98        20.78        70.13         0.16        15.75 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 
       86.76        53.95        37.81        12.59        53.92        17.72 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       11.54        27.39         6.97        35.90         0.33       126.18 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
      132.36        22.29         5.92        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 
       38.86         6.41        36.53        34.95        32.91         1.38 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       29.95        18.94        25.15        19.04        24.13        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       14.07        16.87        10.09         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
       16.77         5.29        32.71         0.72         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       13.94        12.59         0.10        15.62        25.68        19.33 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 
       14.96        24.36        19.73        16.21        14.96         0.79 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
       12.39        24.92         2.93        11.77        14.07        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
       22.62        10.59         4.01         2.30        21.04         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 TCGA-94-A5I6 
       11.70         4.01         5.03        26.63        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       49.87        57.07        18.31        17.46        16.57         8.42 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.81        30.67        21.34        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 
       21.21        20.32        20.71        19.10        16.11        13.18 
TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ 
       13.41         0.07        64.08         4.54         1.22        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
        4.21         2.89        37.22        22.78        83.57        65.49 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A5IB 
       16.80         0.43        11.18 

  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                          0.20                           0.03 
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                        174.08                         154.32 
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                         20.12                          19.00 
[1] "0.2 - 174.1 (20.1)" "0.0 - 154.3 (19.0)"
[1] "hr=" "1.3"
D19V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(14Q13.3) MUTATED         2       21       45        1        23
  AMP PEAK 19(14Q13.3) WILD-TYPE       0       66      106        1        40
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(14Q13.3) MUTATED          31         2         25          5
  AMP PEAK 19(14Q13.3) WILD-TYPE        61         1         37         16
                                vv
clus                             STAGE IV
  AMP PEAK 19(14Q13.3) MUTATED          2
  AMP PEAK 19(14Q13.3) WILD-TYPE        5
D19V3, multiclass
            clus
vv           AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             21                             66
  STAGE IB                             45                            106
  STAGE II                              1                              1
  STAGE IIA                            23                             40
  STAGE IIB                            31                             61
  STAGE III                             2                              1
  STAGE IIIA                           25                             37
  STAGE IIIB                            5                             16
  STAGE IV                              2                              5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 19(14Q13.3) MUTATED    28  96  26   7
  AMP PEAK 19(14Q13.3) WILD-TYPE  83 194  43  16
D19V4, multiclass
    clus
vv   AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  T1                           28                             83
  T2                           96                            194
  T3                           26                             43
  T4                            7                             16
[1] 4 2
[1] TRUE
[1] "dimension of 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(14Q13.3) MUTATED    96  40  19   1
  AMP PEAK 19(14Q13.3) WILD-TYPE 216  91  20   4
D19V5, multiclass
    clus
vv   AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  N0                           96                            216
  N1                           40                             91
  N2                           19                             20
  N3                            1                              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(14Q13.3) MUTATED   131   2
  AMP PEAK 19(14Q13.3) WILD-TYPE 273   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(14Q13.3) MUTATED    131    2
  AMP PEAK 19(14Q13.3) WILD-TYPE  273    5
   clus
vv  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  0                          131                            273
  1                            2                              5
[1] 2 2
[1] FALSE
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(14Q13.3) MUTATED    41 116
  AMP PEAK 19(14Q13.3) WILD-TYPE  86 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(14Q13.3) MUTATED     41  116
  AMP PEAK 19(14Q13.3) WILD-TYPE   86  250
        clus
vv       AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  FEMALE                           41                             86
  MALE                            116                            250
[1] 2 2
[1] FALSE
D19V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(14Q13.3) MUTATED                                       4
  AMP PEAK 19(14Q13.3) WILD-TYPE                                    11
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(14Q13.3) MUTATED                                         0
  AMP PEAK 19(14Q13.3) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 19(14Q13.3) MUTATED                                        1
  AMP PEAK 19(14Q13.3) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 19(14Q13.3) MUTATED                                         0
  AMP PEAK 19(14Q13.3) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(14Q13.3) MUTATED                                                           152
  AMP PEAK 19(14Q13.3) WILD-TYPE                                                         318
D19V9, multiclass
                                                             clus
vv                                                            AMP PEAK 19(14Q13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          152
                                                             clus
vv                                                            AMP PEAK 19(14Q13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            318
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, binary
                                cls
clus                               0   1
  AMP PEAK 19(14Q13.3) MUTATED     3 154
  AMP PEAK 19(14Q13.3) WILD-TYPE  10 326
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(14Q13.3) MUTATED      3  154
  AMP PEAK 19(14Q13.3) WILD-TYPE   10  326
     clus
vv    AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  NO                             3                             10
  YES                          154                            326
[1] 2 2
[1] FALSE
D19V11, continuous
D19V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(14Q13.3) MUTATED   123   5   1  10
  AMP PEAK 19(14Q13.3) WILD-TYPE 271   7   3  12
D19V13, multiclass
    clus
vv   AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  R0                          123                            271
  R1                            5                              7
  R2                            1                              3
  RX                           10                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(14Q13.3) MUTATED       3                        10   105
  AMP PEAK 19(14Q13.3) WILD-TYPE     6                        21   235
D19V14, multiclass
                           clus
vv                          AMP PEAK 19(14Q13.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              105
                           clus
vv                          AMP PEAK 19(14Q13.3) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             21
  WHITE                                                235
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V15, binary
                                cls
clus                               0   1
  AMP PEAK 19(14Q13.3) MUTATED     6  88
  AMP PEAK 19(14Q13.3) WILD-TYPE   2 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(14Q13.3) MUTATED      6   88
  AMP PEAK 19(14Q13.3) WILD-TYPE    2  221
                        clus
vv                       AMP PEAK 19(14Q13.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           88
                        clus
vv                       AMP PEAK 19(14Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            221
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(14Q32.33) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 20(14Q32.33) MUTATED    93  57
  AMP PEAK 20(14Q32.33) WILD-TYPE 188 139
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                            150                             327 
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                             57                             139 
$`AMP PEAK 20(14Q32.33) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 
       75.75       117.57        11.34        92.15         1.64        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1076 
        6.18         2.79       154.32        49.94       119.54        60.89 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-5783 TCGA-21-5786 TCGA-22-1016 
       31.73         9.34       119.80        88.11        33.93        27.02 
TCGA-22-4591 TCGA-22-4595 TCGA-22-5471 TCGA-22-5473 TCGA-22-5482 TCGA-22-5483 
       20.48        24.13        31.73        63.55        11.74        18.84 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4566 TCGA-33-4582 TCGA-33-4589 
       22.06         7.63       133.74       174.08       103.53         1.55 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-5240 TCGA-34-5241 TCGA-34-8455 
      110.99        44.19       118.36        12.00        16.93         4.04 
TCGA-34-8456 TCGA-37-3789 TCGA-37-3792 TCGA-37-4133 TCGA-37-5819 TCGA-39-5011 
       26.43         0.43         0.39         7.82         3.39        47.80 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-2578 TCGA-43-6143 
       24.33        27.39        35.64        35.70        22.49        12.36 
TCGA-43-6771 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-6025 
        5.46         2.93        11.61         9.73        12.03        10.65 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 TCGA-56-6546 
       29.95        28.34         5.46         8.75        18.25         0.62 
TCGA-56-7580 TCGA-56-7730 TCGA-56-8304 TCGA-56-8504 TCGA-56-8624 TCGA-56-A49D 
        1.32         6.51         3.48        16.77         1.18        20.94 
TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8391 TCGA-58-A46N TCGA-60-2706 
       18.74         2.76         0.03        71.24        29.92        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2722 TCGA-60-2724 TCGA-63-A5MG TCGA-63-A5MI 
       21.93        80.45        29.85        23.57        70.62        58.65 
TCGA-63-A5MU TCGA-66-2744 TCGA-66-2756 TCGA-66-2763 TCGA-66-2771 TCGA-66-2781 
       25.41         0.99         0.99         0.99        19.00         3.98 
TCGA-66-2782 TCGA-66-2788 TCGA-66-2789 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 
       12.00        22.98         4.04        30.02        10.06        49.05 
TCGA-68-7755 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-77-6845 TCGA-77-7138 
        2.73         6.94        16.18        14.73        23.28        11.18 
TCGA-77-7140 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8130 TCGA-77-8136 
       20.78       106.95        46.78         6.51        82.92        39.09 
TCGA-77-8139 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
      104.09        26.40         9.63        54.41        65.49        35.90 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 
      117.57        22.29        42.41        27.62         9.67        12.99 
TCGA-85-6798 TCGA-85-7698 TCGA-85-7843 TCGA-85-8071 TCGA-85-8353 TCGA-85-8355 
        6.41        31.30         1.15        14.07         3.09         2.01 
TCGA-85-8582 TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A5B5 TCGA-90-7769 
       13.94        17.72        18.18        12.56         3.65        11.77 
TCGA-92-7340 TCGA-92-7341 TCGA-94-7033 TCGA-94-8491 TCGA-96-A4JK TCGA-98-8020 
        2.70         3.48        21.04        26.63        19.36         2.76 
TCGA-98-A538 TCGA-98-A539 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HD 
       27.16         3.88        12.89        16.11        13.41         0.07 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP 
       51.78        45.37         2.89        39.85        37.22        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52W 
       14.73        29.75        83.57         3.65         3.72         8.58 

$`AMP PEAK 20(14Q32.33) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
       12.20         7.46        79.46         4.80        23.54        31.99 
TCGA-18-3417 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 
       36.07        27.19        46.88        99.16        70.16        34.78 
TCGA-21-1078 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 
       15.58       122.43        43.23        31.63        41.69        10.82 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       32.19        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 
        1.74        14.10        48.82        35.08        48.33         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       38.17        34.75        13.12        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       11.77        64.93        14.63        44.25         0.79        54.28 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       71.34        79.20        30.12        62.86        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6737 
       98.01        79.53       151.27        14.07        54.44        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASL 
       27.02         4.70         0.30        36.62         6.94        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
        2.63        61.61        31.50        28.96        32.88        31.27 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5927 
       65.23        67.79        56.38         9.07        23.24        30.94 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 
       18.15         4.96         1.12        27.19        20.91         3.95 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 
        6.58         8.12         7.46         6.81         0.39        74.07 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
       44.75        68.58        55.20        70.03        60.79         1.71 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
        1.94        36.39        15.58        17.88        17.06        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 
       38.66        27.02        33.11        18.38        27.91        24.89 
TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       21.47         3.81        19.59         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-A56U TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       11.77        14.20         9.99        13.91         0.39         0.39 
TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7221 
       30.35        27.45        28.96         0.10         2.04         0.99 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 
        0.43         0.99         1.45         0.85         0.10        17.49 
TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
       26.89        17.00        14.07         1.35         1.81        22.75 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
       10.36         9.93        20.25        15.81        19.23        13.32 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 
       17.85        21.04         0.13         0.26        13.25        13.55 
TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       29.95        16.47        34.78        85.12        34.36        56.65 
TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       35.24        21.11         3.58        12.23        10.22        96.82 
TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
       37.94        49.48        66.54        41.42         9.01        56.91 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
       50.33        35.34        48.49        42.64         3.19        32.32 
TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ 
       35.90        26.83        11.77       102.67        66.61        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       45.57        14.99        11.34        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       16.37        36.16        53.88        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
        2.01        21.07         1.02         2.01         0.92        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
       21.01        25.05         2.01         1.02         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        7.07        23.01         3.02         2.01        19.00        12.03 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 
       24.95         1.97        25.97        40.01        22.98         5.03 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 
       54.08         4.01         6.64         8.02        13.35        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       73.12        75.09        89.98         0.49        42.28        70.13 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 
        0.16        15.75        86.76        53.95        37.81        12.59 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8156 
       53.92        17.72        11.54        27.39         6.97         0.33 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH 
      126.18       132.36         5.92        42.08        30.81        38.86 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
       11.97        36.53        34.95        32.91         1.38        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
       18.94        25.15        19.04        24.13        31.56        16.87 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       34.52        10.09         0.76        13.22        22.45        16.77 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8584 
        5.29        32.71         0.72         7.76        14.63        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA 
        0.10        15.62        25.68        19.33        14.96        24.36 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       19.73        16.21        15.85        14.96         0.79        12.39 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
       24.92         9.50         2.93        14.07        20.22        22.62 
TCGA-90-A59Q TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7557 TCGA-94-7943 
       10.59         4.01         5.26         2.30         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 
        4.01         5.03        14.14        16.14        17.69        49.87 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       57.07        18.31        17.46        16.57         8.42        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D 
       30.67        21.34        18.15         2.01        27.02        21.21 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-LA-A446 TCGA-MF-A522 
       20.32        18.58        20.71        19.10        13.18        11.84 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HO 
       64.08         4.54         1.22        13.74         4.21        30.58 
TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52S 
       22.78        65.49        16.80         0.43        33.07        12.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                           0.03                            0.10 
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                         174.08                          151.27 
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                          18.92                           19.23 
[1] "0.0 - 174.1 (18.9)" "0.1 - 151.3 (19.2)"
[1] "hr=" "1.3"
D20V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(14Q32.33) MUTATED         1       20       47        0        20
  AMP PEAK 20(14Q32.33) WILD-TYPE       1       67      104        2        43
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(14Q32.33) MUTATED          34         1         24          5
  AMP PEAK 20(14Q32.33) WILD-TYPE        58         2         38         16
                                 vv
clus                              STAGE IV
  AMP PEAK 20(14Q32.33) MUTATED          3
  AMP PEAK 20(14Q32.33) WILD-TYPE        4
D20V3, multiclass
            clus
vv           AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  STAGE I                                1                               1
  STAGE IA                              20                              67
  STAGE IB                              47                             104
  STAGE II                               0                               2
  STAGE IIA                             20                              43
  STAGE IIB                             34                              58
  STAGE III                              1                               2
  STAGE IIIA                            24                              38
  STAGE IIIB                             5                              16
  STAGE IV                               3                               4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 20(14Q32.33) MUTATED    25  95  30   5
  AMP PEAK 20(14Q32.33) WILD-TYPE  86 195  39  18
D20V4, multiclass
    clus
vv   AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  T1                            25                              86
  T2                            95                             195
  T3                            30                              39
  T4                             5                              18
[1] 4 2
[1] TRUE
[1] "dimension of 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(14Q32.33) MUTATED    95  43  14   1
  AMP PEAK 20(14Q32.33) WILD-TYPE 217  88  25   4
D20V5, multiclass
    clus
vv   AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  N0                            95                             217
  N1                            43                              88
  N2                            14                              25
  N3                             1                               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"
D20V6, binary
                                 cls
clus                                0   1
  AMP PEAK 20(14Q32.33) MUTATED   129   3
  AMP PEAK 20(14Q32.33) WILD-TYPE 275   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(14Q32.33) MUTATED    129    3
  AMP PEAK 20(14Q32.33) WILD-TYPE  275    4
   clus
vv  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  0                           129                             275
  1                             3                               4
[1] 2 2
[1] FALSE
D20V7, binary
                                 cls
clus                                0   1
  AMP PEAK 20(14Q32.33) MUTATED    34 121
  AMP PEAK 20(14Q32.33) WILD-TYPE  93 245
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(14Q32.33) MUTATED     34  121
  AMP PEAK 20(14Q32.33) WILD-TYPE   93  245
        clus
vv       AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  FEMALE                            34                              93
  MALE                             121                             245
[1] 2 2
[1] FALSE
D20V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 20(14Q32.33) MUTATED                                       6
  AMP PEAK 20(14Q32.33) WILD-TYPE                                     9
                                 vv
clus                              LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 20(14Q32.33) MUTATED                                         0
  AMP PEAK 20(14Q32.33) WILD-TYPE                                       1
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 20(14Q32.33) MUTATED                                        1
  AMP PEAK 20(14Q32.33) WILD-TYPE                                      5
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 20(14Q32.33) MUTATED                                         0
  AMP PEAK 20(14Q32.33) WILD-TYPE                                       1
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(14Q32.33) MUTATED                                                           148
  AMP PEAK 20(14Q32.33) WILD-TYPE                                                         322
D20V9, multiclass
                                                             clus
vv                                                            AMP PEAK 20(14Q32.33) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           148
                                                             clus
vv                                                            AMP PEAK 20(14Q32.33) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             322
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, binary
                                 cls
clus                                0   1
  AMP PEAK 20(14Q32.33) MUTATED     3 152
  AMP PEAK 20(14Q32.33) WILD-TYPE  10 328
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(14Q32.33) MUTATED      3  152
  AMP PEAK 20(14Q32.33) WILD-TYPE   10  328
     clus
vv    AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  NO                              3                              10
  YES                           152                             328
[1] 2 2
[1] FALSE
D20V11, continuous
D20V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 20(14Q32.33) MUTATED   129   5   1   5
  AMP PEAK 20(14Q32.33) WILD-TYPE 265   7   3  17
D20V13, multiclass
    clus
vv   AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  R0                           129                             265
  R1                             5                               7
  R2                             1                               3
  RX                             5                              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(14Q32.33) MUTATED       2                        11   101
  AMP PEAK 20(14Q32.33) WILD-TYPE     7                        20   239
D20V14, multiclass
                           clus
vv                          AMP PEAK 20(14Q32.33) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               101
                           clus
vv                          AMP PEAK 20(14Q32.33) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              20
  WHITE                                                 239
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V15, binary
                                 cls
clus                                0   1
  AMP PEAK 20(14Q32.33) MUTATED     5  88
  AMP PEAK 20(14Q32.33) WILD-TYPE   3 221
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(14Q32.33) MUTATED      5   88
  AMP PEAK 20(14Q32.33) WILD-TYPE    3  221
                        clus
vv                       AMP PEAK 20(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            88
                        clus
vv                       AMP PEAK 20(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             221
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(15Q26.3) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(15Q26.3) MUTATED    99  68
  AMP PEAK 21(15Q26.3) WILD-TYPE 182 128
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                           167                            310 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            68                            128 
$`AMP PEAK 21(15Q26.3) MUTATED`
TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
        4.80       117.57        23.54        92.15        31.99        36.07 
TCGA-18-4083 TCGA-18-4086 TCGA-21-1072 TCGA-21-1077 TCGA-21-1079 TCGA-21-1082 
        6.18         2.79        99.16        34.78        31.73       119.80 
TCGA-21-5786 TCGA-22-0944 TCGA-22-4591 TCGA-22-4593 TCGA-22-4604 TCGA-22-4605 
       33.93         7.33        20.48        35.08        13.12        32.02 
TCGA-22-4613 TCGA-22-5472 TCGA-22-5474 TCGA-22-5482 TCGA-22-5483 TCGA-33-4532 
       11.77        64.93        14.63        11.74        18.84         7.63 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4589 TCGA-33-6737 
       98.01        79.53       174.08       151.27         1.55        19.76 
TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
      110.99        44.19         2.63        61.61        31.50        28.96 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 TCGA-34-5240 TCGA-34-5929 TCGA-34-8455 
       31.27        65.23        56.38        12.00         4.96         4.04 
TCGA-34-8456 TCGA-37-3789 TCGA-37-3792 TCGA-39-5031 TCGA-39-5037 TCGA-43-2578 
       26.43         0.43         0.39        27.39        35.70        22.49 
TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-A475 TCGA-46-6025 
       27.02        27.91        12.36        21.47         9.73        10.65 
TCGA-46-6026 TCGA-52-7809 TCGA-56-5898 TCGA-56-7222 TCGA-56-7582 TCGA-56-7730 
       13.91         5.46        18.25         0.43         0.85         6.51 
TCGA-56-8308 TCGA-56-8504 TCGA-56-8626 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DR 
       17.00        16.77         9.93        19.23        18.74         0.13 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-60-2695 
       29.95        71.24        34.78        85.12        34.36        21.11 
TCGA-60-2696 TCGA-60-2706 TCGA-60-2710 TCGA-60-2711 TCGA-60-2722 TCGA-60-2724 
        3.58        92.71        66.54        41.42        29.85        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5ML 
       26.83        11.77       102.67        66.61        58.65        45.57 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2734 
       25.28        89.29        78.28        36.16        34.59        43.10 
TCGA-66-2754 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 
        2.01         2.01         1.02         2.01         7.07        23.01 
TCGA-66-2773 TCGA-66-2781 TCGA-66-2787 TCGA-66-2789 TCGA-66-2791 TCGA-66-2795 
        3.02         3.98        40.01         4.04         5.03         4.01 
TCGA-68-7755 TCGA-68-A59I TCGA-68-A59J TCGA-77-7140 TCGA-77-7141 TCGA-77-7338 
        2.73        16.18        14.73        20.78         0.49         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8133 TCGA-77-8136 TCGA-77-8143 
       46.78        15.75        53.95        53.92        39.09        26.40 
TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6561 
       54.41        65.49       132.36       117.57        27.62        12.99 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 
        6.41        36.53        29.95        18.94        19.04        24.13 
TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 
       31.56        34.52        10.09        16.77         5.29        32.71 
TCGA-85-8481 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A50Z 
        7.76        12.59         0.10        25.68        14.96        16.21 
TCGA-85-A510 TCGA-90-7766 TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-94-7557 
       15.85         9.50        10.59         3.48         4.01         0.16 
TCGA-94-7943 TCGA-94-8491 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
       11.70        26.63        16.14        17.69        49.87        57.07 
TCGA-98-8020 TCGA-98-A538 TCGA-98-A53B TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HD 
        2.76        27.16         2.01        16.11        13.18         0.07 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HN TCGA-NC-A5HR TCGA-NC-A5HT 
       64.08        51.78        13.74        37.22        29.75        22.78 
TCGA-NK-A5CR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52V TCGA-O2-A5IB 
       83.57        16.80         0.43        43.89        11.18 

$`AMP PEAK 21(15Q26.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3412 TCGA-18-3419 
       12.20         7.46        75.75        79.46        11.34         1.64 
TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
       86.96       154.32        49.94        27.19       119.54        46.88 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 
       70.16        60.89        15.58       122.43         9.34        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
       31.63        88.11        41.69        10.82        32.19        21.99 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       14.93         4.31        64.21         1.74        14.10        27.02 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       48.82        48.33        24.13         0.56        38.17        34.75 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5471 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
       19.30         9.57        31.73        63.55        44.25         0.79 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       54.28        71.34        79.20        30.12        62.86        56.32 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 
       16.64        22.06       133.74       103.53        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ 
       27.02         4.70         0.30        36.62         6.94       118.36 
TCGA-33-AASL TCGA-34-2608 TCGA-34-5232 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 
       27.16        32.88        67.79         9.07        23.24        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 
       30.94        18.15         1.12        27.19        20.91         3.95 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        6.58         8.12         7.46         7.82         6.81         0.39 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        3.39        47.80        74.07        44.75        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 
       70.03        60.79         1.71        24.33         1.94        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
       15.58        35.64        17.88        17.06        40.21        38.66 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       33.11        18.38        24.89         5.46         3.81        19.59 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
        7.76        66.51        13.38        11.77         2.93        11.61 
TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
       14.20        12.03         9.99         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
       28.34        30.35         8.75        27.45        28.96         0.10 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
        2.04         0.62         0.99         0.99         1.45         1.32 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
        0.10        17.49         3.48        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 
        1.81        22.75         1.18        10.36        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DS TCGA-56-A62T 
       20.94        13.32        17.85        21.04         0.26         2.76 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8392 TCGA-58-A46L TCGA-58-A46M 
        0.03        13.25        13.55        16.47        56.65        35.24 
TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 
       29.92        12.23        10.22        96.82        37.94        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       80.45        49.48         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-63-A5MG 
       48.49        42.64         3.19        32.32        35.90        70.62 
TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MW 
       59.97        14.99        11.34        16.37        25.41        53.88 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 
       16.96         2.01        21.07         0.99         1.02         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2768 
        0.99        43.99        21.01        25.05         0.99         2.01 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
       19.00         2.01        19.00        12.03        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 
        1.97        25.97        22.98        22.98        30.02        10.06 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       54.08        49.05         6.64         6.94         8.02        13.35 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       29.56        73.12        75.09        23.28        11.18        89.98 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 
       42.28        70.13       106.95         6.51        86.76        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
       82.92        12.59        17.72       104.09        11.54        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G6 
        6.97         9.63        35.90         0.33       126.18        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 
        5.92        42.41        42.08        30.81        38.86         9.67 
TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       11.97        34.95        31.30        32.91         1.38         1.15 
TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       25.15        14.07        16.87         0.76        13.22        22.45 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 
        3.09         2.01         0.72        14.63        13.94        15.62 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       19.33        17.72        24.36        18.18        19.73        12.56 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 
       14.96         0.79        12.39         3.65        24.92         2.93 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-8064 
       11.77        14.07        20.22        22.62         2.70         5.26 
TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-96-8169 
        2.30        21.04         4.01         5.03        14.14        18.31 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       17.46        19.36        16.57         8.42        30.81        30.67 
TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       21.34         3.88        18.15        27.02        21.21        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 
       18.58        20.71        19.10        12.89        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
        4.54         1.22        45.37         4.21         2.89        39.85 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CT TCGA-NK-A5CX TCGA-O2-A52N 
       30.58        24.00        14.73        65.49         3.65        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52W TCGA-XC-AA0X 
        3.72        12.72         8.58         0.20 

  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                          0.07                           0.03 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                        174.08                         154.32 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                        21.110                         18.345 
[1] "0.1 - 174.1 (21.1)" "0.0 - 154.3 (18.3)"
[1] "hr=" "1.2"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(15Q26.3) MUTATED         0       26       53        1        28
  AMP PEAK 21(15Q26.3) WILD-TYPE       2       61       98        1        35
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(15Q26.3) MUTATED          31         1         24          7
  AMP PEAK 21(15Q26.3) WILD-TYPE        61         2         38         14
                                vv
clus                             STAGE IV
  AMP PEAK 21(15Q26.3) MUTATED          3
  AMP PEAK 21(15Q26.3) WILD-TYPE        4
D21V3, multiclass
            clus
vv           AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                             26                             61
  STAGE IB                             53                             98
  STAGE II                              1                              1
  STAGE IIA                            28                             35
  STAGE IIB                            31                             61
  STAGE III                             1                              2
  STAGE IIIA                           24                             38
  STAGE IIIB                            7                             14
  STAGE IV                              3                              4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 21(15Q26.3) MUTATED    33 113  23   6
  AMP PEAK 21(15Q26.3) WILD-TYPE  78 177  46  17
D21V4, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  T1                           33                             78
  T2                          113                            177
  T3                           23                             46
  T4                            6                             17
[1] 4 2
[1] TRUE
[1] "dimension of 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(15Q26.3) MUTATED   100  56  14   3
  AMP PEAK 21(15Q26.3) WILD-TYPE 212  75  25   2
D21V5, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  N0                          100                            212
  N1                           56                             75
  N2                           14                             25
  N3                            3                              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"
D21V6, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED   150   3
  AMP PEAK 21(15Q26.3) WILD-TYPE 254   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED    150    3
  AMP PEAK 21(15Q26.3) WILD-TYPE  254    4
   clus
vv  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  0                          150                            254
  1                            3                              4
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED    41 134
  AMP PEAK 21(15Q26.3) WILD-TYPE  86 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED     41  134
  AMP PEAK 21(15Q26.3) WILD-TYPE   86  232
        clus
vv       AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  FEMALE                           41                             86
  MALE                            134                            232
[1] 2 2
[1] FALSE
D21V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(15Q26.3) MUTATED                                       8
  AMP PEAK 21(15Q26.3) WILD-TYPE                                     7
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(15Q26.3) MUTATED                                         1
  AMP PEAK 21(15Q26.3) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 21(15Q26.3) MUTATED                                        2
  AMP PEAK 21(15Q26.3) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 21(15Q26.3) MUTATED                                         0
  AMP PEAK 21(15Q26.3) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(15Q26.3) MUTATED                                                           164
  AMP PEAK 21(15Q26.3) WILD-TYPE                                                         306
D21V9, multiclass
                                                             clus
vv                                                            AMP PEAK 21(15Q26.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          164
                                                             clus
vv                                                            AMP PEAK 21(15Q26.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            306
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED     4 171
  AMP PEAK 21(15Q26.3) WILD-TYPE   9 309
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED      4  171
  AMP PEAK 21(15Q26.3) WILD-TYPE    9  309
     clus
vv    AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  NO                             4                              9
  YES                          171                            309
[1] 2 2
[1] FALSE
D21V11, continuous
D21V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(15Q26.3) MUTATED   138   7   1   9
  AMP PEAK 21(15Q26.3) WILD-TYPE 256   5   3  13
D21V13, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  R0                          138                            256
  R1                            7                              5
  R2                            1                              3
  RX                            9                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(15Q26.3) MUTATED       1                        11   117
  AMP PEAK 21(15Q26.3) WILD-TYPE     8                        20   223
D21V14, multiclass
                           clus
vv                          AMP PEAK 21(15Q26.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              117
                           clus
vv                          AMP PEAK 21(15Q26.3) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             20
  WHITE                                                223
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V15, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED     2 108
  AMP PEAK 21(15Q26.3) WILD-TYPE   6 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED      2  108
  AMP PEAK 21(15Q26.3) WILD-TYPE    6  201
                        clus
vv                       AMP PEAK 21(15Q26.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          108
                        clus
vv                       AMP PEAK 21(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            201
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(17Q25.1) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 22(17Q25.1) MUTATED   141  85
  AMP PEAK 22(17Q25.1) WILD-TYPE 140 111
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                           226                            251 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                            85                            111 
$`AMP PEAK 22(17Q25.1) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 
       12.20         7.46         4.80       117.57        11.34        92.15 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-21-1071 
       31.99        36.07         1.64        86.96         6.18        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
       99.16        70.16        34.78         9.34       119.80        43.23 
TCGA-21-5786 TCGA-21-5787 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
       33.93        10.82        14.10        20.48        35.08        48.33 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4609 
       24.13        38.17        34.75        13.12        19.30         9.57 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       11.77        31.73        14.63        44.25         0.79        54.28 
TCGA-22-5483 TCGA-22-5491 TCGA-33-4532 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 
       18.84        56.32         7.63       103.53        14.07        27.02 
TCGA-33-A4WN TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2604 TCGA-34-2609 
        4.70        44.19       118.36         2.63        31.50        31.27 
TCGA-34-5231 TCGA-34-5236 TCGA-34-5240 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 
       65.23         9.07        12.00         4.04        26.43         3.95 
TCGA-37-3792 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        0.39         7.46         7.82         6.81         0.39         3.39 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5027 TCGA-39-5035 TCGA-39-5037 
       74.07        44.75        55.20        60.79        15.58        35.70 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       17.06        40.21        22.49        38.66        27.02        33.11 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6770 TCGA-43-7657 TCGA-43-8115 TCGA-43-A475 
       18.38        27.91        21.47         7.76        13.38         9.73 
TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-52-7812 
       12.03         9.99        10.65        13.91         0.39        27.45 
TCGA-56-1622 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 
       28.96         0.43         0.99         1.45         0.85         6.51 
TCGA-56-8304 TCGA-56-8308 TCGA-56-8504 TCGA-56-8629 TCGA-56-A4BX TCGA-56-A4BY 
        3.48        17.00        16.77        15.81        13.32        17.85 
TCGA-56-A4ZJ TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J 
       21.04         0.03        13.25        29.95        71.24        85.12 
TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 
       34.36        35.24        29.92        96.82        92.71        21.93 
TCGA-60-2708 TCGA-60-2711 TCGA-60-2715 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
       80.45        41.42        35.34        29.85        35.90        26.83 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MU 
       11.77       102.67        66.61        58.65        59.97        25.41 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2742 TCGA-66-2754 TCGA-66-2756 
       36.16        53.88        34.59        21.07         2.01         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 
       43.99        21.01         0.99         2.01        23.01        19.00 
TCGA-66-2777 TCGA-66-2781 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        2.01         3.98        40.01        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 
        5.03        30.02        10.06         4.01         2.73         6.64 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 
        8.02        13.35        16.18        14.73        29.56        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7465 
       11.18        89.98        20.78         0.49        42.28        15.75 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 
        6.51        53.95        37.81        53.92        39.09       104.09 
TCGA-77-8144 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       27.39        65.49         0.33       117.57        22.29         5.92 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7843 
       42.08        27.62         9.67        11.97        36.53         1.15 
TCGA-85-7844 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 
       29.95        31.56        16.87        10.09        22.45        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
        5.29         3.09        32.71         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A53L 
       19.33        14.96        19.73        16.21        15.85        12.39 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        3.65         2.93        11.77        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-94-7033 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 
        2.70         3.48        21.04        26.63        14.14        16.14 
TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A 
       49.87        57.07        19.36        21.34        27.16        18.15 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HG 
       18.58        20.71        19.10        16.11        11.84        51.78 
TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT 
        2.89        39.85        37.22        14.73        29.75        22.78 
TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52S 
       83.57         0.43        33.07        12.72 

$`AMP PEAK 22(17Q25.1) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3414 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       75.75        79.46        23.54         2.79       154.32        49.94 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       27.19       119.54        60.89        15.58        31.73       122.43 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
       31.63        88.11        41.69        32.19        21.99         7.33 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 
       14.93         4.31        64.21         1.74        27.02        48.82 
TCGA-22-4596 TCGA-22-4605 TCGA-22-5472 TCGA-22-5473 TCGA-22-5480 TCGA-22-5481 
        0.56        32.02        64.93        63.55        71.34        79.20 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 
       11.74        30.12        62.86        16.64        22.06       133.74 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 
       98.01        79.53       174.08       151.27        54.44         1.55 
TCGA-33-6737 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASL 
       19.76         0.30        36.62         6.94       110.99        27.16 
TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
       61.61        28.96        32.88        67.79        56.38        23.24 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       16.93        30.94        18.15         4.96         1.12        27.19 
TCGA-34-A5IX TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-39-5011 TCGA-39-5021 
       20.91         0.43         6.58         8.12        47.80        68.58 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       70.03         1.71        24.33         1.94        27.39        36.39 
TCGA-39-5036 TCGA-39-5039 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 
       35.64        17.88        12.36        24.89         5.46         3.81 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U 
       19.59        66.51        11.77         2.93        11.61        14.20 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
        0.39        29.95        28.34         5.46        30.35         8.75 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7580 
        0.10        18.25         2.04         0.62         0.99         1.32 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        0.10        17.49        26.89        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D 
       22.75         1.18        10.36         9.93        20.25        20.94 
TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8388 
       19.23        18.74         0.13         0.26         2.76        13.55 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 
       16.47        34.78        56.65        21.11         3.58        12.23 
TCGA-60-2698 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 
       10.22        37.94        49.48        66.54         9.01        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
       50.33        48.49        42.64         3.19        32.32        23.57 
TCGA-63-A5MG TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       70.62        45.57        14.99        11.34        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 
       78.28        16.37        16.96        43.10         2.01         0.99 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
        1.02         0.92        25.05         2.01         1.02         2.01 
TCGA-66-2769 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
        7.07         3.02        19.00        12.03        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2794 TCGA-66-2800 TCGA-68-7757 TCGA-77-6843 
        1.97        25.97        54.08        49.05         6.94        73.12 
TCGA-77-6844 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 
       75.09        70.13       106.95         0.16        46.78        86.76 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 
       82.92        12.59        17.72        11.54        26.40         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G8 
        9.63        54.41        35.90       126.18       132.36        42.41 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 
       30.81        38.86        12.99         6.41        34.95        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
       32.91         1.38        18.94        25.15        19.04        24.13 
TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8355 TCGA-85-8479 
       14.07        34.52         0.76        13.22         2.01         0.72 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB TCGA-85-A4PA 
        7.76        14.63        13.94        12.59        17.72        24.36 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 
       18.18        12.56        14.96         0.79        24.92         9.50 
TCGA-90-7964 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7557 TCGA-94-7943 
       14.07         4.01         5.26         2.30         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
        4.01         5.03        17.69        18.31        17.46        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-A539 TCGA-98-A53B 
        8.42         2.76        30.81        30.67         3.88         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW 
       27.02        21.21        20.32        12.89        13.18        13.41 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
        0.07        64.08         4.54         1.22        45.37        13.74 
TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
        4.21        30.58        24.00        65.49         3.65        16.80 
TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        43.89         8.58        11.18         0.20 

  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                          0.03                           0.07 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                        119.80                         174.08 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                         20.35                          18.25 
[1] "0.0 - 119.8 (20.4)" "0.1 - 174.1 (18.2)"
[1] "hr=" "1.1"
D22V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(17Q25.1) MUTATED         1       31       65        0        40
  AMP PEAK 22(17Q25.1) WILD-TYPE       1       56       86        2        23
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(17Q25.1) MUTATED          44         1         33         10
  AMP PEAK 22(17Q25.1) WILD-TYPE        48         2         29         11
                                vv
clus                             STAGE IV
  AMP PEAK 22(17Q25.1) MUTATED          5
  AMP PEAK 22(17Q25.1) WILD-TYPE        2
D22V3, multiclass
            clus
vv           AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             31                             56
  STAGE IB                             65                             86
  STAGE II                              0                              2
  STAGE IIA                            40                             23
  STAGE IIB                            44                             48
  STAGE III                             1                              2
  STAGE IIIA                           33                             29
  STAGE IIIB                           10                             11
  STAGE IV                              5                              2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 22(17Q25.1) MUTATED    39 156  26  10
  AMP PEAK 22(17Q25.1) WILD-TYPE  72 134  43  13
D22V4, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  T1                           39                             72
  T2                          156                            134
  T3                           26                             43
  T4                           10                             13
[1] 4 2
[1] TRUE
[1] "dimension of 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(17Q25.1) MUTATED   128  76  23   3
  AMP PEAK 22(17Q25.1) WILD-TYPE 184  55  16   2
D22V5, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  N0                          128                            184
  N1                           76                             55
  N2                           23                             16
  N3                            3                              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"
D22V6, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED   190   5
  AMP PEAK 22(17Q25.1) WILD-TYPE 214   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED    190    5
  AMP PEAK 22(17Q25.1) WILD-TYPE  214    2
   clus
vv  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  0                          190                            214
  1                            5                              2
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED    45 186
  AMP PEAK 22(17Q25.1) WILD-TYPE  82 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     45  186
  AMP PEAK 22(17Q25.1) WILD-TYPE   82  180
        clus
vv       AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  FEMALE                           45                             82
  MALE                            186                            180
[1] 2 2
[1] FALSE
D22V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(17Q25.1) MUTATED                                       7
  AMP PEAK 22(17Q25.1) WILD-TYPE                                     8
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(17Q25.1) MUTATED                                         1
  AMP PEAK 22(17Q25.1) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 22(17Q25.1) MUTATED                                        1
  AMP PEAK 22(17Q25.1) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 22(17Q25.1) MUTATED                                         0
  AMP PEAK 22(17Q25.1) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(17Q25.1) MUTATED                                                           222
  AMP PEAK 22(17Q25.1) WILD-TYPE                                                         248
D22V9, multiclass
                                                             clus
vv                                                            AMP PEAK 22(17Q25.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          222
                                                             clus
vv                                                            AMP PEAK 22(17Q25.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            248
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED     8 223
  AMP PEAK 22(17Q25.1) WILD-TYPE   5 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED      8  223
  AMP PEAK 22(17Q25.1) WILD-TYPE    5  257
     clus
vv    AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  NO                             8                              5
  YES                          223                            257
[1] 2 2
[1] FALSE
D22V11, continuous
D22V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(17Q25.1) MUTATED   190   5   2   7
  AMP PEAK 22(17Q25.1) WILD-TYPE 204   7   2  15
D22V13, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  R0                          190                            204
  R1                            5                              7
  R2                            2                              2
  RX                            7                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(17Q25.1) MUTATED       3                        12   159
  AMP PEAK 22(17Q25.1) WILD-TYPE     6                        19   181
D22V14, multiclass
                           clus
vv                          AMP PEAK 22(17Q25.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              159
                           clus
vv                          AMP PEAK 22(17Q25.1) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             19
  WHITE                                                181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V15, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED     3 139
  AMP PEAK 22(17Q25.1) WILD-TYPE   5 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED      3  139
  AMP PEAK 22(17Q25.1) WILD-TYPE    5  170
                        clus
vv                       AMP PEAK 22(17Q25.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          139
                        clus
vv                       AMP PEAK 22(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            170
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(18P11.32) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 23(18P11.32) MUTATED   105  66
  AMP PEAK 23(18P11.32) WILD-TYPE 176 130
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                            171                             306 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                             66                             130 
$`AMP PEAK 23(18P11.32) MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3416 TCGA-18-4083 TCGA-21-1075 
        7.46       117.57        11.34        31.99         6.18        70.16 
TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
       31.73       119.80        43.23        31.63        41.69        33.93 
TCGA-22-0944 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4604 TCGA-22-5471 
        7.33        20.48        35.08        24.13        13.12        31.73 
TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4566 
       71.34        18.84        62.86        56.32         7.63       174.08 
TCGA-33-6737 TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 TCGA-34-2604 
       19.76        36.62       110.99        44.19         2.63        31.50 
TCGA-34-5231 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-A5IX 
       65.23         9.07        23.24        12.00        16.93        20.91 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 
        0.43         0.39         8.12         6.81         0.39        74.07 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 
       44.75        68.58        60.79        24.33        27.39        35.70 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
       17.06        40.21        22.49        18.38        27.91        12.36 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V 
        7.76        66.51         2.93        11.61         9.73        12.03 
TCGA-46-3768 TCGA-46-6026 TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 
        9.99        13.91        29.95         5.46         8.75        18.25 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-8304 TCGA-56-8309 
        0.43         0.99         1.32         6.51         3.48        14.07 
TCGA-56-A49D TCGA-56-A4BY TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8391 
       20.94        17.85         0.13         0.26         0.03        71.24 
TCGA-58-8392 TCGA-60-2698 TCGA-60-2711 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
       16.47        10.22        41.42        29.85        35.90        26.83 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MU 
       11.77       102.67        66.61        58.65        45.57        25.41 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2758 TCGA-66-2759 
       53.88        16.96        43.10        21.07        21.01        25.05 
TCGA-66-2763 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 TCGA-66-2781 
        0.99         2.01         7.07        23.01         2.01         3.98 
TCGA-66-2783 TCGA-66-2787 TCGA-66-2789 TCGA-66-2794 TCGA-66-2800 TCGA-68-8250 
       24.95        40.01         4.04        54.08        49.05         8.02 
TCGA-68-A59J TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7463 TCGA-77-7465 
       14.73        20.78         0.49        70.13        46.78        15.75 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8140 TCGA-77-8143 TCGA-77-8150 
       53.95        37.81        82.92        11.54        26.40        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 
       65.49         0.33       117.57        27.62        12.99         6.41 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
        1.15        29.95        19.04        31.56        14.07        34.52 
TCGA-85-8277 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8580 TCGA-85-8664 
       10.09         5.29         3.09        32.71        14.63         0.10 
TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A50M TCGA-85-A510 TCGA-85-A5B5 
       15.62        19.33        17.72        12.56        15.85         3.65 
TCGA-90-7766 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8064 TCGA-94-8491 
        9.50        11.77        22.62        10.59         5.26        26.63 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-98-8021 
       14.14        16.14        57.07        18.31        19.36        30.81 
TCGA-98-A538 TCGA-98-A53B TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
       27.16         2.01        18.58        19.10        12.89        16.11 
TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NC-A5HT 
       11.84         1.22        45.37         2.89        14.73        22.78 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A5IB 
        3.65        33.07        11.18 

$`AMP PEAK 23(18P11.32) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
       12.20        75.75        79.46         4.80        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       36.07         1.64        86.96         2.79       154.32        49.94 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 
       27.19       119.54        46.88        99.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-5783 TCGA-21-5787 TCGA-21-A5DI 
       15.58       122.43         9.34        88.11        10.82        32.19 
TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       21.99        14.93         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       27.02        48.82        48.33         0.56        38.17        34.75 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 
       32.02        19.30         9.57        11.77        64.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 
       14.63        44.25         0.79        54.28        79.20        11.74 
TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
       30.12        16.64        22.06       133.74        98.01        79.53 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 
      103.53       151.27        14.07        54.44         1.55        27.02 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 
        4.70         0.30         6.94       118.36        27.16        61.61 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 
       28.96        32.88        31.27        67.79        56.38        30.94 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       18.15         4.96         1.12        27.19         4.04        26.43 
TCGA-37-3783 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-39-5011 
        3.95         6.58         7.46         7.82         3.39        47.80 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
       55.20        70.03         1.71         1.94        36.39        15.58 
TCGA-39-5036 TCGA-39-5039 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6647 
       35.64        17.88        38.66        27.02        33.11        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       21.47         5.46         3.81        19.59        13.38        11.77 
TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7810 
       14.20        10.65         0.39         0.39        28.34        30.35 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
       27.45        28.96         0.10         2.04         0.62         0.99 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 
        1.45         0.85         0.10        17.49        26.89        17.00 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ 
        9.93        20.25        15.81        19.23        13.32        21.04 
TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 
       18.74         2.76        13.25        13.55        29.95        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       85.12        34.36        56.65        35.24        29.92        21.11 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
        3.58        12.23        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
       80.45        49.48        66.54         9.01        56.91        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
       35.34        48.49        42.64         3.19        32.32        23.57 
TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       70.62        59.97        14.99        11.34        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2737 TCGA-66-2744 
       78.28        16.37        36.16        34.59         2.01         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2765 
        1.02         2.01         0.92         0.99        43.99         2.01 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
        1.02         2.01        19.00         3.02        19.00        12.03 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 
       12.00         1.97        25.97        22.98        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
       30.02        10.06         4.01         2.73         6.64         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       13.35        16.18        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 
       11.18        89.98        42.28       106.95         0.16         6.51 
TCGA-77-8008 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       86.76        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
       27.39         6.97         9.63        35.90       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH 
       22.29         5.92        42.41        42.08        30.81        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
        9.67        11.97        36.53        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 TCGA-85-8072 TCGA-85-8287 
        1.38        18.94        25.15        24.13        16.87         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       13.22        22.45        16.77         2.01         0.72         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       13.94        12.59        25.68        14.96        24.36        18.18 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       19.73        16.21        14.96         0.79        12.39        24.92 
TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
        2.93        14.07        20.22         2.70         3.48         4.01 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        2.30        21.04         0.16        11.70         4.01         5.03 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       17.69        49.87        17.46        16.57         8.42         2.76 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D 
       30.67        21.34         3.88        18.15        27.02        21.21 
TCGA-98-A53H TCGA-98-A53J TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HE 
       20.32        20.71        13.18        13.41         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN 
        4.54        51.78        13.74         4.21        39.85        37.22 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 
       30.58        24.00        29.75        83.57        65.49        16.80 
TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
        0.43         3.72        12.72        43.89         8.58         0.20 

  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                           0.03                            0.07 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                         174.08                          154.32 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                         18.840                          19.445 
[1] "0.0 - 174.1 (18.8)" "0.1 - 154.3 (19.4)"
[1] "hr=" "1.1"
D23V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 23(18P11.32) MUTATED         1       29       57        0        26
  AMP PEAK 23(18P11.32) WILD-TYPE       1       58       94        2        37
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(18P11.32) MUTATED          27         1         25          9
  AMP PEAK 23(18P11.32) WILD-TYPE        65         2         37         12
                                 vv
clus                              STAGE IV
  AMP PEAK 23(18P11.32) MUTATED          2
  AMP PEAK 23(18P11.32) WILD-TYPE        5
D23V3, multiclass
            clus
vv           AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  STAGE I                                1                               1
  STAGE IA                              29                              58
  STAGE IB                              57                              94
  STAGE II                               0                               2
  STAGE IIA                             26                              37
  STAGE IIB                             27                              65
  STAGE III                              1                               2
  STAGE IIIA                            25                              37
  STAGE IIIB                             9                              12
  STAGE IV                               2                               5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 23(18P11.32) MUTATED    37 114  22   5
  AMP PEAK 23(18P11.32) WILD-TYPE  74 176  47  18
D23V4, multiclass
    clus
vv   AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  T1                            37                              74
  T2                           114                             176
  T3                            22                              47
  T4                             5                              18
[1] 4 2
[1] TRUE
[1] "dimension of 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(18P11.32) MUTATED   106  50  17   3
  AMP PEAK 23(18P11.32) WILD-TYPE 206  81  22   2
D23V5, multiclass
    clus
vv   AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  N0                           106                             206
  N1                            50                              81
  N2                            17                              22
  N3                             3                               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"
D23V6, binary
                                 cls
clus                                0   1
  AMP PEAK 23(18P11.32) MUTATED   147   2
  AMP PEAK 23(18P11.32) WILD-TYPE 257   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED    147    2
  AMP PEAK 23(18P11.32) WILD-TYPE  257    5
   clus
vv  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  0                           147                             257
  1                             2                               5
[1] 2 2
[1] FALSE
D23V7, binary
                                 cls
clus                                0   1
  AMP PEAK 23(18P11.32) MUTATED    41 137
  AMP PEAK 23(18P11.32) WILD-TYPE  86 229
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED     41  137
  AMP PEAK 23(18P11.32) WILD-TYPE   86  229
        clus
vv       AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  FEMALE                            41                              86
  MALE                             137                             229
[1] 2 2
[1] FALSE
D23V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(18P11.32) MUTATED                                       5
  AMP PEAK 23(18P11.32) WILD-TYPE                                    10
                                 vv
clus                              LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(18P11.32) MUTATED                                         0
  AMP PEAK 23(18P11.32) WILD-TYPE                                       1
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 23(18P11.32) MUTATED                                        1
  AMP PEAK 23(18P11.32) WILD-TYPE                                      5
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 23(18P11.32) MUTATED                                         0
  AMP PEAK 23(18P11.32) WILD-TYPE                                       1
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(18P11.32) MUTATED                                                           172
  AMP PEAK 23(18P11.32) WILD-TYPE                                                         298
D23V9, multiclass
                                                             clus
vv                                                            AMP PEAK 23(18P11.32) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           172
                                                             clus
vv                                                            AMP PEAK 23(18P11.32) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             298
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                                 cls
clus                                0   1
  AMP PEAK 23(18P11.32) MUTATED     7 171
  AMP PEAK 23(18P11.32) WILD-TYPE   6 309
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED      7  171
  AMP PEAK 23(18P11.32) WILD-TYPE    6  309
     clus
vv    AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  NO                              7                               6
  YES                           171                             309
[1] 2 2
[1] FALSE
D23V11, continuous
D23V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 23(18P11.32) MUTATED   139   3   3   9
  AMP PEAK 23(18P11.32) WILD-TYPE 255   9   1  13
D23V13, multiclass
    clus
vv   AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  R0                           139                             255
  R1                             3                               9
  R2                             3                               1
  RX                             9                              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(18P11.32) MUTATED       4                         6   128
  AMP PEAK 23(18P11.32) WILD-TYPE     5                        25   212
D23V14, multiclass
                           clus
vv                          AMP PEAK 23(18P11.32) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               128
                           clus
vv                          AMP PEAK 23(18P11.32) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                              25
  WHITE                                                 212
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V15, binary
                                 cls
clus                                0   1
  AMP PEAK 23(18P11.32) MUTATED     2 110
  AMP PEAK 23(18P11.32) WILD-TYPE   6 199
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED      2  110
  AMP PEAK 23(18P11.32) WILD-TYPE    6  199
                        clus
vv                       AMP PEAK 23(18P11.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           110
                        clus
vv                       AMP PEAK 23(18P11.32) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             199
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(18Q11.2) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(18Q11.2) MUTATED    85  60
  AMP PEAK 24(18Q11.2) WILD-TYPE 196 136
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           145                            332 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                            60                            136 
$`AMP PEAK 24(18Q11.2) MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-4083 TCGA-21-1082 TCGA-21-1083 
        7.46       117.57        11.34         6.18       119.80        43.23 
TCGA-21-5783 TCGA-21-5784 TCGA-22-1012 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 
       88.11        41.69        14.10        24.13        38.17        13.12 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 
       11.77        31.73         0.79        71.34        79.20        18.84 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4566 TCGA-33-4586 TCGA-33-AASD 
       62.86        56.32         7.63       174.08        14.07       110.99 
TCGA-33-AASI TCGA-34-2596 TCGA-34-2609 TCGA-34-5231 TCGA-34-5236 TCGA-34-5239 
       44.19         2.63        31.27        65.23         9.07        23.24 
TCGA-34-5240 TCGA-34-8456 TCGA-37-3789 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
       12.00        26.43         0.43         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 
        6.81         0.39        47.80        44.75        68.58        60.79 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 TCGA-43-3920 
       24.33        27.39        35.70        17.06        22.49        33.11 
TCGA-43-5668 TCGA-43-6647 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8118 
       18.38        24.89         7.76        66.51        13.38         2.93 
TCGA-43-A475 TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 
        9.73        12.03        13.91         0.39        29.95         5.46 
TCGA-52-7811 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-8304 
        8.75        18.25         0.99         1.32         6.51         3.48 
TCGA-56-A49D TCGA-56-A4BX TCGA-58-8391 TCGA-58-8392 TCGA-58-A46M TCGA-58-A46N 
       20.94        13.32        71.24        16.47        35.24        29.92 
TCGA-60-2695 TCGA-60-2711 TCGA-60-2712 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
       21.11        41.42         9.01        29.85        35.90        26.83 
TCGA-60-2726 TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MU TCGA-66-2734 
       11.77        59.97        45.57        25.28        25.41        43.10 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 
       21.01        25.05         2.01         7.07        23.01         2.01 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
       25.97        40.01        22.98        30.02        10.06        54.08 
TCGA-66-2800 TCGA-68-7755 TCGA-77-6842 TCGA-77-7140 TCGA-77-7463 TCGA-77-7465 
       49.05         2.73        29.56        20.78        46.78        15.75 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8140 TCGA-77-8143 TCGA-77-8150 
       53.95        37.81        82.92        11.54        26.40        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 
       65.49         0.33       117.57        27.62        38.86        12.99 
TCGA-85-6798 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8070 TCGA-85-8071 
        6.41         1.15        29.95        18.94        31.56        14.07 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8352 TCGA-85-8664 TCGA-85-A4CN 
       34.52        10.09        22.45         5.29         0.10        19.33 
TCGA-85-A4JB TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8064 TCGA-96-7545 
       17.72        11.77        22.62        10.59         5.26        57.07 
TCGA-98-8021 TCGA-98-8022 TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A7SW 
       30.81        30.67        18.58        19.10        12.89        13.41 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52S 
       11.84        51.78         2.89        14.73         3.65        12.72 
TCGA-O2-A5IB 
       11.18 

$`AMP PEAK 24(18Q11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
       12.20        75.75        79.46         4.80        23.54        92.15 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       31.99        36.07         1.64        86.96         2.79       154.32 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
       49.94        27.19       119.54        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       60.89        34.78        15.58        31.73       122.43         9.34 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
       31.63        33.93        10.82        32.19        21.99         7.33 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 
       14.93         4.31        64.21         1.74        27.02        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4601 TCGA-22-4605 
       20.48        35.08        48.33         0.56        34.75        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       19.30         9.57        64.93        63.55        14.63        44.25 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 
       54.28        11.74        30.12        16.64        22.06       133.74 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 
       98.01        79.53       103.53       151.27        54.44         1.55 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       19.76        27.02         4.70         0.30        36.62         6.94 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
      118.36        27.16        61.61        31.50        28.96        32.88 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       67.79        56.38        16.93        30.94        18.15         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 
        1.12        27.19         4.04        20.91         3.95         0.39 
TCGA-37-4129 TCGA-37-5819 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
        6.58         3.39        74.07        55.20        70.03         1.71 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 
        1.94        36.39        15.58        35.64        17.88        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 
       38.66        27.02        27.91        12.36        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8116 TCGA-43-A474 TCGA-43-A56U TCGA-46-3768 
        3.81        19.59        11.77        11.61        14.20         9.99 
TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 
       10.65         0.39        28.34        30.35        27.45        28.96 
TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 
        0.10         2.04         0.62         0.99         0.43         1.45 
TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.85         0.10        17.49        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        1.35        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ 
        9.93        20.25        15.81        19.23        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       18.74         0.13         0.26         2.76         0.03        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       13.55        29.95        34.78        85.12        34.36        56.65 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
        3.58        12.23        10.22        96.82        37.94        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       21.93        80.45        49.48        66.54        56.91        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
       35.34        48.49        42.64         3.19        32.32        23.57 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN 
      102.67        70.62        66.61        58.65        14.99        11.34 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       89.29        78.28        16.37        36.16        53.88        34.59 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       16.96         2.01        21.07         0.99         1.02         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
        0.92         0.99        43.99         0.99         2.01         1.02 
TCGA-66-2767 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        2.01        19.00         3.02        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
       12.00        24.95         1.97        22.98         4.04         5.03 
TCGA-66-2795 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
        4.01         6.64         6.94         8.02        13.35        16.18 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       14.73        73.12        75.09        23.28        11.18        89.98 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 
        0.49        42.28        70.13       106.95         0.16         6.51 
TCGA-77-8008 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       86.76        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
       27.39         6.97         9.63        35.90       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-85-6175 
       22.29         5.92        42.41        42.08        30.81         9.67 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
       11.97        36.53        34.95        31.30        32.91         1.38 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 
       25.15        19.04        24.13        16.87         0.76        13.22 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       16.77         3.09        32.71         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC 
       14.63        13.94        12.59        15.62        25.68        14.96 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       24.36        18.18        19.73        12.56        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
       14.96         0.79        12.39         3.65        24.92         9.50 
TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
        2.93        14.07        20.22         2.70         3.48         4.01 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        2.30        21.04         0.16        11.70         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
       26.63        14.14        16.14        17.69        49.87        18.31 
TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8023 
       17.46        19.36        16.57         8.42         2.76        21.34 
TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D 
       27.16         3.88        18.15         2.01        27.02        21.21 
TCGA-98-A53H TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HD TCGA-NC-A5HE 
       20.32        20.71        16.11        13.18         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM 
        4.54         1.22        45.37        13.74         4.21        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
       37.22        30.58        24.00        29.75        22.78        83.57 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V 
       65.49        16.80         0.43        33.07         3.72        43.89 
TCGA-O2-A52W TCGA-XC-AA0X 
        8.58         0.20 

  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                        174.08                         154.32 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                        21.010                         18.525 
[1] "0.1 - 174.1 (21.0)" "0.0 - 154.3 (18.5)"
[1] "hr=" "1"  
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(18Q11.2) MUTATED         0       24       44        0        22
  AMP PEAK 24(18Q11.2) WILD-TYPE       2       63      107        2        41
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(18Q11.2) MUTATED          31         2         19          7
  AMP PEAK 24(18Q11.2) WILD-TYPE        61         1         43         14
                                vv
clus                             STAGE IV
  AMP PEAK 24(18Q11.2) MUTATED          1
  AMP PEAK 24(18Q11.2) WILD-TYPE        6
D24V3, multiclass
            clus
vv           AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                             24                             63
  STAGE IB                             44                            107
  STAGE II                              0                              2
  STAGE IIA                            22                             41
  STAGE IIB                            31                             61
  STAGE III                             2                              1
  STAGE IIIA                           19                             43
  STAGE IIIB                            7                             14
  STAGE IV                              1                              6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 24(18Q11.2) MUTATED    32  97  13   8
  AMP PEAK 24(18Q11.2) WILD-TYPE  79 193  56  15
D24V4, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  T1                           32                             79
  T2                           97                            193
  T3                           13                             56
  T4                            8                             15
[1] 4 2
[1] TRUE
[1] "dimension of 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(18Q11.2) MUTATED    82  52  15   0
  AMP PEAK 24(18Q11.2) WILD-TYPE 230  79  24   5
D24V5, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  N0                           82                            230
  N1                           52                             79
  N2                           15                             24
  N3                            0                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED   126   1
  AMP PEAK 24(18Q11.2) WILD-TYPE 278   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED    126    1
  AMP PEAK 24(18Q11.2) WILD-TYPE  278    6
   clus
vv  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  0                          126                            278
  1                            1                              6
[1] 2 2
[1] FALSE
D24V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED    39 111
  AMP PEAK 24(18Q11.2) WILD-TYPE  88 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED     39  111
  AMP PEAK 24(18Q11.2) WILD-TYPE   88  255
        clus
vv       AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  FEMALE                           39                             88
  MALE                            111                            255
[1] 2 2
[1] FALSE
D24V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                                       5
  AMP PEAK 24(18Q11.2) WILD-TYPE                                    10
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                                         0
  AMP PEAK 24(18Q11.2) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 24(18Q11.2) MUTATED                                        1
  AMP PEAK 24(18Q11.2) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                                         0
  AMP PEAK 24(18Q11.2) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(18Q11.2) MUTATED                                                           144
  AMP PEAK 24(18Q11.2) WILD-TYPE                                                         326
D24V9, multiclass
                                                             clus
vv                                                            AMP PEAK 24(18Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          144
                                                             clus
vv                                                            AMP PEAK 24(18Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            326
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED     6 144
  AMP PEAK 24(18Q11.2) WILD-TYPE   7 336
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED      6  144
  AMP PEAK 24(18Q11.2) WILD-TYPE    7  336
     clus
vv    AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  NO                             6                              7
  YES                          144                            336
[1] 2 2
[1] FALSE
D24V11, continuous
D24V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 24(18Q11.2) MUTATED   122   4   2   5
  AMP PEAK 24(18Q11.2) WILD-TYPE 272   8   2  17
D24V13, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  R0                          122                            272
  R1                            4                              8
  R2                            2                              2
  RX                            5                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(18Q11.2) MUTATED       2                         6   107
  AMP PEAK 24(18Q11.2) WILD-TYPE     7                        25   233
D24V14, multiclass
                           clus
vv                          AMP PEAK 24(18Q11.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                              107
                           clus
vv                          AMP PEAK 24(18Q11.2) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             25
  WHITE                                                233
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V15, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED     2  93
  AMP PEAK 24(18Q11.2) WILD-TYPE   6 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED      2   93
  AMP PEAK 24(18Q11.2) WILD-TYPE    6  216
                        clus
vv                       AMP PEAK 24(18Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           93
                        clus
vv                       AMP PEAK 24(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            216
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(19Q12) MUTATION ANALYSIS
D25V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 25(19Q12) MUTATED   126  86
  AMP PEAK 25(19Q12) WILD-TYPE 155 110
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         212                          265 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          86                          110 
$`AMP PEAK 25(19Q12) MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3416 TCGA-18-3417 TCGA-21-1070 
        7.46         4.80       117.57        31.99        36.07       119.54 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1080 TCGA-21-1081 TCGA-21-5786 TCGA-21-5787 
       46.88        60.89       122.43         9.34        33.93        10.82 
TCGA-22-0940 TCGA-22-1011 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
       21.99         1.74        48.82        20.48        35.08        24.13 
TCGA-22-4599 TCGA-22-4601 TCGA-22-5471 TCGA-22-5474 TCGA-22-5477 TCGA-22-5481 
       38.17        34.75        31.73        14.63        44.25        79.20 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 
       18.84        30.12        62.86        22.06       133.74        98.01 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-6737 TCGA-33-6738 TCGA-33-AASD 
      174.08       103.53        14.07        19.76        27.02       110.99 
TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       44.19         2.63        61.61        31.50        28.96        32.88 
TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 TCGA-34-8456 
       65.23        23.24        12.00        18.15         1.12        26.43 
TCGA-34-A5IX TCGA-37-3792 TCGA-37-4130 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
       20.91         0.39         8.12         3.39        47.80        74.07 
TCGA-39-5019 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 
       44.75        24.33        27.39        36.39        15.58        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
       17.06        40.21        22.49        27.02        33.11        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-7657 TCGA-43-A475 TCGA-43-A56V 
       27.91        12.36        19.59         7.76         9.73        12.03 
TCGA-46-3768 TCGA-46-6026 TCGA-52-7809 TCGA-56-6545 TCGA-56-6546 TCGA-56-7580 
        9.99        13.91         5.46         2.04         0.62         1.32 
TCGA-56-7582 TCGA-56-8304 TCGA-56-8308 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX 
        0.85         3.48        17.00        15.81        20.94        13.32 
TCGA-56-A4BY TCGA-56-A5DR TCGA-58-8386 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L 
       17.85         0.13         0.03        34.78        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 
       35.24        29.92        21.11        10.22        37.94        92.71 
TCGA-60-2708 TCGA-60-2712 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-63-A5MB 
       80.45         9.01        42.64        29.85        35.90       102.67 
TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MV 
       70.62        66.61        58.65        45.57        89.29        36.16 
TCGA-66-2742 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 
       21.07         0.99        21.01        25.05         0.99         1.02 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 
       23.01         2.01         3.98        12.00         1.97        40.01 
TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 
       22.98         5.03        30.02        10.06         4.01        49.05 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 
       13.35        16.18        14.73        29.56        73.12        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7465 
       11.18        89.98         0.49        42.28        70.13        15.75 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8136 TCGA-77-8138 
       86.76        53.95        37.81        82.92        39.09        17.72 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G1 TCGA-77-A5G3 
        6.97         9.63        54.41        65.49       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       22.29         5.92        42.41        27.62        38.86         9.67 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 TCGA-85-8070 
        6.41        36.53        32.91         1.15        25.15        31.56 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
       16.87        10.09        22.45        16.77         3.09        32.71 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50M 
       13.94        12.59        25.68        19.33        19.73        12.56 
TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q 
       15.85        12.39         3.65        11.77        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7943 TCGA-94-A4VJ 
        2.70         3.48         4.01         5.26        11.70        14.14 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-98-8020 TCGA-98-8021 TCGA-98-A53A 
       16.14        17.69        57.07         2.76        30.81        18.15 
TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
        2.01        18.58        20.71        19.10        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP 
       13.18        13.41        13.74         2.89        37.22        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N 
       14.73        29.75        65.49         3.65         0.43        33.07 
TCGA-O2-A52W TCGA-XC-AA0X 
        8.58         0.20 

$`AMP PEAK 25(19Q12) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       12.20        75.75        79.46        11.34        23.54        92.15 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
        1.64        86.96         6.18         2.79       154.32        49.94 
TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       27.19        99.16        70.16        34.78        15.58        31.73 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI 
      119.80        43.23        31.63        88.11        41.69        32.19 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 
        7.33        14.93         4.31        64.21        14.10        27.02 
TCGA-22-4594 TCGA-22-4596 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       48.33         0.56        13.12        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       11.77        64.93        63.55         0.79        54.28        71.34 
TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4547 TCGA-33-4583 
       11.74        56.32        16.64         7.63        79.53       151.27 
TCGA-33-4587 TCGA-33-4589 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       54.44         1.55         4.70         0.30        36.62         6.94 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
      118.36        27.16        31.27        67.79        56.38         9.07 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 
       16.93        30.94         4.96        27.19         4.04         3.95 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        0.43         6.58         7.46         7.82         6.81         0.39 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
       68.58        55.20        70.03        60.79         1.71         1.94 
TCGA-39-5036 TCGA-39-5037 TCGA-43-2581 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       35.64        35.70        38.66        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
        3.81        66.51        13.38        11.77         2.93        11.61 
TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       14.20        10.65         0.39         0.39        29.95        28.34 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       30.35         8.75        27.45        28.96         0.10        18.25 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 
        0.99         0.43         0.99         1.45         6.51         0.10 
TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
       17.49        26.89        14.07         1.35        16.77         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW 
       22.75         1.18        10.36         9.93        20.25        19.23 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 
       21.04        18.74         0.26         2.76        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-60-2696 TCGA-60-2697 
       29.95        71.24        16.47        85.12         3.58        12.23 
TCGA-60-2703 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 
       96.82        21.93        49.48        66.54        41.42        56.91 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
       50.33        35.34        48.49         3.19        32.32        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       26.83        11.77        59.97        14.99        11.34        25.28 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       78.28        16.37        25.41        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       43.10         2.01         0.99         1.02         2.01         0.92 
TCGA-66-2757 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
       43.99         2.01         2.01         2.01         7.07        19.00 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 TCGA-66-2786 TCGA-66-2789 
        3.02        19.00        12.03        24.95        25.97         4.04 
TCGA-66-2790 TCGA-66-2794 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
       22.98        54.08         2.73         6.64         6.94         8.02 
TCGA-77-6844 TCGA-77-7140 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 
       75.09        20.78       106.95         0.16        46.78         6.51 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       12.59        53.92       104.09        11.54        26.40        27.39 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5GA TCGA-77-A5GB TCGA-85-6560 
       35.90         0.33       126.18        42.08        30.81        11.97 
TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
       12.99        34.95        31.30         1.38        29.95        18.94 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
       19.04        24.13        14.07        34.52         0.76        13.22 
TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 
        5.29         2.01         0.72         7.76        14.63         0.10 
TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z 
       15.62        17.72        14.96        24.36        18.18        16.21 
TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 
       14.96         0.79        24.92         9.50         2.93        14.07 
TCGA-90-A4ED TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 
       20.22         2.30        21.04         0.16         4.01         5.03 
TCGA-94-8491 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       26.63        49.87        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53C 
        8.42        30.67        21.34        27.16         3.88        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF 
       21.21        20.32        11.84         0.07        64.08         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HO 
       51.78         1.22        45.37         4.21        39.85        30.58 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       22.78        83.57        16.80         3.72        12.72        43.89 
TCGA-O2-A5IB 
       11.18 

  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                        0.03                         0.07 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                      174.08                       154.32 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                      20.975                       17.720 
[1] "0.0 - 174.1 (21.0)" "0.1 - 154.3 (17.7)"
[1] "hr=" "1.2"
D25V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(19Q12) MUTATED         2       36       60        1        32
  AMP PEAK 25(19Q12) WILD-TYPE       0       51       91        1        31
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(19Q12) MUTATED          36         0         38         10
  AMP PEAK 25(19Q12) WILD-TYPE        56         3         24         11
                              vv
clus                           STAGE IV
  AMP PEAK 25(19Q12) MUTATED          4
  AMP PEAK 25(19Q12) WILD-TYPE        3
D25V3, multiclass
            clus
vv           AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  STAGE I                             2                            0
  STAGE IA                           36                           51
  STAGE IB                           60                           91
  STAGE II                            1                            1
  STAGE IIA                          32                           31
  STAGE IIB                          36                           56
  STAGE III                           0                            3
  STAGE IIIA                         38                           24
  STAGE IIIB                         10                           11
  STAGE IV                            4                            3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 25(19Q12) MUTATED    44 136  28  11
  AMP PEAK 25(19Q12) WILD-TYPE  67 154  41  12
D25V4, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  T1                         44                           67
  T2                        136                          154
  T3                         28                           41
  T4                         11                           12
[1] 4 2
[1] TRUE
[1] "dimension of 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(19Q12) MUTATED   131  59  26   1
  AMP PEAK 25(19Q12) WILD-TYPE 181  72  13   4
D25V5, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  N0                        131                          181
  N1                         59                           72
  N2                         26                           13
  N3                          1                            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"
D25V6, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED   183   4
  AMP PEAK 25(19Q12) WILD-TYPE 221   3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED    183    4
  AMP PEAK 25(19Q12) WILD-TYPE  221    3
   clus
vv  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  0                        183                          221
  1                          4                            3
[1] 2 2
[1] FALSE
D25V7, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED    51 168
  AMP PEAK 25(19Q12) WILD-TYPE  76 198
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     51  168
  AMP PEAK 25(19Q12) WILD-TYPE   76  198
        clus
vv       AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  FEMALE                         51                           76
  MALE                          168                          198
[1] 2 2
[1] FALSE
D25V8, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 25(19Q12) MUTATED                                       9
  AMP PEAK 25(19Q12) WILD-TYPE                                     6
                              vv
clus                           LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 25(19Q12) MUTATED                                         1
  AMP PEAK 25(19Q12) WILD-TYPE                                       0
                              vv
clus                           LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 25(19Q12) MUTATED                                        2
  AMP PEAK 25(19Q12) WILD-TYPE                                      4
                              vv
clus                           LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 25(19Q12) MUTATED                                         0
  AMP PEAK 25(19Q12) WILD-TYPE                                       1
                              vv
clus                           LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(19Q12) MUTATED                                                           207
  AMP PEAK 25(19Q12) WILD-TYPE                                                         263
D25V9, multiclass
                                                             clus
vv                                                            AMP PEAK 25(19Q12) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                              1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        207
                                                             clus
vv                                                            AMP PEAK 25(19Q12) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          263
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED     8 211
  AMP PEAK 25(19Q12) WILD-TYPE   5 269
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED      8  211
  AMP PEAK 25(19Q12) WILD-TYPE    5  269
     clus
vv    AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  NO                           8                            5
  YES                        211                          269
[1] 2 2
[1] FALSE
D25V11, continuous
D25V12, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 25(19Q12) MUTATED   174   5   2  12
  AMP PEAK 25(19Q12) WILD-TYPE 220   7   2  10
D25V13, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  R0                        174                          220
  R1                          5                            7
  R2                          2                            2
  RX                         12                           10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(19Q12) MUTATED       5                        15   145
  AMP PEAK 25(19Q12) WILD-TYPE     4                        16   195
D25V14, multiclass
                           clus
vv                          AMP PEAK 25(19Q12) MUTATED
  ASIAN                                              5
  BLACK OR AFRICAN AMERICAN                         15
  WHITE                                            145
                           clus
vv                          AMP PEAK 25(19Q12) WILD-TYPE
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              195
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V15, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED     3 129
  AMP PEAK 25(19Q12) WILD-TYPE   5 180
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED      3  129
  AMP PEAK 25(19Q12) WILD-TYPE    5  180
                        clus
vv                       AMP PEAK 25(19Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        129
                        clus
vv                       AMP PEAK 25(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          180
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(19Q13.2) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 26(19Q13.2) MUTATED   136  90
  AMP PEAK 26(19Q13.2) WILD-TYPE 145 106
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                           226                            251 
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                            90                            106 
$`AMP PEAK 26(19Q13.2) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3417 
       12.20         7.46         4.80       117.57        11.34        36.07 
TCGA-18-3421 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1080 TCGA-21-1081 
       86.96       119.54        46.88        60.89       122.43         9.34 
TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-1005 TCGA-22-1011 
       88.11        33.93        10.82        21.99        64.21         1.74 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-5471 
       20.48        35.08        24.13        38.17        34.75        31.73 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 
       63.55        14.63        44.25        79.20        18.84        30.12 
TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4582 
       62.86        22.06         7.63       133.74        98.01       103.53 
TCGA-33-4586 TCGA-33-6737 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 
       14.07        19.76        27.02       110.99        44.19         2.63 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
       61.61        31.50        28.96        32.88        31.27        65.23 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-34-8456 
       23.24        12.00        16.93        18.15         1.12        26.43 
TCGA-34-A5IX TCGA-37-3792 TCGA-37-4130 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
       20.91         0.39         8.12         3.39        74.07        44.75 
TCGA-39-5029 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
       24.33        36.39        15.58        17.88        17.06        40.21 
TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
       22.49        27.02        33.11        18.38        27.91        12.36 
TCGA-43-7657 TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-52-7809 
        7.76         9.73         9.99        10.65        13.91         5.46 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7580 TCGA-56-7582 
       28.96        18.25         2.04         0.62         1.32         0.85 
TCGA-56-8304 TCGA-56-8308 TCGA-56-8622 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX 
        3.48        17.00         1.81        15.81        20.94        13.32 
TCGA-56-A4BY TCGA-56-A5DR TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L 
       17.85         0.13        16.47        34.78        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 
       35.24        29.92        21.11        10.22        37.94        92.71 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2712 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 
       80.45        49.48         9.01        42.64        29.85        35.90 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MR 
      102.67        70.62        66.61        58.65        45.57        89.29 
TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2742 TCGA-66-2756 TCGA-66-2758 
       78.28        36.16        34.59        21.07         0.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2777 
       25.05         0.99         1.02         2.01        23.01         2.01 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 
        3.98        12.00         1.97        40.01        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-8251 TCGA-68-A59I 
       30.02        10.06         4.01        49.05        13.35        16.18 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       14.73        29.56        73.12        23.28        11.18        89.98 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
        0.49        42.28        70.13        15.75        86.76        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8136 TCGA-77-8138 TCGA-77-8145 TCGA-77-8148 
       37.81        82.92        39.09        17.72         6.97         9.63 
TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
       54.41       132.36       117.57        22.29         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-7696 TCGA-85-7699 
       42.08        27.62        38.86         9.67        36.53        32.91 
TCGA-85-7843 TCGA-85-8048 TCGA-85-8070 TCGA-85-8276 TCGA-85-8350 TCGA-85-8351 
        1.15        25.15        31.56        34.52        22.45        16.77 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
        3.09        32.71         2.01        13.94        12.59         0.10 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A50M TCGA-85-A510 TCGA-85-A513 
       25.68        19.33        17.72        12.56        15.85         0.79 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q 
       12.39         3.65        11.77        14.07        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7943 TCGA-94-A4VJ 
        2.70         3.48         4.01         5.26        11.70        14.14 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       16.14        17.69        57.07         2.76        30.81        30.67 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       18.15         2.01        18.58        20.71        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HL 
       16.11        13.18        13.41         1.22        13.74         2.89 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5CX 
       37.22        24.00        14.73        29.75        65.49         3.65 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52W TCGA-XC-AA0X 
        0.43        33.07         8.58         0.20 

$`AMP PEAK 26(19Q13.2) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 
       75.75        79.46        23.54        92.15        31.99         1.64 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 
        6.18         2.79       154.32        49.94        27.19        99.16 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 
       70.16        34.78        15.58        31.73       119.80        43.23 
TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       31.63        41.69        32.19         7.33        14.93         4.31 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-22-4604 
       14.10        27.02        48.82        48.33         0.56        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 TCGA-22-5478 
       32.02        19.30         9.57        11.77        64.93         0.79 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 
       54.28        71.34        11.74        56.32        16.64        79.53 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-33-A4WN TCGA-33-A5GW 
      174.08       151.27        54.44         1.55         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-5232 TCGA-34-5234 
       36.62         6.94       118.36        27.16        67.79        56.38 
TCGA-34-5236 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 
        9.07        30.94         4.96        27.19         4.04         3.95 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        0.43         6.58         7.46         7.82         6.81         0.39 
TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
       47.80        68.58        55.20        70.03        60.79         1.71 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-2581 TCGA-43-6647 
        1.94        27.39        35.64        35.70        38.66        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 
       21.47         5.46         3.81        19.59        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-51-4079 
       11.77         2.93        11.61        14.20        12.03         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
        0.39        29.95        28.34        30.35         8.75        27.45 
TCGA-56-5897 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 
        0.10         0.99         0.43         0.99         1.45         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
        0.10        17.49        26.89        14.07         1.35        16.77 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW 
       22.75         1.18        10.36         9.93        20.25        19.23 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       21.04        18.74         0.26         2.76         0.03        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-60-2696 TCGA-60-2697 
       13.55        29.95        71.24        85.12         3.58        12.23 
TCGA-60-2703 TCGA-60-2707 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
       96.82        21.93        66.54        41.42        56.91        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 
       35.34        48.49         3.19        32.32        23.57        26.83 
TCGA-60-2726 TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MT 
       11.77        59.97        14.99        11.34        25.28        16.37 
TCGA-63-A5MU TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 
       25.41        53.88        16.96        43.10         2.01         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2765 TCGA-66-2768 
        1.02         2.01         0.92        43.99         2.01         2.01 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 
        7.07        19.00         3.02        19.00        12.03        24.95 
TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 TCGA-68-7755 TCGA-68-7756 
       25.97         4.04        22.98        54.08         2.73         6.64 
TCGA-68-7757 TCGA-68-8250 TCGA-77-6844 TCGA-77-7140 TCGA-77-7337 TCGA-77-7338 
        6.94         8.02        75.09        20.78       106.95         0.16 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8131 TCGA-77-8133 TCGA-77-8139 TCGA-77-8140 
       46.78         6.51        12.59        53.92       104.09        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       26.40        27.39        65.49        35.90         0.33       126.18 
TCGA-77-A5GB TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 
       30.81        11.97        12.99         6.41        34.95        31.30 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
        1.38        29.95        18.94        19.04        24.13        14.07 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8352 TCGA-85-8479 
       16.87        10.09         0.76        13.22         5.29         0.72 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
        7.76        14.63        15.62        14.96        24.36        18.18 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
       19.73        16.21        14.96        24.92         9.50         2.93 
TCGA-90-A4ED TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 
       20.22         2.30        21.04         0.16         4.01         5.03 
TCGA-94-8491 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       26.63        49.87        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53C TCGA-98-A53D 
        8.42        21.34        27.16         3.88        27.02        21.21 
TCGA-98-A53H TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       20.32        11.84         0.07        64.08         4.54        51.78 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CR 
       45.37         4.21        39.85        30.58        22.78        83.57 
TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       16.80         3.72        12.72        43.89        11.18 

  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                          0.10                           0.03 
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                        133.74                         174.08 
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                        20.925                         18.310 
[1] "0.1 - 133.7 (20.9)" "0.0 - 174.1 (18.3)"
[1] "hr=" "1.2"
D26V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(19Q13.2) MUTATED         2       39       69        1        32
  AMP PEAK 26(19Q13.2) WILD-TYPE       0       48       82        1        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(19Q13.2) MUTATED          39         0         35         11
  AMP PEAK 26(19Q13.2) WILD-TYPE        53         3         27         10
                                vv
clus                             STAGE IV
  AMP PEAK 26(19Q13.2) MUTATED          3
  AMP PEAK 26(19Q13.2) WILD-TYPE        4
D26V3, multiclass
            clus
vv           AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             39                             48
  STAGE IB                             69                             82
  STAGE II                              1                              1
  STAGE IIA                            32                             31
  STAGE IIB                            39                             53
  STAGE III                             0                              3
  STAGE IIIA                           35                             27
  STAGE IIIB                           11                             10
  STAGE IV                              3                              4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 26(19Q13.2) MUTATED    48 146  26  11
  AMP PEAK 26(19Q13.2) WILD-TYPE  63 144  43  12
D26V4, multiclass
    clus
vv   AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  T1                           48                             63
  T2                          146                            144
  T3                           26                             43
  T4                           11                             12
[1] 4 2
[1] TRUE
[1] "dimension of 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(19Q13.2) MUTATED   142  60  25   2
  AMP PEAK 26(19Q13.2) WILD-TYPE 170  71  14   3
D26V5, multiclass
    clus
vv   AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  N0                          142                            170
  N1                           60                             71
  N2                           25                             14
  N3                            2                              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"
D26V6, binary
                                cls
clus                               0   1
  AMP PEAK 26(19Q13.2) MUTATED   196   3
  AMP PEAK 26(19Q13.2) WILD-TYPE 208   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19Q13.2) MUTATED    196    3
  AMP PEAK 26(19Q13.2) WILD-TYPE  208    4
   clus
vv  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  0                          196                            208
  1                            3                              4
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(19Q13.2) MUTATED    48 183
  AMP PEAK 26(19Q13.2) WILD-TYPE  79 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19Q13.2) MUTATED     48  183
  AMP PEAK 26(19Q13.2) WILD-TYPE   79  183
        clus
vv       AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  FEMALE                           48                             79
  MALE                            183                            183
[1] 2 2
[1] FALSE
D26V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 26(19Q13.2) MUTATED                                      10
  AMP PEAK 26(19Q13.2) WILD-TYPE                                     5
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 26(19Q13.2) MUTATED                                         1
  AMP PEAK 26(19Q13.2) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 26(19Q13.2) MUTATED                                        1
  AMP PEAK 26(19Q13.2) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 26(19Q13.2) MUTATED                                         0
  AMP PEAK 26(19Q13.2) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(19Q13.2) MUTATED                                                           219
  AMP PEAK 26(19Q13.2) WILD-TYPE                                                         251
D26V9, multiclass
                                                             clus
vv                                                            AMP PEAK 26(19Q13.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          219
                                                             clus
vv                                                            AMP PEAK 26(19Q13.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            251
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, binary
                                cls
clus                               0   1
  AMP PEAK 26(19Q13.2) MUTATED     8 223
  AMP PEAK 26(19Q13.2) WILD-TYPE   5 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19Q13.2) MUTATED      8  223
  AMP PEAK 26(19Q13.2) WILD-TYPE    5  257
     clus
vv    AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  NO                             8                              5
  YES                          223                            257
[1] 2 2
[1] FALSE
D26V11, continuous
D26V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 26(19Q13.2) MUTATED   189   5   2  10
  AMP PEAK 26(19Q13.2) WILD-TYPE 205   7   2  12
D26V13, multiclass
    clus
vv   AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  R0                          189                            205
  R1                            5                              7
  R2                            2                              2
  RX                           10                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(19Q13.2) MUTATED       5                        15   157
  AMP PEAK 26(19Q13.2) WILD-TYPE     4                        16   183
D26V14, multiclass
                           clus
vv                          AMP PEAK 26(19Q13.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           15
  WHITE                                              157
                           clus
vv                          AMP PEAK 26(19Q13.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             16
  WHITE                                                183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V15, binary
                                cls
clus                               0   1
  AMP PEAK 26(19Q13.2) MUTATED     3 140
  AMP PEAK 26(19Q13.2) WILD-TYPE   5 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19Q13.2) MUTATED      3  140
  AMP PEAK 26(19Q13.2) WILD-TYPE    5  169
                        clus
vv                       AMP PEAK 26(19Q13.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          140
                        clus
vv                       AMP PEAK 26(19Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            169
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(20P12.2) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 27(20P12.2) MUTATED   151 116
  AMP PEAK 27(20P12.2) WILD-TYPE 130  80
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           267                            210 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           116                             80 
$`AMP PEAK 27(20P12.2) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        7.46        79.46         4.80       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 
       92.15        36.07        49.94       119.54        46.88        60.89 
TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       34.78       122.43         9.34       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-1011 TCGA-22-1016 
       88.11        41.69        33.93        32.19         1.74        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 
       20.48        35.08        48.33        38.17        13.12        32.02 
TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
        9.57        31.73        64.93        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 
        0.79        71.34        11.74        18.84        30.12        56.32 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 TCGA-33-4587 TCGA-33-4589 
       22.06         7.63        98.01       103.53        54.44         1.55 
TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 
       27.02       110.99        44.19       118.36         2.63        61.61 
TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 
       28.96        32.88        65.23        23.24        12.00        18.15 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-4130 
        1.12         4.04        26.43        20.91         3.95         8.12 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5028 
        0.39         3.39        74.07        44.75        68.58         1.71 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 
       24.33        27.39        35.64        35.70        17.88        40.21 
TCGA-43-2578 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6773 TCGA-43-7656 
       22.49        33.11        27.91        12.36         3.81        19.59 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 
        7.76        66.51         2.93        11.61        12.03         9.99 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       10.65        13.91         0.39        29.95        28.34         5.46 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 
        8.75        28.96        18.25         2.04         0.62         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 
        0.99         1.45         1.32         0.85         6.51        17.49 
TCGA-56-8308 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-A49D TCGA-56-A4BW 
       17.00        16.77         1.81         1.18        20.94        19.23 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-8391 
       21.04        18.74         0.13         2.76         0.03        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 TCGA-60-2698 
       16.47        34.78        34.36        35.24        21.11        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2715 
       96.82        37.94        21.93        80.45        41.42        35.34 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 
       42.64         3.19        32.32        29.85        35.90        11.77 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MS 
      102.67        70.62        59.97        45.57        14.99        78.28 
TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2756 
       36.16        53.88        16.96         2.01        21.07         0.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 
       21.01        25.05         0.99         7.07        23.01         3.02 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2787 
        2.01        12.03         3.98        12.00        24.95        40.01 
TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 
       22.98         5.03        30.02        10.06        49.05         6.64 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 
        8.02        13.35        16.18        29.56        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
       11.18        89.98        20.78         0.49        42.28         0.16 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
        6.51        86.76        53.95        82.92        53.92        39.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 
       11.54        26.40         6.97         0.33       117.57        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        5.92        42.41        42.08        30.81        27.62        38.86 
TCGA-85-6175 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 TCGA-85-7950 
        9.67         6.41        36.53        31.30         1.15        18.94 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       19.04        24.13        31.56        34.52        10.09         0.76 
TCGA-85-8350 TCGA-85-8353 TCGA-85-8354 TCGA-85-8481 TCGA-85-8664 TCGA-85-8666 
       22.45         3.09        32.71         7.76         0.10        15.62 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A510 
       19.33        17.72        14.96        18.18        12.56        15.85 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
       12.39         3.65         2.93        11.77        20.22        22.62 
TCGA-92-7341 TCGA-92-8064 TCGA-94-7557 TCGA-94-7943 TCGA-94-8490 TCGA-94-A5I4 
        3.48         5.26         0.16        11.70         5.03        16.14 
TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       17.69        57.07        19.36         2.76        30.81        30.67 
TCGA-98-A539 TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
        3.88         2.01        18.58        20.71        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF 
       16.11        13.18        13.41        11.84         0.07         4.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
        1.22        45.37        13.74         4.21         2.89        37.22 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N 
       24.00        14.73        83.57         3.65         0.43        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52W 
        3.72        12.72         8.58 

$`AMP PEAK 27(20P12.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
       12.20        75.75        31.99         1.64        86.96         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 
        2.79       154.32        27.19        99.16        70.16        15.58 
TCGA-21-1079 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       31.73        10.82        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1012 TCGA-22-1017 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 
       64.21        14.10        48.82        24.13         0.56        34.75 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5479 TCGA-22-5481 TCGA-22-5489 TCGA-22-5492 
       19.30        11.77        54.28        79.20        62.86        16.64 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-6737 
      133.74        79.53       174.08       151.27        14.07        19.76 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASL TCGA-34-2604 
        4.70         0.30        36.62         6.94        27.16        31.50 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 
       31.27        67.79        56.38         9.07        16.93        30.94 
TCGA-34-5929 TCGA-34-8454 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
        4.96        27.19         0.43         0.39         6.58         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        7.82         6.81        47.80        55.20        70.03        60.79 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 
        1.94        36.39        15.58        17.06        38.66        27.02 
TCGA-43-5668 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 TCGA-43-8116 
       18.38        24.89        21.47         5.46        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-51-4080 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 
        9.73        14.20         0.39        30.35        27.45         0.10 
TCGA-56-7221 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
        0.99         0.10         3.48        26.89        14.07         1.35 
TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BX 
       22.75        10.36         9.93        20.25        15.81        13.32 
TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J 
       17.85         0.26        13.25        13.55        29.95        85.12 
TCGA-58-A46L TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 TCGA-60-2706 TCGA-60-2709 
       56.65        29.92         3.58        12.23        92.71        49.48 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2724 
       66.54         9.01        56.91        50.33        48.49        23.57 
TCGA-60-2725 TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       26.83        66.61        58.65        11.34        25.28        89.29 
TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MY TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 
       16.37        25.41        34.59        43.10         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
        2.01         0.92        43.99         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 
        2.01        19.00        19.00         1.97        25.97         4.04 
TCGA-66-2790 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59J 
       22.98        54.08         4.01         2.73         6.94        14.73 
TCGA-77-6843 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8128 
       73.12        70.13       106.95        46.78        15.75        37.81 
TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 
       12.59        17.72       104.09        27.39         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-85-6560 TCGA-85-6561 
       65.49        35.90       126.18       132.36        11.97        12.99 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8071 
       34.95        32.91         1.38        29.95        25.15        14.07 
TCGA-85-8072 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 
       16.87        13.22        16.77         5.29         2.01         0.72 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR 
       14.63        13.94        12.59        25.68        24.36        19.73 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 
       16.21        14.96         0.79        24.92         9.50        14.07 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 
       10.59         2.70         4.01         2.30        21.04         4.01 
TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
       26.63        14.14        49.87        18.31        17.46        16.57 
TCGA-98-7454 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D 
        8.42        21.34        27.16        18.15        27.02        21.21 
TCGA-98-A53H TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HR 
       20.32        64.08        51.78        39.85        30.58        29.75 
TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       22.78        65.49        16.80        43.89        11.18         0.20 

  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                          0.03                           0.10 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                        122.43                         174.08 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                         19.33                          18.69 
[1] "0.0 - 122.4 (19.3)" "0.1 - 174.1 (18.7)"
[1] "hr=" "1.2"
D27V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(20P12.2) MUTATED         2       39       92        1        32
  AMP PEAK 27(20P12.2) WILD-TYPE       0       48       59        1        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(20P12.2) MUTATED          54         2         33         11
  AMP PEAK 27(20P12.2) WILD-TYPE        38         1         29         10
                                vv
clus                             STAGE IV
  AMP PEAK 27(20P12.2) MUTATED          6
  AMP PEAK 27(20P12.2) WILD-TYPE        1
D27V3, multiclass
            clus
vv           AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             39                             48
  STAGE IB                             92                             59
  STAGE II                              1                              1
  STAGE IIA                            32                             31
  STAGE IIB                            54                             38
  STAGE III                             2                              1
  STAGE IIIA                           33                             29
  STAGE IIIB                           11                             10
  STAGE IV                              6                              1
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 27(20P12.2) MUTATED    48 173  39  14
  AMP PEAK 27(20P12.2) WILD-TYPE  63 117  30   9
D27V4, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  T1                           48                             63
  T2                          173                            117
  T3                           39                             30
  T4                           14                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  AMP PEAK 27(20P12.2) MUTATED   177  72  20   2
  AMP PEAK 27(20P12.2) WILD-TYPE 135  59  19   3
D27V5, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  N0                          177                            135
  N1                           72                             59
  N2                           20                             19
  N3                            2                              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"
D27V6, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED   227   6
  AMP PEAK 27(20P12.2) WILD-TYPE 177   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED    227    6
  AMP PEAK 27(20P12.2) WILD-TYPE  177    1
   clus
vv  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  0                          227                            177
  1                            6                              1
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED    56 218
  AMP PEAK 27(20P12.2) WILD-TYPE  71 148
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     56  218
  AMP PEAK 27(20P12.2) WILD-TYPE   71  148
        clus
vv       AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  FEMALE                           56                             71
  MALE                            218                            148
[1] 2 2
[1] FALSE
D27V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 27(20P12.2) MUTATED                                       8
  AMP PEAK 27(20P12.2) WILD-TYPE                                     7
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 27(20P12.2) MUTATED                                         1
  AMP PEAK 27(20P12.2) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 27(20P12.2) MUTATED                                        2
  AMP PEAK 27(20P12.2) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 27(20P12.2) MUTATED                                         1
  AMP PEAK 27(20P12.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(20P12.2) MUTATED                                                           262
  AMP PEAK 27(20P12.2) WILD-TYPE                                                         208
D27V9, multiclass
                                                             clus
vv                                                            AMP PEAK 27(20P12.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          262
                                                             clus
vv                                                            AMP PEAK 27(20P12.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            208
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED     7 267
  AMP PEAK 27(20P12.2) WILD-TYPE   6 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED      7  267
  AMP PEAK 27(20P12.2) WILD-TYPE    6  213
     clus
vv    AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  NO                             7                              6
  YES                          267                            213
[1] 2 2
[1] FALSE
D27V11, continuous
D27V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 27(20P12.2) MUTATED   217   8   3  13
  AMP PEAK 27(20P12.2) WILD-TYPE 177   4   1   9
D27V13, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  R0                          217                            177
  R1                            8                              4
  R2                            3                              1
  RX                           13                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20P12.2) MUTATED       6                        16   187
  AMP PEAK 27(20P12.2) WILD-TYPE     3                        15   153
D27V14, multiclass
                           clus
vv                          AMP PEAK 27(20P12.2) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              187
                           clus
vv                          AMP PEAK 27(20P12.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                153
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V15, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED     7 165
  AMP PEAK 27(20P12.2) WILD-TYPE   1 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED      7  165
  AMP PEAK 27(20P12.2) WILD-TYPE    1  144
                        clus
vv                       AMP PEAK 27(20P12.2) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          165
                        clus
vv                       AMP PEAK 27(20P12.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            144
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(20Q11.21) MUTATION ANALYSIS
D28V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 28(20Q11.21) MUTATED   172 123
  AMP PEAK 28(20Q11.21) WILD-TYPE 109  73
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                            295                             182 
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                            123                              73 
$`AMP PEAK 28(20Q11.21) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        79.46         4.80       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-5592 TCGA-21-1070 
       23.54        92.15        36.07         1.64        49.94       119.54 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 
       46.88        60.89        34.78        15.58        31.73         9.34 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
      119.80        43.23        88.11        41.69        33.93        10.82 
TCGA-21-A5DI TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       32.19         1.74        14.10        27.02        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4604 TCGA-22-4605 TCGA-22-5471 TCGA-22-5472 
       48.33        24.13        13.12        32.02        31.73        64.93 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       44.25         0.79        71.34        11.74        18.84        30.12 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 
       56.32        22.06         7.63        98.01       103.53       151.27 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI 
       14.07         1.55        27.02        36.62       110.99        44.19 
TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
      118.36         2.63        61.61        31.50        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 
       31.27        65.23        23.24        12.00        18.15         1.12 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 
        4.04        26.43        20.91         3.95         0.39         8.12 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
        7.82         6.81         0.39         3.39        47.80        74.07 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 
       44.75        68.58         1.71        24.33        27.39        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-3920 TCGA-43-5668 
       35.70        17.88        40.21        22.49        33.11        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 
       27.91        12.36         5.46         3.81         7.76        66.51 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
        2.93        11.61        12.03         9.99        10.65        13.91 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 
       28.34         5.46        30.35         8.75        28.96        18.25 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
        2.04         0.62         0.43         0.99         1.45         1.32 
TCGA-56-7582 TCGA-56-7822 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
        0.85        17.49        16.77         1.81         1.18        10.36 
TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK 
        9.93        15.81        20.94        19.23        21.04        18.74 
TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
        0.13         2.76         0.03        29.95        71.24        34.78 
TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 
       34.36        35.24        21.11         3.58        10.22        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2714 
       37.94        92.71        21.93        80.45        41.42        50.33 
TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2726 TCGA-63-A5MB 
       35.34        42.64         3.19        29.85        11.77       102.67 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MS 
       70.62        58.65        59.97        45.57        14.99        78.28 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       36.16        53.88        34.59         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        1.02         0.99        43.99        21.01        25.05         0.99 
TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 
        1.02         7.07        23.01         3.02         2.01        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2793 
        3.98        12.00         1.97        40.01        22.98        10.06 
TCGA-66-2800 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
       49.05         6.64         8.02        13.35        16.18        14.73 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 
       29.56        73.12        23.28        11.18        89.98        20.78 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        0.49        42.28       106.95         0.16        46.78        15.75 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
        6.51        86.76        53.95        82.92        53.92        39.09 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G3 
       26.40        27.39         6.97         9.63         0.33       117.57 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
       22.29        42.41        42.08        30.81        27.62        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 
        9.67        11.97        12.99        36.53        31.30         1.15 
TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
       29.95        19.04        24.13        31.56        14.07        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
       10.09         0.76        22.45        16.77         5.29         3.09 
TCGA-85-8354 TCGA-85-8481 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB 
       32.71         7.76        13.94         0.10        15.62        17.72 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 
       14.96        18.18        19.73        12.56        15.85        14.96 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
       12.39         3.65         2.93        11.77        20.22        22.62 
TCGA-92-7341 TCGA-92-8064 TCGA-94-7557 TCGA-94-7943 TCGA-94-A4VJ TCGA-94-A5I4 
        3.48         5.26         0.16        11.70        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-8022 TCGA-98-A538 
       17.69        57.07        19.36         2.76        30.67        27.16 
TCGA-98-A539 TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
        3.88         2.01        18.58        20.71        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF 
       16.11        13.18        13.41        11.84         0.07         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
       51.78         1.22        45.37        13.74         4.21         2.89 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR 
       39.85        37.22        24.00        14.73        29.75        83.57 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
        3.65        16.80         0.43        33.07         3.72        12.72 
TCGA-O2-A52W 
        8.58 

$`AMP PEAK 28(20Q11.21) WILD-TYPE`
TCGA-18-3408 TCGA-18-3416 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       75.75        31.99        86.96         6.18         2.79       154.32 
TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1080 TCGA-21-5782 TCGA-22-0940 
       27.19        99.16        70.16       122.43        31.63        21.99 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1017 TCGA-22-4596 
        7.33        14.93         4.31        64.21        48.82         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       38.17        34.75        19.30         9.57        11.77        63.55 
TCGA-22-5474 TCGA-22-5479 TCGA-22-5481 TCGA-22-5489 TCGA-22-5492 TCGA-33-4533 
       14.63        54.28        79.20        62.86        16.64       133.74 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4587 TCGA-33-6737 TCGA-33-A4WN TCGA-33-A5GW 
       79.53       174.08        54.44        19.76         4.70         0.30 
TCGA-33-AASB TCGA-33-AASL TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 
        6.94        27.16        67.79        56.38         9.07        16.93 
TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 
       30.94         4.96        27.19         0.43         6.58         7.46 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
       55.20        70.03        60.79         1.94        36.39        15.58 
TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 
       17.06        38.66        27.02        24.89        21.47        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 TCGA-51-4080 
       13.38        11.77         9.73        14.20         0.39         0.39 
TCGA-51-4081 TCGA-52-7812 TCGA-56-5897 TCGA-56-7221 TCGA-56-7730 TCGA-56-7731 
       29.95        27.45         0.10         0.99         6.51         0.10 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 
        3.48        26.89        17.00        14.07         1.35        22.75 
TCGA-56-8628 TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 
       20.25        13.32        17.85         0.26        13.25        13.55 
TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2697 TCGA-60-2709 
       16.47        85.12        56.65        29.92        12.23        49.48 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2716 TCGA-60-2721 TCGA-60-2723 
       66.54         9.01        56.91        48.49        32.32        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MH TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       23.57        26.83        66.61        11.34        25.28        89.29 
TCGA-63-A5MT TCGA-63-A5MU TCGA-66-2727 TCGA-66-2734 TCGA-66-2754 TCGA-66-2755 
       16.37        25.41        16.96        43.10         2.01         0.92 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2783 
        2.01         2.01         2.01        19.00        19.00        24.95 
TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
       25.97         4.04        22.98         5.03        30.02        54.08 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-77-6844 TCGA-77-7335 TCGA-77-8128 
        4.01         2.73         6.94        75.09        70.13        37.81 
TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8150 TCGA-77-8153 
       12.59        17.72       104.09        11.54        54.41        65.49 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-85-6798 TCGA-85-7697 
       35.90       126.18       132.36         5.92         6.41        34.95 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8072 TCGA-85-8288 
       32.91         1.38        18.94        25.15        16.87        13.22 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4CN 
        2.01         0.72        14.63        12.59        25.68        19.33 
TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 
       24.36        16.21         0.79        24.92         9.50        14.07 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 
       10.59         2.70         4.01         2.30        21.04         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
        5.03        26.63        49.87        18.31        17.46        16.57 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D 
        8.42        30.81        21.34        18.15        27.02        21.21 
TCGA-98-A53H TCGA-NC-A5HE TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CT TCGA-O2-A52V 
       20.32        64.08        30.58        22.78        65.49        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                           0.03                            0.10 
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                         151.27                          174.08 
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                          18.84                           19.46 
[1] "0.0 - 151.3 (18.8)" "0.1 - 174.1 (19.5)"
[1] "hr=" "1.1"
D28V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(20Q11.21) MUTATED         2       46       93        1        40
  AMP PEAK 28(20Q11.21) WILD-TYPE       0       41       58        1        23
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 28(20Q11.21) MUTATED          57         2         41         11
  AMP PEAK 28(20Q11.21) WILD-TYPE        35         1         21         10
                                 vv
clus                              STAGE IV
  AMP PEAK 28(20Q11.21) MUTATED          6
  AMP PEAK 28(20Q11.21) WILD-TYPE        1
D28V3, multiclass
            clus
vv           AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  STAGE I                                2                               0
  STAGE IA                              46                              41
  STAGE IB                              93                              58
  STAGE II                               1                               1
  STAGE IIA                             40                              23
  STAGE IIB                             57                              35
  STAGE III                              2                               1
  STAGE IIIA                            41                              21
  STAGE IIIB                            11                              10
  STAGE IV                               6                               1
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 28(20Q11.21) MUTATED    58 187  40  16
  AMP PEAK 28(20Q11.21) WILD-TYPE  53 103  29   7
D28V4, multiclass
    clus
vv   AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  T1                            58                              53
  T2                           187                             103
  T3                            40                              29
  T4                            16                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 28(20Q11.21) MUTATED   188  83  26   0
  AMP PEAK 28(20Q11.21) WILD-TYPE 124  48  13   5
D28V5, multiclass
    clus
vv   AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  N0                           188                             124
  N1                            83                              48
  N2                            26                              13
  N3                             0                               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"
D28V6, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.21) MUTATED   251   6
  AMP PEAK 28(20Q11.21) WILD-TYPE 153   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.21) MUTATED    251    6
  AMP PEAK 28(20Q11.21) WILD-TYPE  153    1
   clus
vv  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  0                           251                             153
  1                             6                               1
[1] 2 2
[1] FALSE
D28V7, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.21) MUTATED    59 242
  AMP PEAK 28(20Q11.21) WILD-TYPE  68 124
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.21) MUTATED     59  242
  AMP PEAK 28(20Q11.21) WILD-TYPE   68  124
        clus
vv       AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  FEMALE                            59                              68
  MALE                             242                             124
[1] 2 2
[1] FALSE
D28V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 28(20Q11.21) MUTATED                                      11
  AMP PEAK 28(20Q11.21) WILD-TYPE                                     4
                                 vv
clus                              LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 28(20Q11.21) MUTATED                                         1
  AMP PEAK 28(20Q11.21) WILD-TYPE                                       0
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 28(20Q11.21) MUTATED                                        1
  AMP PEAK 28(20Q11.21) WILD-TYPE                                      5
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 28(20Q11.21) MUTATED                                         0
  AMP PEAK 28(20Q11.21) WILD-TYPE                                       1
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(20Q11.21) MUTATED                                                           288
  AMP PEAK 28(20Q11.21) WILD-TYPE                                                         182
D28V9, multiclass
                                                             clus
vv                                                            AMP PEAK 28(20Q11.21) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           288
                                                             clus
vv                                                            AMP PEAK 28(20Q11.21) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             182
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.21) MUTATED     9 292
  AMP PEAK 28(20Q11.21) WILD-TYPE   4 188
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.21) MUTATED      9  292
  AMP PEAK 28(20Q11.21) WILD-TYPE    4  188
     clus
vv    AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  NO                              9                               4
  YES                           292                             188
[1] 2 2
[1] FALSE
D28V11, continuous
D28V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 28(20Q11.21) MUTATED   241   6   2  14
  AMP PEAK 28(20Q11.21) WILD-TYPE 153   6   2   8
D28V13, multiclass
    clus
vv   AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  R0                           241                             153
  R1                             6                               6
  R2                             2                               2
  RX                            14                               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(20Q11.21) MUTATED       5                        19   209
  AMP PEAK 28(20Q11.21) WILD-TYPE     4                        12   131
D28V14, multiclass
                           clus
vv                          AMP PEAK 28(20Q11.21) MUTATED
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            19
  WHITE                                               209
                           clus
vv                          AMP PEAK 28(20Q11.21) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                              12
  WHITE                                                 131
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V15, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.21) MUTATED     7 184
  AMP PEAK 28(20Q11.21) WILD-TYPE   1 125
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.21) MUTATED      7  184
  AMP PEAK 28(20Q11.21) WILD-TYPE    1  125
                        clus
vv                       AMP PEAK 28(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           184
                        clus
vv                       AMP PEAK 28(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             125
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(22Q11.21) MUTATION ANALYSIS
D29V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 29(22Q11.21) MUTATED   148  92
  AMP PEAK 29(22Q11.21) WILD-TYPE 133 104
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                            240                             237 
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                             92                             104 
$`AMP PEAK 29(22Q11.21) MUTATED`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3421 
       75.75        79.46       117.57        11.34        23.54        86.96 
TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
      154.32        27.19       119.54        99.16        70.16        60.89 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1081 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 
       34.78        31.73         9.34        43.23        88.11        41.69 
TCGA-21-5786 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 
       33.93         4.31         1.74        14.10        20.48        35.08 
TCGA-22-4595 TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 
       24.13        13.12        32.02        11.77        63.55        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 
        0.79        54.28        79.20        11.74        56.32        16.64 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-AASD 
       22.06         7.63       103.53        14.07         1.55       110.99 
TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
      118.36         2.63        61.61        28.96        32.88        31.27 
TCGA-34-5231 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 
       65.23         9.07        23.24        12.00        16.93        18.15 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4130 TCGA-37-4133 
        1.12         4.04        26.43        20.91         8.12         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5029 
        6.81         0.39        74.07        44.75        68.58        24.33 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-3920 TCGA-43-5668 
       36.39        35.64        35.70        17.88        33.11        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7657 TCGA-43-8118 
       27.91        12.36        24.89        21.47         7.76         2.93 
TCGA-43-A474 TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 TCGA-51-4081 TCGA-52-7809 
       11.61         9.73         9.99        10.65        29.95         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
       30.35         8.75        28.96         0.10        18.25         2.04 
TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
        0.99         1.45         1.32         0.85         6.51         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
       17.49         3.48        17.00         1.35        16.77         1.81 
TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ 
        9.93        15.81        20.94        19.23        13.32        21.04 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-A46M 
        0.13         0.26         0.03        13.25        29.95        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       29.92        21.11        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2711 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       80.45        41.42        50.33        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       35.90        26.83        11.77       102.67        70.62        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       59.97        45.57        25.28        78.28        16.37        36.16 
TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 
       53.88        43.10         2.01        21.07         0.99         0.92 
TCGA-66-2766 TCGA-66-2769 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2788 
        1.02         7.07         3.02         2.01         3.98        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2800 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
        5.03        30.02        49.05        16.18        14.73        29.56 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 
       23.28        89.98        20.78         0.49        42.28       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 
        0.16        46.78        15.75        86.76        37.81        82.92 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8150 
       12.59        53.92        11.54        26.40         6.97        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       65.49         0.33       132.36       117.57        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       42.41        42.08        30.81        27.62        38.86         9.67 
TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-8052 TCGA-85-8070 
       12.99        36.53        34.95        31.30        24.13        31.56 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8354 TCGA-85-8580 TCGA-85-A4CN 
       34.52        10.09        22.45        32.71        14.63        19.33 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 
       17.72        14.96        18.18        19.73        12.56        15.85 
TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-92-7341 TCGA-94-7033 
       14.96         3.65         2.93        11.77         3.48        21.04 
TCGA-94-7943 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8169 
       11.70        14.14        16.14        17.69        57.07        18.31 
TCGA-96-8170 TCGA-96-A4JK TCGA-98-8020 TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 
       17.46        19.36         2.76        30.67        27.16         3.88 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HD TCGA-NC-A5HG 
       20.71        19.10        16.11        13.18         0.07        51.78 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP 
        1.22        45.37         4.21         2.89        37.22        24.00 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52W TCGA-XC-AA0X 
       22.78        83.57         3.65        33.07         8.58         0.20 

$`AMP PEAK 29(22Q11.21) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
       12.20         7.46         4.80        92.15        31.99        36.07 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-21-1071 TCGA-21-1078 
        1.64         6.18         2.79        49.94        46.88        15.58 
TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
      122.43       119.80        31.63        10.82        32.19        21.99 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 
        7.33        14.93        64.21        27.02        48.82        48.33 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 TCGA-22-5471 
        0.56        38.17        34.75        19.30         9.57        31.73 
TCGA-22-5472 TCGA-22-5474 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
       64.93        14.63        71.34        18.84        30.12        62.86 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 
      133.74        98.01        79.53       174.08       151.27        54.44 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       19.76        27.02         4.70         0.30        36.62         6.94 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2604 TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 
       44.19        27.16        31.50        67.79        56.38        30.94 
TCGA-34-5929 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
        4.96        27.19         3.95         0.43         0.39         6.58 
TCGA-37-4132 TCGA-37-5819 TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        7.46         3.39        47.80        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 
        1.71         1.94        27.39        15.58        17.06        40.21 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       22.49        38.66        27.02         5.46         3.81        19.59 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 
       66.51        13.38        11.77        14.20        12.03        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7812 TCGA-56-6546 TCGA-56-7222 
        0.39         0.39        28.34        27.45         0.62         0.43 
TCGA-56-7223 TCGA-56-8307 TCGA-56-8309 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        0.99        26.89        14.07        22.75         1.18        10.36 
TCGA-56-8628 TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8388 TCGA-58-8391 
       20.25        17.85        18.74         2.76        13.55        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2696 
       16.47        34.78        85.12        34.36        56.65         3.58 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 
       12.23        10.22        49.48        66.54         9.01        56.91 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 TCGA-60-2724 TCGA-63-A5MH TCGA-63-A5MM 
       35.34        48.49        32.32        23.57        66.61        14.99 
TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MU TCGA-63-A5MY TCGA-66-2727 TCGA-66-2753 
       11.34        89.29        25.41        34.59        16.96         1.02 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        2.01         0.99        43.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2778 
        2.01         2.01         2.01        23.01        19.00        19.00 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
       12.03        12.00        24.95         1.97        25.97        40.01 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 
        4.04        22.98        10.06        54.08         4.01         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-77-6843 TCGA-77-6844 
        6.64         6.94         8.02        13.35        73.12        75.09 
TCGA-77-7138 TCGA-77-7335 TCGA-77-8007 TCGA-77-8009 TCGA-77-8136 TCGA-77-8138 
       11.18        70.13         6.51        53.95        39.09        17.72 
TCGA-77-8139 TCGA-77-8144 TCGA-77-8148 TCGA-77-8154 TCGA-77-A5FZ TCGA-85-6560 
      104.09        27.39         9.63        35.90       126.18        11.97 
TCGA-85-6798 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
        6.41        32.91         1.38         1.15        29.95        18.94 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 
       25.15        19.04        14.07        16.87         0.76        13.22 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       16.77         5.29         3.09         2.01         0.72         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA 
       13.94        12.59         0.10        15.62        25.68        24.36 
TCGA-85-A50Z TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 
       16.21         0.79        12.39        24.92         9.50        14.07 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 
       20.22        22.62        10.59         2.70         4.01         5.26 
TCGA-92-8065 TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 
        2.30         0.16         4.01         5.03        26.63        49.87 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B 
       16.57         8.42        30.81        21.34        18.15         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-LA-A7SW 
       27.02        21.21        20.32        18.58        12.89        13.41 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HJ TCGA-NC-A5HM TCGA-NC-A5HO 
       11.84        64.08         4.54        13.74        39.85        30.58 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52Q 
       14.73        29.75        65.49        16.80         0.43         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       12.72        43.89        11.18 

  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                           0.03                            0.10 
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                         154.32                          174.08 
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                          20.99                           17.72 
[1] "0.0 - 154.3 (21.0)" "0.1 - 174.1 (17.7)"
[1] "hr=" "1.3"
D29V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 29(22Q11.21) MUTATED         2       37       80        1        33
  AMP PEAK 29(22Q11.21) WILD-TYPE       0       50       71        1        30
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(22Q11.21) MUTATED          58         0         25          8
  AMP PEAK 29(22Q11.21) WILD-TYPE        34         3         37         13
                                 vv
clus                              STAGE IV
  AMP PEAK 29(22Q11.21) MUTATED          5
  AMP PEAK 29(22Q11.21) WILD-TYPE        2
D29V3, multiclass
            clus
vv           AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  STAGE I                                2                               0
  STAGE IA                              37                              50
  STAGE IB                              80                              71
  STAGE II                               1                               1
  STAGE IIA                             33                              30
  STAGE IIB                             58                              34
  STAGE III                              0                               3
  STAGE IIIA                            25                              37
  STAGE IIIB                             8                              13
  STAGE IV                               5                               2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 29(22Q11.21) MUTATED    47 159  36   9
  AMP PEAK 29(22Q11.21) WILD-TYPE  64 131  33  14
D29V4, multiclass
    clus
vv   AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  T1                            47                              64
  T2                           159                             131
  T3                            36                              33
  T4                             9                              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  AMP PEAK 29(22Q11.21) MUTATED   165  66  14   1
  AMP PEAK 29(22Q11.21) WILD-TYPE 147  65  25   4
D29V5, multiclass
    clus
vv   AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  N0                           165                             147
  N1                            66                              65
  N2                            14                              25
  N3                             1                               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                                 cls
clus                                0   1
  AMP PEAK 29(22Q11.21) MUTATED   214   5
  AMP PEAK 29(22Q11.21) WILD-TYPE 190   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(22Q11.21) MUTATED    214    5
  AMP PEAK 29(22Q11.21) WILD-TYPE  190    2
   clus
vv  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  0                           214                             190
  1                             5                               2
[1] 2 2
[1] FALSE
D29V7, binary
                                 cls
clus                                0   1
  AMP PEAK 29(22Q11.21) MUTATED    57 194
  AMP PEAK 29(22Q11.21) WILD-TYPE  70 172
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(22Q11.21) MUTATED     57  194
  AMP PEAK 29(22Q11.21) WILD-TYPE   70  172
        clus
vv       AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  FEMALE                            57                              70
  MALE                             194                             172
[1] 2 2
[1] FALSE
D29V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 29(22Q11.21) MUTATED                                       9
  AMP PEAK 29(22Q11.21) WILD-TYPE                                     6
                                 vv
clus                              LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 29(22Q11.21) MUTATED                                         1
  AMP PEAK 29(22Q11.21) WILD-TYPE                                       0
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 29(22Q11.21) MUTATED                                        1
  AMP PEAK 29(22Q11.21) WILD-TYPE                                      5
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 29(22Q11.21) MUTATED                                         0
  AMP PEAK 29(22Q11.21) WILD-TYPE                                       1
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(22Q11.21) MUTATED                                                           240
  AMP PEAK 29(22Q11.21) WILD-TYPE                                                         230
D29V9, multiclass
                                                             clus
vv                                                            AMP PEAK 29(22Q11.21) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           240
                                                             clus
vv                                                            AMP PEAK 29(22Q11.21) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             230
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                                 cls
clus                                0   1
  AMP PEAK 29(22Q11.21) MUTATED     5 246
  AMP PEAK 29(22Q11.21) WILD-TYPE   8 234
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(22Q11.21) MUTATED      5  246
  AMP PEAK 29(22Q11.21) WILD-TYPE    8  234
     clus
vv    AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  NO                              5                               8
  YES                           246                             234
[1] 2 2
[1] FALSE
D29V11, continuous
D29V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 29(22Q11.21) MUTATED   207   8   0   8
  AMP PEAK 29(22Q11.21) WILD-TYPE 187   4   4  14
D29V13, multiclass
    clus
vv   AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  R0                           207                             187
  R1                             8                               4
  R2                             0                               4
  RX                             8                              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(22Q11.21) MUTATED       4                        10   179
  AMP PEAK 29(22Q11.21) WILD-TYPE     5                        21   161
D29V14, multiclass
                           clus
vv                          AMP PEAK 29(22Q11.21) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               179
                           clus
vv                          AMP PEAK 29(22Q11.21) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                              21
  WHITE                                                 161
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V15, binary
                                 cls
clus                                0   1
  AMP PEAK 29(22Q11.21) MUTATED     4 155
  AMP PEAK 29(22Q11.21) WILD-TYPE   4 154
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(22Q11.21) MUTATED      4  155
  AMP PEAK 29(22Q11.21) WILD-TYPE    4  154
                        clus
vv                       AMP PEAK 29(22Q11.21) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           155
                        clus
vv                       AMP PEAK 29(22Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             154
[1] 2 2
[1] FALSE

Clustering(30) Variable = AMP PEAK 30(XQ28) MUTATION ANALYSIS
D30V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 30(XQ28) MUTATED    68  51
  AMP PEAK 30(XQ28) WILD-TYPE 213 145
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                        119                         358 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                         51                         145 
$`AMP PEAK 30(XQ28) MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-5595 
        7.46        75.75        92.15        36.07        86.96        27.19 
TCGA-21-1081 TCGA-22-0940 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
        9.34        21.99        14.10        20.48        35.08        48.33 
TCGA-22-4595 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
       24.13        63.55        44.25         0.79        71.34        79.20 
TCGA-22-5483 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4566 TCGA-33-AASJ 
       18.84        22.06         7.63        79.53       174.08       118.36 
TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-34-5240 TCGA-34-5927 
        2.63        31.50        28.96        31.27        12.00        30.94 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3792 TCGA-37-4133 TCGA-37-5819 TCGA-39-5011 
       18.15        27.19         0.39         7.82         3.39        47.80 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5028 TCGA-39-5037 TCGA-43-5670 TCGA-43-7657 
       44.75        68.58         1.71        35.70        27.91         7.76 
TCGA-43-8118 TCGA-43-A475 TCGA-51-4079 TCGA-56-7222 TCGA-56-7223 TCGA-56-8504 
        2.93         9.73         0.39         0.43         0.99        16.77 
TCGA-56-8624 TCGA-56-8629 TCGA-56-A49D TCGA-56-A5DR TCGA-58-8386 TCGA-58-A46M 
        1.18        15.81        20.94         0.13         0.03        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2708 TCGA-60-2709 TCGA-60-2724 TCGA-63-A5MI 
       29.92        21.11        80.45        49.48        23.57        58.65 
TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MW TCGA-66-2753 TCGA-66-2756 
       25.28        16.37        25.41        53.88         1.02         0.99 
TCGA-66-2758 TCGA-66-2766 TCGA-66-2769 TCGA-66-2773 TCGA-66-2778 TCGA-66-2781 
       21.01         1.02         7.07         3.02        19.00         3.98 
TCGA-66-2782 TCGA-66-2792 TCGA-66-2793 TCGA-68-7756 TCGA-77-6842 TCGA-77-6845 
       12.00        30.02        10.06         6.64        29.56        23.28 
TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 TCGA-77-7338 TCGA-77-8009 TCGA-77-8136 
       11.18        20.78         0.49         0.16        53.95        39.09 
TCGA-77-8144 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 
       27.39         0.33       117.57        42.08        27.62         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-8070 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
       12.99         6.41        31.56        16.77         3.09        32.71 
TCGA-85-A4QR TCGA-85-A50M TCGA-90-7769 TCGA-90-A4EE TCGA-92-8064 TCGA-94-7557 
       19.73        12.56        11.77        22.62         5.26         0.16 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-A4JK TCGA-98-8023 
       26.63        14.14        16.14        17.69        19.36        21.34 
TCGA-98-A53B TCGA-J1-A4AH TCGA-LA-A446 TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HL 
        2.01        19.10        13.18         1.22        13.74         2.89 
TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A5IB 
       37.22        14.73         0.43         3.72        11.18 

$`AMP PEAK 30(XQ28) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       12.20        79.46         4.80       117.57        11.34        23.54 
TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       31.99         1.64         6.18         2.79       154.32        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
      119.54        46.88        99.16        70.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       15.58        31.73       122.43       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 
       88.11        41.69        33.93        10.82        32.19         7.33 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 
       14.93         4.31        64.21         1.74        27.02        48.82 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
        0.56        38.17        34.75        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5479 
        9.57        11.77        31.73        64.93        14.63        54.28 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4533 
       11.74        30.12        62.86        56.32        16.64       133.74 
TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
       98.01       103.53       151.27        14.07        54.44         1.55 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       19.76        27.02         4.70         0.30        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
      110.99        44.19        27.16        61.61        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5929 
       67.79        56.38         9.07        23.24        16.93         4.96 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
        1.12         4.04        26.43        20.91         3.95         0.43 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 
        6.58         8.12         7.46         6.81         0.39        74.07 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       55.20        70.03        60.79        24.33         1.94        27.39 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
       36.39        15.58        35.64        17.88        17.06        40.21 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 
       22.49        38.66        27.02        33.11        18.38        12.36 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 
       24.89        21.47         5.46         3.81        19.59        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
       13.38        11.77        11.61        14.20        12.03         9.99 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       10.65        13.91         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       30.35         8.75        27.45        28.96         0.10        18.25 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
        2.04         0.62         0.99         1.45         1.32         0.85 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 
        6.51         0.10        17.49         3.48        26.89        17.00 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 
       14.07         1.35         1.81        22.75        10.36         9.93 
TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       20.25        19.23        13.32        17.85        21.04        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        0.26         2.76        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2696 
       16.47        34.78        85.12        34.36        56.65         3.58 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       12.23        10.22        96.82        37.94        92.71        21.93 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       66.54        41.42         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
       48.49        42.64         3.19        32.32        29.85        35.90 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MJ 
       26.83        11.77       102.67        70.62        66.61        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV 
       45.57        14.99        11.34        89.29        78.28        36.16 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       34.59        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        2.01         0.92        43.99        25.05         0.99         2.01 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 
        2.01         2.01        23.01        19.00         2.01        12.03 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
       24.95         1.97        25.97        40.01        22.98         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
       22.98         5.03        54.08         4.01        49.05         2.73 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 
        6.94         8.02        13.35        16.18        14.73        73.12 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 
       75.09        89.98        42.28        70.13       106.95        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
       15.75         6.51        86.76        37.81        82.92        12.59 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 
       53.92        17.72       104.09        11.54        26.40         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
        9.63        54.41        65.49        35.90       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 
       22.29         5.92        42.41        30.81        38.86        11.97 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       36.53        34.95        31.30        32.91         1.38         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
       29.95        18.94        25.15        19.04        24.13        14.07 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       16.87        34.52        10.09         0.76        13.22        22.45 
TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
        5.29         2.01         0.72         7.76        14.63        13.94 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
       12.59         0.10        15.62        25.68        19.33        17.72 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       14.96        24.36        18.18        16.21        15.85        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        0.79        12.39         3.65        24.92         9.50         2.93 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       14.07        20.22        10.59         2.70         3.48         4.01 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-96-7544 
        2.30        21.04        11.70         4.01         5.03        49.87 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       57.07        18.31        17.46        16.57         8.42         2.76 
TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C 
       30.81        30.67        27.16         3.88        18.15        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 
       21.21        20.32        18.58        20.71        12.89        16.11 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       13.41        11.84         0.07        64.08         4.54        51.78 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR 
       45.37         4.21        39.85        30.58        24.00        29.75 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52N 
       22.78        83.57        65.49         3.65        16.80        33.07 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       12.72        43.89         8.58         0.20 

  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                       0.03                        0.07 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                     174.08                      154.32 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                     19.000                      19.265 
[1] "0.0 - 174.1 (19.0)" "0.1 - 154.3 (19.3)"
[1] "hr=" "1.2"
D30V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 30(XQ28) MUTATED         0       10       39        0        18
  AMP PEAK 30(XQ28) WILD-TYPE       2       77      112        2        45
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 30(XQ28) MUTATED          26         2         16          7
  AMP PEAK 30(XQ28) WILD-TYPE        66         1         46         14
                             vv
clus                          STAGE IV
  AMP PEAK 30(XQ28) MUTATED          2
  AMP PEAK 30(XQ28) WILD-TYPE        5
D30V3, multiclass
            clus
vv           AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                          10                          77
  STAGE IB                          39                         112
  STAGE II                           0                           2
  STAGE IIA                         18                          45
  STAGE IIB                         26                          66
  STAGE III                          2                           1
  STAGE IIIA                        16                          46
  STAGE IIIB                         7                          14
  STAGE IV                           2                           5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 30(XQ28) MUTATED    13  76  23   9
  AMP PEAK 30(XQ28) WILD-TYPE  98 214  46  14
D30V4, multiclass
    clus
vv   AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  T1                        13                          98
  T2                        76                         214
  T3                        23                          46
  T4                         9                          14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  AMP PEAK 30(XQ28) MUTATED    69  40   9   1
  AMP PEAK 30(XQ28) WILD-TYPE 243  91  30   4
D30V5, multiclass
    clus
vv   AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  N0                        69                         243
  N1                        40                          91
  N2                         9                          30
  N3                         1                           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"
D30V6, binary
                             cls
clus                            0   1
  AMP PEAK 30(XQ28) MUTATED    98   2
  AMP PEAK 30(XQ28) WILD-TYPE 306   5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED     98    2
  AMP PEAK 30(XQ28) WILD-TYPE  306    5
   clus
vv  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  0                        98                         306
  1                         2                           5
[1] 2 2
[1] FALSE
D30V7, binary
                             cls
clus                            0   1
  AMP PEAK 30(XQ28) MUTATED    24  97
  AMP PEAK 30(XQ28) WILD-TYPE 103 269
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED     24   97
  AMP PEAK 30(XQ28) WILD-TYPE  103  269
        clus
vv       AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  FEMALE                        24                         103
  MALE                          97                         269
[1] 2 2
[1] FALSE
D30V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 30(XQ28) MUTATED                                       4
  AMP PEAK 30(XQ28) WILD-TYPE                                    11
                             vv
clus                          LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 30(XQ28) MUTATED                                         0
  AMP PEAK 30(XQ28) WILD-TYPE                                       1
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  AMP PEAK 30(XQ28) MUTATED                                        1
  AMP PEAK 30(XQ28) WILD-TYPE                                      5
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  AMP PEAK 30(XQ28) MUTATED                                         0
  AMP PEAK 30(XQ28) WILD-TYPE                                       1
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 30(XQ28) MUTATED                                                           116
  AMP PEAK 30(XQ28) WILD-TYPE                                                         354
D30V9, multiclass
                                                             clus
vv                                                            AMP PEAK 30(XQ28) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       116
                                                             clus
vv                                                            AMP PEAK 30(XQ28) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         354
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                             cls
clus                            0   1
  AMP PEAK 30(XQ28) MUTATED     3 118
  AMP PEAK 30(XQ28) WILD-TYPE  10 362
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED      3  118
  AMP PEAK 30(XQ28) WILD-TYPE   10  362
     clus
vv    AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  NO                          3                          10
  YES                       118                         362
[1] 2 2
[1] FALSE
D30V11, continuous
D30V12, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 30(XQ28) MUTATED    97   4   1   4
  AMP PEAK 30(XQ28) WILD-TYPE 297   8   3  18
D30V13, multiclass
    clus
vv   AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  R0                        97                         297
  R1                         4                           8
  R2                         1                           3
  RX                         4                          18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(XQ28) MUTATED       3                         6    82
  AMP PEAK 30(XQ28) WILD-TYPE     6                        25   258
D30V14, multiclass
                           clus
vv                          AMP PEAK 30(XQ28) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         6
  WHITE                                            82
                           clus
vv                          AMP PEAK 30(XQ28) WILD-TYPE
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          25
  WHITE                                             258
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V15, binary
                             cls
clus                            0   1
  AMP PEAK 30(XQ28) MUTATED     0  72
  AMP PEAK 30(XQ28) WILD-TYPE   8 237
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED      0   72
  AMP PEAK 30(XQ28) WILD-TYPE    8  237
                        clus
vv                       AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             0                           8
  NOT HISPANIC OR LATINO                        72                         237
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   132  84
  DEL PEAK  1(1P36.11) WILD-TYPE 149 112
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           216                            261 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            84                            112 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       12.20        75.75       117.57        11.34        23.54        92.15 
TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        6.18       154.32        49.94        46.88        99.16        70.16 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
       34.78        31.73       119.80        43.23        33.93        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1017 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 
       21.99         7.33        48.82        35.08         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4609 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 
       34.75        13.12         9.57        31.73        63.55        14.63 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5483 TCGA-22-5491 TCGA-33-4533 TCGA-33-4538 
       44.25        54.28        18.84        56.32       133.74        98.01 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-A5GW TCGA-33-AAS8 
      103.53       151.27        14.07        54.44         0.30        36.62 
TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 
        6.94        44.19        27.16         2.63        61.61        28.96 
TCGA-34-2608 TCGA-34-5231 TCGA-34-7107 TCGA-34-8456 TCGA-37-3792 TCGA-37-4129 
       32.88        65.23         1.12        26.43         0.39         6.58 
TCGA-37-4130 TCGA-37-4133 TCGA-37-5819 TCGA-39-5016 TCGA-39-5027 TCGA-39-5031 
        8.12         7.82         3.39        74.07        60.79        27.39 
TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-6770 
       35.64        35.70        40.21        38.66        27.02        21.47 
TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 
        7.76         2.93        11.61        12.03         9.99        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       13.91         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 
       30.35         8.75        27.45        28.96        18.25         2.04 
TCGA-56-7221 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 
        0.99         0.99         1.32         0.85         6.51        17.49 
TCGA-56-8308 TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8390 TCGA-58-8391 
       17.00        13.32        18.74         2.76        29.95        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2698 
       16.47        34.78        34.36        56.65        35.24        10.22 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
       92.71        21.93        80.45        41.42        56.91        50.33 
TCGA-60-2722 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP 
       29.85        11.77       102.67        59.97        45.57        25.28 
TCGA-63-A5MR TCGA-63-A5MV TCGA-66-2737 TCGA-66-2742 TCGA-66-2755 TCGA-66-2758 
       89.29        36.16         2.01        21.07         0.92        21.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 
        1.02         2.01        23.01         3.02         2.01        12.03 
TCGA-66-2781 TCGA-66-2785 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
        3.98         1.97        40.01        22.98         5.03        30.02 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 
       10.06        54.08         4.01        49.05         2.73         6.94 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       14.73        73.12        23.28        89.98         0.49        42.28 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8144 
        0.16        15.75        53.95        37.81        53.92        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G8 
        6.97         9.63        54.41        65.49       117.57        42.41 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 
       27.62         9.67        12.99        36.53        31.30        32.91 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 
       19.04        24.13        31.56        14.07        16.87        10.09 
TCGA-85-8287 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8580 TCGA-85-A4CL 
        0.76        16.77         5.29         3.09        14.63        25.68 
TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 
       19.33        14.96        19.73        14.96        12.39         3.65 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 TCGA-94-8490 
       20.22        22.62         3.48         5.26        11.70         5.03 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8023 
       16.14        17.69        57.07        19.36        30.81        21.34 
TCGA-98-A539 TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 
        3.88        18.58        20.71        19.10        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       13.41        11.84        64.08         4.54        51.78        45.37 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
        4.21         2.89        39.85        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       14.73        29.75        83.57         3.72        12.72        43.89 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
        7.46        79.46         4.80        31.99        36.07         1.64 
TCGA-18-3421 TCGA-18-4086 TCGA-18-5595 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 
       86.96         2.79        27.19       119.54        60.89        15.58 
TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI 
      122.43         9.34        31.63        88.11        41.69        32.19 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       14.93         4.31        64.21         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
       20.48        48.33        24.13        32.02        19.30        11.77 
TCGA-22-5472 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 
       64.93         0.79        71.34        79.20        11.74        30.12 
TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4566 
       62.86        16.64        22.06         7.63        79.53       174.08 
TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASD TCGA-33-AASJ 
        1.55        19.76        27.02         4.70       110.99       118.36 
TCGA-34-2604 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       31.50        31.27        67.79        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 
       12.00        16.93        30.94        18.15         4.96        27.19 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4132 TCGA-37-4135 
        4.04        20.91         3.95         0.43         7.46         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        0.39        47.80        44.75        68.58        55.20        70.03 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 
        1.71        24.33         1.94        36.39        15.58        17.88 
TCGA-39-5040 TCGA-43-2578 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
       17.06        22.49        33.11        18.38        27.91        12.36 
TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 
       24.89         5.46         3.81        19.59        66.51        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-56-5897 TCGA-56-6546 TCGA-56-7222 
       11.77         9.73        14.20         0.10         0.62         0.43 
TCGA-56-7579 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
        1.45         0.10         3.48        26.89        14.07         1.35 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       16.77         1.81        22.75         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ 
       20.25        15.81        20.94        19.23        17.85        21.04 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-A46J 
        0.13         0.26         0.03        13.25        13.55        85.12 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 
       29.92        21.11         3.58        12.23        96.82        37.94 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
       49.48        66.54         9.01        35.34        48.49        42.64 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG 
        3.19        32.32        35.90        23.57        26.83        70.62 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MT 
       66.61        58.65        14.99        11.34        78.28        16.37 
TCGA-63-A5MU TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2744 
       25.41        53.88        34.59        16.96        43.10         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 
        1.02         2.01         0.99        43.99        25.05         0.99 
TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2778 TCGA-66-2782 
        2.01         2.01         7.07        19.00        19.00        12.00 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-68-7756 TCGA-68-8250 
       24.95        25.97        22.98         4.04         6.64         8.02 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7140 
       13.35        16.18        29.56        75.09        11.18        20.78 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 
       70.13       106.95        46.78         6.51        86.76        82.92 
TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       12.59        39.09        17.72       104.09        11.54        26.40 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
       35.90         0.33       126.18       132.36        22.29         5.92 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 
       42.08        30.81        38.86        11.97         6.41        34.95 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8276 
        1.38         1.15        29.95        18.94        25.15        34.52 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       13.22        22.45        32.71         2.01         0.72         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4PA 
       13.94        12.59         0.10        15.62        17.72        24.36 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 TCGA-90-6837 
       18.18        12.56        16.21        15.85         0.79        24.92 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 
        9.50         2.93        11.77        14.07        10.59         2.70 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-8491 
        4.01         2.30        21.04         0.16         4.01        26.63 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       14.14        49.87        18.31        17.46        16.57         8.42 
TCGA-98-8020 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
        2.76        30.67        27.16        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-NC-A5HD TCGA-NC-A5HH TCGA-NC-A5HJ 
       21.21        20.32        12.89         0.07         1.22        13.74 
TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N 
       22.78        65.49         3.65        16.80         0.43        33.07 
TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        8.58        11.18         0.20 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.16                           0.03 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        154.32                         174.08 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        21.405                         17.880 
[1] "0.2 - 154.3 (21.4)" "0.0 - 174.1 (17.9)"
[1] "hr=" "1.2"
D31V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.11) MUTATED         0       33       69        2        35
  DEL PEAK  1(1P36.11) WILD-TYPE       2       54       82        0        28
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED          37         2         30         11
  DEL PEAK  1(1P36.11) WILD-TYPE        55         1         32         10
                                vv
clus                             STAGE IV
  DEL PEAK  1(1P36.11) MUTATED          3
  DEL PEAK  1(1P36.11) WILD-TYPE        4
D31V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                             33                             54
  STAGE IB                             69                             82
  STAGE II                              2                              0
  STAGE IIA                            35                             28
  STAGE IIB                            37                             55
  STAGE III                             2                              1
  STAGE IIIA                           30                             32
  STAGE IIIB                           11                             10
  STAGE IV                              3                              4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  1(1P36.11) MUTATED    45 134  31  13
  DEL PEAK  1(1P36.11) WILD-TYPE  66 156  38  10
D31V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                           45                             66
  T2                          134                            156
  T3                           31                             38
  T4                           13                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK  1(1P36.11) MUTATED   133  69  17   2
  DEL PEAK  1(1P36.11) WILD-TYPE 179  62  22   3
D31V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                          133                            179
  N1                           69                             62
  N2                           17                             22
  N3                            2                              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"
D31V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   187   3
  DEL PEAK  1(1P36.11) WILD-TYPE 217   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    187    3
  DEL PEAK  1(1P36.11) WILD-TYPE  217    4
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                          187                            217
  1                            3                              4
[1] 2 2
[1] FALSE
D31V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    47 176
  DEL PEAK  1(1P36.11) WILD-TYPE  80 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     47  176
  DEL PEAK  1(1P36.11) WILD-TYPE   80  190
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           47                             80
  MALE                            176                            190
[1] 2 2
[1] FALSE
D31V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                                       7
  DEL PEAK  1(1P36.11) WILD-TYPE                                     8
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                                         1
  DEL PEAK  1(1P36.11) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  1(1P36.11) MUTATED                                        1
  DEL PEAK  1(1P36.11) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                                         1
  DEL PEAK  1(1P36.11) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                           213
  DEL PEAK  1(1P36.11) WILD-TYPE                                                         257
D31V9, multiclass
                                                             clus
vv                                                            DEL PEAK  1(1P36.11) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          213
                                                             clus
vv                                                            DEL PEAK  1(1P36.11) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            257
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     7 216
  DEL PEAK  1(1P36.11) WILD-TYPE   6 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      7  216
  DEL PEAK  1(1P36.11) WILD-TYPE    6  264
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             7                              6
  YES                          216                            264
[1] 2 2
[1] FALSE
D31V11, continuous
D31V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED   184   7   2  10
  DEL PEAK  1(1P36.11) WILD-TYPE 210   5   2  12
D31V13, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                          184                            210
  R1                            7                              5
  R2                            2                              2
  RX                           10                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED       4                        15   157
  DEL PEAK  1(1P36.11) WILD-TYPE     5                        16   183
D31V14, multiclass
                           clus
vv                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           15
  WHITE                                              157
                           clus
vv                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             16
  WHITE                                                183
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V15, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     5 137
  DEL PEAK  1(1P36.11) WILD-TYPE   3 172
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      5  137
  DEL PEAK  1(1P36.11) WILD-TYPE    3  172
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          137
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            172
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  2(1P13.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.1) MUTATED   124  87
  DEL PEAK  2(1P13.1) WILD-TYPE 157 109
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          211                           266 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           87                           109 
$`DEL PEAK  2(1P13.1) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3421 
       12.20        75.75        11.34        23.54        92.15        86.96 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
      154.32        49.94       119.54        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 
       60.89        34.78        31.73        33.93        21.99         7.33 
TCGA-22-1012 TCGA-22-1017 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       14.10        48.82        35.08         0.56        38.17        34.75 
TCGA-22-4604 TCGA-22-4609 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       13.12         9.57        31.73        63.55        14.63        44.25 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 
       54.28        79.20        18.84        30.12        62.86        22.06 
TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-A4WN TCGA-33-A5GW 
       98.01       103.53       151.27        14.07         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
       36.62         6.94        44.19        27.16         2.63        61.61 
TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-7107 TCGA-34-8456 TCGA-37-4129 
       28.96        32.88        65.23         1.12        26.43         6.58 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5029 TCGA-39-5034 TCGA-39-5037 TCGA-43-2578 
        3.39        74.07        24.33        36.39        35.70        22.49 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-7657 TCGA-43-7658 
       38.66        27.02        33.11        12.36         7.76        66.51 
TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       11.61        12.03         9.99        10.65        13.91         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
        0.39        29.95        28.34         5.46        30.35         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7223 
       27.45        28.96        18.25         2.04         0.99         0.99 
TCGA-56-7730 TCGA-56-7822 TCGA-56-8308 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BX 
        6.51        17.49        17.00        10.36        20.94        13.32 
TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46L 
       18.74         2.76        71.24        16.47        34.78        56.65 
TCGA-58-A46M TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 
       35.24        10.22        21.93        80.45        50.33        42.64 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5MP 
       32.32        29.85        11.77       102.67        59.97        25.28 
TCGA-63-A5MR TCGA-66-2727 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 
       89.29        16.96         2.01         0.92         0.99        21.01 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
        0.99         1.02         2.01        23.01        19.00         3.02 
TCGA-66-2777 TCGA-66-2781 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
        2.01         3.98        40.01        22.98         5.03        30.02 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J 
       10.06        54.08         4.01        49.05         2.73        14.73 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7338 TCGA-77-7463 
       73.12        23.28        89.98         0.49         0.16        46.78 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8136 TCGA-77-8145 
       15.75        53.95        37.81        53.92        39.09         6.97 
TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
        9.63         0.33       117.57        42.41        42.08        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 TCGA-85-7710 TCGA-85-7843 
       38.86         9.67        12.99        36.53         1.38         1.15 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       18.94        19.04        24.13        14.07        16.87        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 TCGA-85-8584 TCGA-85-8664 
       10.09         0.76         5.29         3.09        12.59         0.10 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 
       25.68        19.33        17.72        19.73        16.21        14.96 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 
       12.39         3.65         2.93        22.62        10.59         3.48 
TCGA-92-8064 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 
        5.26        11.70         4.01         5.03        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-98-8021 
       17.69        49.87        57.07        18.31        19.36        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53B TCGA-98-A53I TCGA-J1-A4AH 
       30.67        21.34         3.88         2.01        18.58        19.10 
TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HK TCGA-NC-A5HL 
       16.11        11.84        64.08        51.78         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-O2-A52N 
       37.22        30.58        24.00        14.73        29.75        33.07 
TCGA-O2-A52S 
       12.72 

$`DEL PEAK  2(1P13.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3416 TCGA-18-3417 
        7.46        79.46         4.80       117.57        31.99        36.07 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-5595 TCGA-21-1078 TCGA-21-1080 
        1.64         6.18         2.79        27.19        15.58       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
        9.34       119.80        43.23        31.63        88.11        41.69 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       10.82        32.19        14.93         4.31        64.21         1.74 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4605 TCGA-22-4607 
       27.02        20.48        48.33        24.13        32.02        19.30 
TCGA-22-4613 TCGA-22-5472 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5491 
       11.77        64.93         0.79        71.34        11.74        56.32 
TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4587 
       16.64         7.63       133.74        79.53       174.08        54.44 
TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASJ TCGA-34-2604 
        1.55        19.76        27.02       110.99       118.36        31.50 
TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       31.27        67.79        56.38         9.07        23.24        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 
       16.93        30.94        18.15         4.96        27.19         4.04 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 
       20.91         3.95         0.43         0.39         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
        7.82         6.81         0.39        47.80        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 
       55.20        70.03        60.79         1.71         1.94        27.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-5668 
       15.58        35.64        17.88        17.06        40.21        18.38 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.91        24.89        21.47         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-56-5897 
       13.38        11.77         2.93         9.73        14.20         0.10 
TCGA-56-6546 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 
        0.62         0.43         1.45         1.32         0.85         0.10 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
        3.48        26.89        14.07         1.35        16.77         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
       22.75         1.18         9.93        20.25        15.81        19.23 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 
       17.85        21.04         0.13         0.26         0.03        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46N TCGA-60-2695 
       13.55        29.95        85.12        34.36        29.92        21.11 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2709 
        3.58        12.23        96.82        37.94        92.71        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 
       66.54        41.42         9.01        56.91        35.34        48.49 
TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MH 
        3.19        35.90        23.57        26.83        70.62        66.61 
TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MT 
       58.65        45.57        14.99        11.34        78.28        16.37 
TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 
       25.41        36.16        53.88        34.59        43.10         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 
       21.07         0.99         1.02        43.99        25.05         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
        2.01         7.07        19.00        12.03        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-68-7756 TCGA-68-7757 
        1.97        25.97        22.98         4.04         6.64         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 
        8.02        13.35        16.18        29.56        75.09        11.18 
TCGA-77-7140 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8007 TCGA-77-8008 
       20.78        42.28        70.13       106.95         6.51        86.76 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       82.92        12.59        17.72       104.09        11.54        26.40 
TCGA-77-8144 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
       27.39        54.41        65.49        35.90       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GB TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 
       22.29         5.92        30.81        11.97         6.41        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7844 TCGA-85-8048 TCGA-85-8070 TCGA-85-8288 
       31.30        32.91        29.95        25.15        31.56        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       22.45        16.77        32.71         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       14.63        13.94        15.62        14.96        24.36        18.18 
TCGA-85-A50M TCGA-85-A510 TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 
       12.56        15.85         0.79        24.92         9.50        11.77 
TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 
       14.07        20.22         2.70         4.01         2.30        21.04 
TCGA-94-7557 TCGA-94-8491 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
        0.16        26.63        17.46        16.57         8.42         2.76 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J 
       27.16        18.15        27.02        21.21        20.32        20.71 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HH 
       12.89        13.18        13.41         0.07         4.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HM TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
       45.37        13.74        39.85        22.78        83.57        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W 
        3.65        16.80         0.43         3.72        43.89         8.58 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                       154.32                        174.08 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                        19.36                         18.28 
[1] "0.1 - 154.3 (19.4)" "0.0 - 174.1 (18.3)"
[1] "hr=" "1"  
D32V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.1) MUTATED         1       33       60        1        36
  DEL PEAK  2(1P13.1) WILD-TYPE       1       54       91        1        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P13.1) MUTATED          44         1         27         10
  DEL PEAK  2(1P13.1) WILD-TYPE        48         2         35         11
                               vv
clus                            STAGE IV
  DEL PEAK  2(1P13.1) MUTATED          2
  DEL PEAK  2(1P13.1) WILD-TYPE        5
D32V3, multiclass
            clus
vv           DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            33                            54
  STAGE IB                            60                            91
  STAGE II                             1                             1
  STAGE IIA                           36                            27
  STAGE IIB                           44                            48
  STAGE III                            1                             2
  STAGE IIIA                          27                            35
  STAGE IIIB                          10                            11
  STAGE IV                             2                             5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  2(1P13.1) MUTATED    46 128  31  11
  DEL PEAK  2(1P13.1) WILD-TYPE  65 162  38  12
D32V4, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  T1                          46                            65
  T2                         128                           162
  T3                          31                            38
  T4                          11                            12
[1] 4 2
[1] TRUE
[1] "dimension of 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(1P13.1) MUTATED   125  71  16   2
  DEL PEAK  2(1P13.1) WILD-TYPE 187  60  23   3
D32V5, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  N0                         125                           187
  N1                          71                            60
  N2                          16                            23
  N3                           2                             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"
D32V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED   183   2
  DEL PEAK  2(1P13.1) WILD-TYPE 221   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED    183    2
  DEL PEAK  2(1P13.1) WILD-TYPE  221    5
   clus
vv  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  0                         183                           221
  1                           2                             5
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED    50 166
  DEL PEAK  2(1P13.1) WILD-TYPE  77 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED     50  166
  DEL PEAK  2(1P13.1) WILD-TYPE   77  200
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  FEMALE                          50                            77
  MALE                           166                           200
[1] 2 2
[1] FALSE
D32V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                                       7
  DEL PEAK  2(1P13.1) WILD-TYPE                                     8
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                                         0
  DEL PEAK  2(1P13.1) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  2(1P13.1) MUTATED                                        2
  DEL PEAK  2(1P13.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                                         0
  DEL PEAK  2(1P13.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.1) MUTATED                                                           207
  DEL PEAK  2(1P13.1) WILD-TYPE                                                         263
D32V9, multiclass
                                                             clus
vv                                                            DEL PEAK  2(1P13.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         207
                                                             clus
vv                                                            DEL PEAK  2(1P13.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           263
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED     4 212
  DEL PEAK  2(1P13.1) WILD-TYPE   9 268
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      4  212
  DEL PEAK  2(1P13.1) WILD-TYPE    9  268
     clus
vv    DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  NO                            4                             9
  YES                         212                           268
[1] 2 2
[1] FALSE
D32V11, continuous
D32V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P13.1) MUTATED   177   7   2  11
  DEL PEAK  2(1P13.1) WILD-TYPE 217   5   2  11
D32V13, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  R0                         177                           217
  R1                           7                             5
  R2                           2                             2
  RX                          11                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.1) MUTATED       3                        11   159
  DEL PEAK  2(1P13.1) WILD-TYPE     6                        20   181
D32V14, multiclass
                           clus
vv                          DEL PEAK  2(1P13.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             159
                           clus
vv                          DEL PEAK  2(1P13.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V15, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED     6 132
  DEL PEAK  2(1P13.1) WILD-TYPE   2 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      6  132
  DEL PEAK  2(1P13.1) WILD-TYPE    2  177
                        clus
vv                       DEL PEAK  2(1P13.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         132
                        clus
vv                       DEL PEAK  2(1P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           177
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  3(2P25.3) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2P25.3) MUTATED    28  21
  DEL PEAK  3(2P25.3) WILD-TYPE 253 175
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           49                           428 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           21                           175 
$`DEL PEAK  3(2P25.3) MUTATED`
TCGA-18-3406 TCGA-18-3414 TCGA-18-3421 TCGA-22-4594 TCGA-22-4601 TCGA-22-5489 
       12.20        23.54        86.96        48.33        34.75        62.86 
TCGA-33-4587 TCGA-34-A5IX TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5028 
       54.44        20.91         6.81         3.39        47.80         1.71 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-43-2578 TCGA-43-7657 TCGA-52-7810 
       24.33        27.39        36.39        22.49         7.76        30.35 
TCGA-56-1622 TCGA-56-8307 TCGA-56-A49D TCGA-58-8392 TCGA-60-2713 TCGA-60-2722 
       28.96        26.89        20.94        16.47        56.91        29.85 
TCGA-60-2726 TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MY TCGA-66-2756 TCGA-66-2766 
       11.77        45.57        25.28        34.59         0.99         1.02 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2791 TCGA-68-A59J TCGA-77-7140 TCGA-77-7337 
       12.03         3.98         5.03        14.73        20.78       106.95 
TCGA-77-8130 TCGA-77-8153 TCGA-77-A5GH TCGA-85-7699 TCGA-85-7710 TCGA-85-8352 
       82.92        65.49        38.86        32.91         1.38         5.29 
TCGA-85-8354 TCGA-85-A511 TCGA-92-8063 TCGA-96-A4JL TCGA-NC-A5HH TCGA-NC-A5HM 
       32.71        14.96         4.01        16.57         1.22        39.85 
TCGA-O2-A52S 
       12.72 

$`DEL PEAK  3(2P25.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
        7.46        75.75        79.46         4.80       117.57        11.34 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 
       92.15        31.99        36.07         1.64         6.18         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
      154.32        49.94        27.19       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       70.16        60.89        34.78        15.58        31.73       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
        9.34       119.80        43.23        31.63        88.11        41.69 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
       33.93        10.82        32.19        21.99         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
        4.31        64.21         1.74        14.10        27.02        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
       20.48        35.08        24.13         0.56        38.17        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
       32.02        19.30         9.57        11.77        31.73        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       63.55        14.63        44.25         0.79        54.28        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 
       79.20        11.74        18.84        30.12        56.32        16.64 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       22.06         7.63       133.74        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
      103.53       151.27        14.07         1.55        19.76        27.02 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI 
        4.70         0.30        36.62         6.94       110.99        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
      118.36        27.16         2.63        61.61        31.50        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       32.88        31.27        65.23        67.79        56.38         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       23.24        12.00        16.93        30.94        18.15         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 
        1.12        27.19         4.04        26.43         3.95         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 
        0.39         6.58         8.12         7.46         7.82         0.39 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
       74.07        44.75        68.58        55.20        70.03        60.79 
TCGA-39-5030 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
        1.94        15.58        35.64        35.70        17.88        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
       40.21        38.66        27.02        33.11        18.38        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       12.36        24.89        21.47         5.46         3.81        19.59 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
       66.51        13.38        11.77         2.93        11.61         9.73 
TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       14.20        12.03         9.99        10.65        13.91         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
        0.39        29.95        28.34         5.46         8.75        27.45 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
        0.10        18.25         2.04         0.62         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
        0.99         1.45         1.32         0.85         6.51         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
       17.49         3.48        17.00        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75         1.18        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       15.81        19.23        13.32        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        0.13         0.26         2.76         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       29.95        71.24        34.78        85.12        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 
       35.24        29.92        21.11         3.58        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       96.82        37.94        92.71        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       66.54        41.42         9.01        50.33        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       42.64         3.19        32.32        35.90        23.57        26.83 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM 
      102.67        70.62        66.61        58.65        59.97        14.99 
TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV 
       11.34        89.29        78.28        16.37        25.41        36.16 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       53.88        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        1.02         2.01         0.92        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
        0.99         2.01         2.01         2.01         7.07        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 
       19.00         3.02         2.01        19.00        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        1.97        25.97        40.01        22.98         4.04        22.98 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
       30.02        10.06        54.08         4.01        49.05         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 
        6.64         6.94         8.02        13.35        16.18        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
       73.12        75.09        23.28        11.18        89.98         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       42.28        70.13         0.16        46.78        15.75         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       86.76        53.95        37.81        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 
       17.72       104.09        11.54        26.40        27.39         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
        9.63        54.41        35.90         0.33       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
      117.57        22.29         5.92        42.41        42.08        30.81 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       27.62         9.67        11.97        12.99         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       34.95        31.30         1.15        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       19.04        24.13        31.56        14.07        16.87        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
       10.09         0.76        13.22        22.45        16.77         3.09 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        2.01         0.72         7.76        14.63        13.94        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC 
        0.10        15.62        25.68        19.33        17.72        14.96 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       24.36        18.18        19.73        12.56        16.21        15.85 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
        0.79        12.39         3.65        24.92         9.50         2.93 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       11.77        14.07        20.22        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        3.48         5.26         2.30        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
        4.01         5.03        26.63        14.14        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-7454 
       49.87        57.07        18.31        17.46        19.36         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        2.76        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I 
       18.15         2.01        27.02        21.21        20.32        18.58 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
       20.71        19.10        12.89        16.11        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       11.84         0.07        64.08         4.54        51.78        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       13.74         4.21         2.89        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX 
       14.73        29.75        22.78        83.57        65.49         3.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W 
       16.80         0.43        33.07         3.72        43.89         8.58 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                         0.99                          0.03 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                       106.95                        174.08 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                        23.54                         18.89 
[1] "1.0 - 107.0 (23.5)" "0.0 - 174.1 (18.9)"
[1] "hr=" "1.1"
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(2P25.3) MUTATED         0        9       13        0         2
  DEL PEAK  3(2P25.3) WILD-TYPE       2       78      138        2        61
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(2P25.3) MUTATED          10         1         10          3
  DEL PEAK  3(2P25.3) WILD-TYPE        82         2         52         18
                               vv
clus                            STAGE IV
  DEL PEAK  3(2P25.3) MUTATED          1
  DEL PEAK  3(2P25.3) WILD-TYPE        6
D33V3, multiclass
            clus
vv           DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                             9                            78
  STAGE IB                            13                           138
  STAGE II                             0                             2
  STAGE IIA                            2                            61
  STAGE IIB                           10                            82
  STAGE III                            1                             2
  STAGE IIIA                          10                            52
  STAGE IIIB                           3                            18
  STAGE IV                             1                             6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  3(2P25.3) MUTATED    10  27   6   6
  DEL PEAK  3(2P25.3) WILD-TYPE 101 263  63  17
D33V4, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  T1                          10                           101
  T2                          27                           263
  T3                           6                            63
  T4                           6                            17
[1] 4 2
[1] TRUE
[1] "dimension of 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(2P25.3) MUTATED    30  11   7   1
  DEL PEAK  3(2P25.3) WILD-TYPE 282 120  32   4
D33V5, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  N0                          30                           282
  N1                          11                           120
  N2                           7                            32
  N3                           1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED    42   1
  DEL PEAK  3(2P25.3) WILD-TYPE 362   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED     42    1
  DEL PEAK  3(2P25.3) WILD-TYPE  362    6
   clus
vv  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  0                          42                           362
  1                           1                             6
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED    16  33
  DEL PEAK  3(2P25.3) WILD-TYPE 111 333
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED     16   33
  DEL PEAK  3(2P25.3) WILD-TYPE  111  333
        clus
vv       DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  FEMALE                          16                           111
  MALE                            33                           333
[1] 2 2
[1] FALSE
D33V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(2P25.3) MUTATED                                       1
  DEL PEAK  3(2P25.3) WILD-TYPE                                    14
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(2P25.3) MUTATED                                         0
  DEL PEAK  3(2P25.3) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  3(2P25.3) MUTATED                                        0
  DEL PEAK  3(2P25.3) WILD-TYPE                                      6
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  3(2P25.3) MUTATED                                         1
  DEL PEAK  3(2P25.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(2P25.3) MUTATED                                                            47
  DEL PEAK  3(2P25.3) WILD-TYPE                                                         423
D33V9, multiclass
                                                             clus
vv                                                            DEL PEAK  3(2P25.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 1
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          47
                                                             clus
vv                                                            DEL PEAK  3(2P25.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  14
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           423
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED     1  48
  DEL PEAK  3(2P25.3) WILD-TYPE  12 432
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      1   48
  DEL PEAK  3(2P25.3) WILD-TYPE   12  432
     clus
vv    DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  NO                            1                            12
  YES                          48                           432
[1] 2 2
[1] FALSE
D33V11, continuous
D33V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(2P25.3) MUTATED    42   1   0   1
  DEL PEAK  3(2P25.3) WILD-TYPE 352  11   4  21
D33V13, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  R0                          42                           352
  R1                           1                            11
  R2                           0                             4
  RX                           1                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2P25.3) MUTATED       2                         0    34
  DEL PEAK  3(2P25.3) WILD-TYPE     7                        31   306
D33V14, multiclass
                           clus
vv                          DEL PEAK  3(2P25.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              34
                           clus
vv                          DEL PEAK  3(2P25.3) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            31
  WHITE                                               306
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V15, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED     1  28
  DEL PEAK  3(2P25.3) WILD-TYPE   7 281
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      1   28
  DEL PEAK  3(2P25.3) WILD-TYPE    7  281
                        clus
vv                       DEL PEAK  3(2P25.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          28
                        clus
vv                       DEL PEAK  3(2P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           281
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  4(2Q22.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q22.1) MUTATED    78  47
  DEL PEAK  4(2Q22.1) WILD-TYPE 203 149
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          125                           352 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           47                           149 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-18-3406 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-21-1075 
       12.20        11.34        92.15        31.99        36.07        70.16 
TCGA-21-1077 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 
       34.78       119.80        31.63        88.11        33.93        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4604 
       21.99         7.33        35.08        48.33        24.13        13.12 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5481 TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4587 
       14.63        44.25        79.20        22.06        98.01        54.44 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-5231 TCGA-37-3783 
       36.62         6.94       118.36        27.16        65.23         3.95 
TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5035 
        8.12         6.81         0.39         3.39        47.80        15.58 
TCGA-39-5037 TCGA-43-6770 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 
       35.70        21.47         7.76        13.38        11.77        11.61 
TCGA-46-3768 TCGA-46-6025 TCGA-51-4081 TCGA-52-7810 TCGA-56-7223 TCGA-56-7822 
        9.99        10.65        29.95        30.35         0.99        17.49 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8503 TCGA-56-8629 TCGA-56-A5DR TCGA-56-A62T 
        3.48        26.89         1.35        15.81         0.13         2.76 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46M TCGA-60-2698 TCGA-60-2713 
       71.24        16.47        34.36        35.24        10.22        56.91 
TCGA-60-2715 TCGA-60-2722 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH 
       35.34        29.85        23.57        11.77       102.67        66.61 
TCGA-63-A5MJ TCGA-63-A5MR TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2754 TCGA-66-2758 
       59.97        89.29        53.88        34.59         2.01        21.01 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2781 
        0.99         1.02         2.01         2.01        23.01         3.98 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2800 
       25.97        40.01        22.98         5.03        10.06        49.05 
TCGA-68-A59J TCGA-77-6843 TCGA-77-7138 TCGA-77-7338 TCGA-77-7465 TCGA-77-8007 
       14.73        73.12        11.18         0.16        15.75         6.51 
TCGA-77-8009 TCGA-77-8136 TCGA-77-8148 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 
       53.95        39.09         9.63        36.53        34.95        32.91 
TCGA-85-7710 TCGA-85-7843 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
        1.38         1.15        14.07        16.87        34.52        10.09 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 TCGA-85-8664 TCGA-85-A4CL 
       13.22        22.45        16.77        32.71         0.10        25.68 
TCGA-85-A4JC TCGA-90-A4EE TCGA-92-8064 TCGA-92-8065 TCGA-94-8491 TCGA-94-A5I4 
       14.96        22.62         5.26         2.30        26.63        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-98-8023 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       17.69        49.87        21.34        13.18        13.41        11.84 
TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52S TCGA-XC-AA0X 
       29.75        16.80        33.07        12.72         0.20 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 
        7.46        75.75        79.46         4.80       117.57        23.54 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
        1.64        86.96         6.18         2.79       154.32        49.94 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 
       27.19       119.54        46.88        99.16        60.89        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5784 TCGA-21-A5DI 
       31.73       122.43         9.34        43.23        41.69        32.19 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       14.93         4.31        64.21         1.74        14.10        27.02 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 
       48.82        20.48         0.56        38.17        34.75        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        63.55 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        0.79        54.28        71.34        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 
       62.86        56.32        16.64         7.63       133.74        79.53 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 
      174.08       103.53       151.27        14.07         1.55        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 
       27.02         4.70         0.30       110.99        44.19         2.63 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 
       61.61        31.50        28.96        32.88        31.27        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       56.38         9.07        23.24        12.00        16.93        30.94 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       18.15         4.96         1.12        27.19         4.04        26.43 
TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
       20.91         0.43         0.39         6.58         7.46         7.82 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
       74.07        44.75        68.58        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
        1.71        24.33         1.94        27.39        36.39        35.64 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
       17.88        17.06        40.21        22.49        38.66        27.02 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 
       33.11        18.38        27.91        12.36        24.89         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U 
        3.81        19.59        66.51         2.93         9.73        14.20 
TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 
       12.03        13.91         0.39         0.39        28.34         5.46 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        8.75        27.45        28.96         0.10        18.25         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
        0.62         0.99         0.43         1.45         1.32         0.85 
TCGA-56-7730 TCGA-56-7731 TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 
        6.51         0.10        17.00        14.07        16.77         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D 
       22.75         1.18        10.36         9.93        20.25        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS 
       19.23        13.32        17.85        21.04        18.74         0.26 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J 
        0.03        13.25        13.55        29.95        34.78        85.12 
TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 
       56.65        29.92        21.11         3.58        12.23        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       41.42         9.01        50.33        48.49        42.64         3.19 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5ML 
       32.32        35.90        26.83        70.62        58.65        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       14.99        11.34        25.28        78.28        16.37        25.41 
TCGA-63-A5MV TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       36.16        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 
        1.02         0.92         0.99        43.99        25.05         2.01 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        7.07        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2792 
       12.00        24.95         1.97        22.98         4.04        30.02 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
       54.08         4.01         2.73         6.64         6.94         8.02 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 
       13.35        16.18        29.56        75.09        23.28        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 
       20.78         0.49        42.28        70.13       106.95        46.78 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 
       86.76        37.81        82.92        12.59        53.92        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8150 
      104.09        11.54        26.40        27.39         6.97        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       65.49        35.90         0.33       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
       22.29         5.92        42.41        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 
       38.86         9.67        11.97        12.99         6.41        31.30 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       29.95        18.94        25.15        19.04        24.13        31.56 
TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
        0.76         5.29         3.09         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
       14.63        13.94        12.59        15.62        19.33        17.72 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       24.36        18.18        19.73        12.56        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
       14.96         0.79        12.39         3.65        24.92         9.50 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 
        2.93        11.77        14.07        20.22        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 
        3.48         4.01        21.04         0.16        11.70         4.01 
TCGA-94-8490 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
        5.03        14.14        57.07        18.31        17.46        19.36 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 
       16.57         8.42         2.76        30.81        30.67        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
        3.88        18.15         2.01        27.02        21.21        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HD 
       18.58        20.71        19.10        12.89        16.11         0.07 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
       64.08         4.54        51.78         1.22        45.37        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
        4.21         2.89        39.85        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE 
       14.73        22.78        83.57        65.49         3.65         0.43 
TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
        3.72        43.89         8.58        11.18 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       119.80                        174.08 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                        21.01                         19.07 
[1] "0.1 - 119.8 (21.0)" "0.0 - 174.1 (19.1)"
[1] "hr=" "1.1"
D34V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(2Q22.1) MUTATED         1       25       28        0        25
  DEL PEAK  4(2Q22.1) WILD-TYPE       1       62      123        2        38
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(2Q22.1) MUTATED          25         1         18          5
  DEL PEAK  4(2Q22.1) WILD-TYPE        67         2         44         16
                               vv
clus                            STAGE IV
  DEL PEAK  4(2Q22.1) MUTATED          1
  DEL PEAK  4(2Q22.1) WILD-TYPE        6
D34V3, multiclass
            clus
vv           DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            25                            62
  STAGE IB                            28                           123
  STAGE II                             0                             2
  STAGE IIA                           25                            38
  STAGE IIB                           25                            67
  STAGE III                            1                             2
  STAGE IIIA                          18                            44
  STAGE IIIB                           5                            16
  STAGE IV                             1                             6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  4(2Q22.1) MUTATED    32  76  17   4
  DEL PEAK  4(2Q22.1) WILD-TYPE  79 214  52  19
D34V4, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  T1                          32                            79
  T2                          76                           214
  T3                          17                            52
  T4                           4                            19
[1] 4 2
[1] TRUE
[1] "dimension of 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(2Q22.1) MUTATED    70  46  11   2
  DEL PEAK  4(2Q22.1) WILD-TYPE 242  85  28   3
D34V5, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  N0                          70                           242
  N1                          46                            85
  N2                          11                            28
  N3                           2                             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"
D34V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED   103   1
  DEL PEAK  4(2Q22.1) WILD-TYPE 301   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED    103    1
  DEL PEAK  4(2Q22.1) WILD-TYPE  301    6
   clus
vv  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  0                         103                           301
  1                           1                             6
[1] 2 2
[1] FALSE
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED    27 102
  DEL PEAK  4(2Q22.1) WILD-TYPE 100 264
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     27  102
  DEL PEAK  4(2Q22.1) WILD-TYPE  100  264
        clus
vv       DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  FEMALE                          27                           100
  MALE                           102                           264
[1] 2 2
[1] FALSE
D34V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q22.1) MUTATED                                       3
  DEL PEAK  4(2Q22.1) WILD-TYPE                                    12
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q22.1) MUTATED                                         0
  DEL PEAK  4(2Q22.1) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  4(2Q22.1) MUTATED                                        1
  DEL PEAK  4(2Q22.1) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  4(2Q22.1) MUTATED                                         1
  DEL PEAK  4(2Q22.1) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(2Q22.1) MUTATED                                                           124
  DEL PEAK  4(2Q22.1) WILD-TYPE                                                         346
D34V9, multiclass
                                                             clus
vv                                                            DEL PEAK  4(2Q22.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         124
                                                             clus
vv                                                            DEL PEAK  4(2Q22.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           346
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     2 127
  DEL PEAK  4(2Q22.1) WILD-TYPE  11 353
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      2  127
  DEL PEAK  4(2Q22.1) WILD-TYPE   11  353
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                            2                            11
  YES                         127                           353
[1] 2 2
[1] FALSE
D34V11, continuous
D34V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(2Q22.1) MUTATED   105   3   0   9
  DEL PEAK  4(2Q22.1) WILD-TYPE 289   9   4  13
D34V13, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  R0                         105                           289
  R1                           3                             9
  R2                           0                             4
  RX                           9                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q22.1) MUTATED       1                        10    86
  DEL PEAK  4(2Q22.1) WILD-TYPE     8                        21   254
D34V14, multiclass
                           clus
vv                          DEL PEAK  4(2Q22.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              86
                           clus
vv                          DEL PEAK  4(2Q22.1) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               254
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V15, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED     1  83
  DEL PEAK  4(2Q22.1) WILD-TYPE   7 226
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      1   83
  DEL PEAK  4(2Q22.1) WILD-TYPE    7  226
                        clus
vv                       DEL PEAK  4(2Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          83
                        clus
vv                       DEL PEAK  4(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           226
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  5(2Q37.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q37.1) MUTATED    91  57
  DEL PEAK  5(2Q37.1) WILD-TYPE 190 139
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          148                           329 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                           57                           139 
$`DEL PEAK  5(2Q37.1) MUTATED`
TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-21-1070 
       92.15        36.07        86.96         6.18         2.79       119.54 
TCGA-21-1075 TCGA-21-1083 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1011 
       70.16        43.23        33.93        21.99         7.33         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 
       14.10        27.02        34.75        13.12        32.02        11.77 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5481 TCGA-22-5482 TCGA-22-5491 TCGA-33-4532 
       14.63        44.25        79.20        11.74        56.32         7.63 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4582 TCGA-33-AAS8 TCGA-33-AASJ TCGA-34-2605 
      133.74        98.01       103.53        36.62       118.36        28.96 
TCGA-34-5231 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-7107 TCGA-37-4141 
       65.23         9.07        12.00        16.93         1.12         0.39 
TCGA-39-5029 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-2578 TCGA-43-3394 
       24.33        15.58        35.64        35.70        22.49        27.02 
TCGA-43-6143 TCGA-43-7657 TCGA-43-8115 TCGA-43-8118 TCGA-43-A56U TCGA-51-4081 
       12.36         7.76        13.38         2.93        14.20        29.95 
TCGA-52-7810 TCGA-52-7811 TCGA-56-7579 TCGA-56-7582 TCGA-56-8304 TCGA-56-8307 
       30.35         8.75         1.45         0.85         3.48        26.89 
TCGA-56-8504 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A62T 
       16.77        15.81        20.94        17.85        18.74         2.76 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L TCGA-60-2696 TCGA-60-2711 
       16.47        34.78        34.36        56.65         3.58        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2722 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI 
        9.01        56.91        29.85       102.67        66.61        58.65 
TCGA-63-A5MJ TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MY TCGA-66-2727 TCGA-66-2755 
       59.97        25.28        89.29        34.59        16.96         0.92 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 TCGA-66-2777 
       21.01         0.99         1.02         2.01         7.07         2.01 
TCGA-66-2787 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 TCGA-68-8250 
       40.01        30.02        10.06        49.05         2.73         8.02 
TCGA-68-A59J TCGA-77-6845 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7465 
       14.73        23.28         0.49        42.28       106.95        15.75 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8136 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
        6.51        53.95        39.09         9.63        54.41        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       35.90         0.33         6.41        36.53        34.95        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       32.91         1.38         1.15        16.87        34.52        10.09 
TCGA-85-8288 TCGA-85-8352 TCGA-85-8479 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN 
       13.22         5.29         0.72         0.10        15.62        19.33 
TCGA-85-A4QR TCGA-85-A511 TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE 
       19.73        14.96        12.39         2.93        11.77        22.62 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-8491 TCGA-94-A5I4 
        2.70         3.48         5.26         2.30        26.63        16.14 
TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A53B TCGA-J1-A4AH 
       49.87        57.07        19.36         2.76         2.01        19.10 
TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HN TCGA-NC-A5HO 
       16.11        13.18        64.08        51.78        37.22        30.58 
TCGA-NC-A5HR TCGA-NK-A5CR TCGA-O2-A52Q TCGA-O2-A5IB 
       29.75        83.57         3.72        11.18 

$`DEL PEAK  5(2Q37.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 TCGA-18-3419 TCGA-18-4721 TCGA-18-5592 
       11.34        23.54        31.99         1.64       154.32        49.94 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       27.19        46.88        99.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 
       31.73       122.43         9.34       119.80        31.63        88.11 
TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       41.69        10.82        32.19        14.93         4.31        64.21 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       48.82        20.48        35.08        48.33        24.13         0.56 
TCGA-22-4599 TCGA-22-4607 TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       38.17        19.30         9.57        31.73        64.93        63.55 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        0.79        54.28        71.34        18.84        30.12        62.86 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 
       16.64        22.06        79.53       174.08       151.27        14.07 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       54.44         1.55        19.76        27.02         4.70         0.30 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
        6.94       110.99        44.19        27.16         2.63        61.61 
TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
       31.50        32.88        31.27        67.79        56.38        23.24 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       30.94        18.15         4.96        27.19         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       20.91         3.95         0.43         0.39         6.58         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
        7.46         7.82         6.81         3.39        47.80        74.07 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
       44.75        68.58        55.20        70.03        60.79         1.71 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
        1.94        27.39        36.39        17.88        17.06        40.21 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
       38.66        33.11        18.38        27.91        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8116 TCGA-43-A474 
        5.46         3.81        19.59        66.51        11.77        11.61 
TCGA-43-A475 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
        9.73        12.03         9.99        10.65        13.91         0.39 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
        0.39        28.34         5.46        27.45        28.96         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
       18.25         2.04         0.62         0.99         0.43         0.99 
TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8308 TCGA-56-8309 
        1.32         6.51         0.10        17.49        17.00        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35         1.81        22.75         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
       20.25        19.23        13.32        21.04         0.13         0.26 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J 
        0.03        13.25        13.55        29.95        71.24        85.12 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       35.24        29.92        21.11        12.23        10.22        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
       50.33        35.34        48.49        42.64         3.19        32.32 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5ML 
       35.90        23.57        26.83        11.77        70.62        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV 
       14.99        11.34        78.28        16.37        25.41        36.16 
TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       53.88        43.10         2.01        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 
        2.01         0.99        43.99        25.05         2.01         2.01 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
       23.01        19.00         3.02        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 
       12.00        24.95         1.97        25.97        22.98         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7756 TCGA-68-7757 
       22.98         5.03        54.08         4.01         6.64         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 
       13.35        16.18        29.56        73.12        75.09        11.18 
TCGA-77-7139 TCGA-77-7140 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 
       89.98        20.78        70.13         0.16        46.78        86.76 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 
       37.81        82.92        12.59        53.92        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-A5FZ TCGA-77-A5G1 
       11.54        26.40        27.39         6.97       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
      117.57        22.29         5.92        42.41        42.08        30.81 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7844 
       27.62        38.86         9.67        11.97        12.99        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       18.94        25.15        19.04        24.13        31.56        14.07 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
        0.76        22.45        16.77         3.09        32.71         2.01 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB 
        7.76        14.63        13.94        12.59        25.68        17.72 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       14.96        24.36        18.18        12.56        16.21        15.85 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED 
        0.79         3.65        24.92         9.50        14.07        20.22 
TCGA-90-A59Q TCGA-92-8063 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 
       10.59         4.01        21.04         0.16        11.70         4.01 
TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
        5.03        14.14        17.69        18.31        17.46        16.57 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        8.42        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
       18.15        27.02        21.21        20.32        18.58        20.71 
TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HH 
       12.89        13.41        11.84         0.07         4.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HP 
       45.37        13.74         4.21         2.89        39.85        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE 
       14.73        22.78        65.49         3.65        16.80         0.43 
TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       33.07        12.72        43.89         8.58         0.20 

  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                         0.10                          0.03 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                       133.74                        174.08 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                        18.92                         19.23 
[1] "0.1 - 133.7 (18.9)" "0.0 - 174.1 (19.2)"
[1] "hr=" "1.1"
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(2Q37.1) MUTATED         0       27       47        1        23
  DEL PEAK  5(2Q37.1) WILD-TYPE       2       60      104        1        40
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q37.1) MUTATED          28         2         20          5
  DEL PEAK  5(2Q37.1) WILD-TYPE        64         1         42         16
                               vv
clus                            STAGE IV
  DEL PEAK  5(2Q37.1) MUTATED          1
  DEL PEAK  5(2Q37.1) WILD-TYPE        6
D35V3, multiclass
            clus
vv           DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                            27                            60
  STAGE IB                            47                           104
  STAGE II                             1                             1
  STAGE IIA                           23                            40
  STAGE IIB                           28                            64
  STAGE III                            2                             1
  STAGE IIIA                          20                            42
  STAGE IIIB                           5                            16
  STAGE IV                             1                             6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  5(2Q37.1) MUTATED    34  95  19   6
  DEL PEAK  5(2Q37.1) WILD-TYPE  77 195  50  17
D35V4, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  T1                          34                            77
  T2                          95                           195
  T3                          19                            50
  T4                           6                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  5(2Q37.1) MUTATED    93  51   9   1
  DEL PEAK  5(2Q37.1) WILD-TYPE 219  80  30   4
D35V5, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  N0                          93                           219
  N1                          51                            80
  N2                           9                            30
  N3                           1                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED   124   1
  DEL PEAK  5(2Q37.1) WILD-TYPE 280   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED    124    1
  DEL PEAK  5(2Q37.1) WILD-TYPE  280    6
   clus
vv  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  0                         124                           280
  1                           1                             6
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED    44 110
  DEL PEAK  5(2Q37.1) WILD-TYPE  83 256
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED     44  110
  DEL PEAK  5(2Q37.1) WILD-TYPE   83  256
        clus
vv       DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  FEMALE                          44                            83
  MALE                           110                           256
[1] 2 2
[1] FALSE
D35V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(2Q37.1) MUTATED                                       6
  DEL PEAK  5(2Q37.1) WILD-TYPE                                     9
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(2Q37.1) MUTATED                                         0
  DEL PEAK  5(2Q37.1) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  5(2Q37.1) MUTATED                                        2
  DEL PEAK  5(2Q37.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  5(2Q37.1) MUTATED                                         0
  DEL PEAK  5(2Q37.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(2Q37.1) MUTATED                                                           146
  DEL PEAK  5(2Q37.1) WILD-TYPE                                                         324
D35V9, multiclass
                                                             clus
vv                                                            DEL PEAK  5(2Q37.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         146
                                                             clus
vv                                                            DEL PEAK  5(2Q37.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           324
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED     2 152
  DEL PEAK  5(2Q37.1) WILD-TYPE  11 328
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED      2  152
  DEL PEAK  5(2Q37.1) WILD-TYPE   11  328
     clus
vv    DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  NO                            2                            11
  YES                         152                           328
[1] 2 2
[1] FALSE
D35V11, continuous
D35V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q37.1) MUTATED   122   4   0   9
  DEL PEAK  5(2Q37.1) WILD-TYPE 272   8   4  13
D35V13, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  R0                         122                           272
  R1                           4                             8
  R2                           0                             4
  RX                           9                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.1) MUTATED       2                        10   106
  DEL PEAK  5(2Q37.1) WILD-TYPE     7                        21   234
D35V14, multiclass
                           clus
vv                          DEL PEAK  5(2Q37.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             106
                           clus
vv                          DEL PEAK  5(2Q37.1) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               234
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V15, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED     3  95
  DEL PEAK  5(2Q37.1) WILD-TYPE   5 214
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED      3   95
  DEL PEAK  5(2Q37.1) WILD-TYPE    5  214
                        clus
vv                       DEL PEAK  5(2Q37.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          95
                        clus
vv                       DEL PEAK  5(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           214
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  6(3P25.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P25.3) MUTATED   225 152
  DEL PEAK  6(3P25.3) WILD-TYPE  56  44
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                          377                           100 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                          152                            44 
$`DEL PEAK  6(3P25.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 
       11.34        92.15        31.99        36.07         6.18         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 
      154.32        49.94       119.54        46.88        70.16        34.78 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 
       31.73       122.43        43.23        31.63        88.11        33.93 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       10.82        32.19        21.99         7.33        14.93         4.31 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
       14.10        27.02        20.48        48.33        24.13        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 
       34.75        13.12        32.02         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       64.93        63.55        44.25         0.79        54.28        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 
       79.20        11.74        18.84        30.12        56.32        16.64 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       22.06         7.63        98.01       103.53       151.27        14.07 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       54.44         1.55        27.02         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
        6.94       110.99       118.36        27.16         2.63        61.61 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5236 
       31.50        28.96        32.88        65.23        67.79         9.07 
TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       23.24        16.93        30.94        18.15         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       27.19         4.04        26.43        20.91         3.95         0.43 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        6.58         8.12         7.46         7.82         6.81         0.39 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
       47.80        74.07        44.75        68.58        55.20        70.03 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
       60.79         1.71         1.94        27.39        36.39        15.58 
TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       35.64        35.70        40.21        38.66        27.02        33.11 
TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       12.36        21.47        19.59         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 
       11.77         2.93        11.61        12.03         9.99        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 
        0.39         0.39        29.95        28.34         5.46         8.75 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
       28.96         0.10        18.25         0.99         0.43         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
        1.45         1.32         0.85         6.51         0.10        17.49 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
        3.48        26.89        17.00        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.81         1.18         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS 
       19.23        13.32        17.85        21.04        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        2.76         0.03        13.55        29.95        71.24        16.47 
TCGA-58-8393 TCGA-58-A46K TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 
       34.78        34.36        21.11         3.58        10.22        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 
       41.42         9.01        56.91        35.34        42.64         3.19 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       32.32        29.85        35.90        23.57        26.83        11.77 
TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP 
      102.67        66.61        58.65        59.97        45.57        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       89.29        78.28        16.37        25.41        36.16        53.88 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 
       16.96        43.10         2.01        21.07         2.01         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
        0.99        43.99        21.01         0.99         2.01         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         7.07        23.01        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
       25.97        40.01        22.98        22.98         5.03        30.02 
TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
       10.06         4.01        49.05         2.73         6.64         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
        8.02        13.35        16.18        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       23.28        11.18        89.98         0.49        42.28        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
      106.95         0.16        46.78        15.75        86.76        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       37.81        82.92        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       11.54        26.40        27.39         6.97         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
       65.49        35.90         0.33       132.36       117.57        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        5.92        42.41        42.08        30.81        27.62        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 
        9.67        11.97        12.99         6.41        34.95        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
       32.91         1.38        29.95        18.94        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       24.13        31.56        14.07        16.87        34.52        10.09 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 
       13.22        22.45        16.77         3.09         2.01         7.76 
TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
       14.63         0.10        15.62        25.68        19.33        17.72 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       14.96        18.18        19.73        16.21        15.85        14.96 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED 
       12.39         3.65         9.50         2.93        14.07        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       22.62        10.59         3.48         4.01         5.26         2.30 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-A5I4 
       21.04         0.16        11.70         4.01         5.03        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
       17.69        49.87        57.07        18.31        17.46        19.36 
TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A 
       16.57        30.81        30.67        27.16         3.88        18.15 
TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 
        2.01        18.58        20.71        19.10        12.89        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       13.41        11.84         0.07        64.08         4.54        51.78 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       45.37        13.74        39.85        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52Q 
       14.73        29.75        83.57         3.65        16.80         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89         8.58        11.18         0.20 

$`DEL PEAK  6(3P25.3) WILD-TYPE`
TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 
       23.54         1.64        86.96        27.19        99.16        60.89 
TCGA-21-1078 TCGA-21-1081 TCGA-21-1082 TCGA-21-5784 TCGA-22-1005 TCGA-22-1011 
       15.58         9.34       119.80        41.69        64.21         1.74 
TCGA-22-1017 TCGA-22-4593 TCGA-22-4596 TCGA-22-4607 TCGA-22-5474 TCGA-22-5489 
       48.82        35.08         0.56        19.30        14.63        62.86 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-6737 TCGA-33-AASI TCGA-34-2609 
      133.74        79.53       174.08        19.76        44.19        31.27 
TCGA-34-5234 TCGA-34-5240 TCGA-37-3792 TCGA-37-5819 TCGA-39-5029 TCGA-39-5039 
       56.38        12.00         0.39         3.39        24.33        17.88 
TCGA-39-5040 TCGA-43-2578 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 
       17.06        22.49        18.38        27.91        24.89         5.46 
TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-52-7810 TCGA-52-7812 
        3.81         9.73        14.20        10.65        30.35        27.45 
TCGA-56-6545 TCGA-56-6546 TCGA-56-8623 TCGA-56-8625 TCGA-56-A5DR TCGA-58-8387 
        2.04         0.62        22.75        10.36         0.13        13.25 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2714 
       85.12        56.65        35.24        29.92        12.23        50.33 
TCGA-60-2716 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MY TCGA-66-2744 
       48.49        70.62        14.99        11.34        34.59         0.99 
TCGA-66-2753 TCGA-66-2759 TCGA-66-2766 TCGA-66-2789 TCGA-66-2794 TCGA-68-A59J 
        1.02        25.05         1.02         4.04        54.08        14.73 
TCGA-77-7140 TCGA-77-8007 TCGA-77-8131 TCGA-77-A5FZ TCGA-85-7696 TCGA-85-7843 
       20.78         6.51        12.59       126.18        36.53         1.15 
TCGA-85-8287 TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8582 TCGA-85-8584 
        0.76         5.29        32.71         0.72        13.94        12.59 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-92-7340 
       24.36        12.56         0.79        24.92        11.77         2.70 
TCGA-94-8491 TCGA-94-A4VJ TCGA-98-7454 TCGA-98-8020 TCGA-98-8023 TCGA-98-A53C 
       26.63        14.14         8.42         2.76        21.34        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-L3-A524 TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HL 
       21.21        20.32        16.11         1.22         4.21         2.89 
TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A7XE TCGA-O2-A52N 
       22.78        65.49         0.43        33.07 

  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                         0.03                          0.13 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                       154.32                        174.08 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                        19.10                         18.84 
[1] "0.0 - 154.3 (19.1)" "0.1 - 174.1 (18.8)"
[1] "hr=" "1.1"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(3P25.3) MUTATED         1       68      125        2        48
  DEL PEAK  6(3P25.3) WILD-TYPE       1       19       26        0        15
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(3P25.3) MUTATED          67         3         50         17
  DEL PEAK  6(3P25.3) WILD-TYPE        25         0         12          4
                               vv
clus                            STAGE IV
  DEL PEAK  6(3P25.3) MUTATED          6
  DEL PEAK  6(3P25.3) WILD-TYPE        1
D36V3, multiclass
            clus
vv           DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            68                            19
  STAGE IB                           125                            26
  STAGE II                             2                             0
  STAGE IIA                           48                            15
  STAGE IIB                           67                            25
  STAGE III                            3                             0
  STAGE IIIA                          50                            12
  STAGE IIIB                          17                             4
  STAGE IV                             6                             1
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  6(3P25.3) MUTATED    88 226  58  18
  DEL PEAK  6(3P25.3) WILD-TYPE  23  64  11   5
D36V4, multiclass
    clus
vv   DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  T1                          88                            23
  T2                         226                            64
  T3                          58                            11
  T4                          18                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  6(3P25.3) MUTATED   251 104  27   4
  DEL PEAK  6(3P25.3) WILD-TYPE  61  27  12   1
D36V5, multiclass
    clus
vv   DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  N0                         251                            61
  N1                         104                            27
  N2                          27                            12
  N3                           4                             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"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P25.3) MUTATED   316   6
  DEL PEAK  6(3P25.3) WILD-TYPE  88   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED    316    6
  DEL PEAK  6(3P25.3) WILD-TYPE   88    1
   clus
vv  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  0                         316                            88
  1                           6                             1
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P25.3) MUTATED    99 291
  DEL PEAK  6(3P25.3) WILD-TYPE  28  75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED     99  291
  DEL PEAK  6(3P25.3) WILD-TYPE   28   75
        clus
vv       DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  FEMALE                          99                            28
  MALE                           291                            75
[1] 2 2
[1] FALSE
D36V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(3P25.3) MUTATED                                      11
  DEL PEAK  6(3P25.3) WILD-TYPE                                     4
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(3P25.3) MUTATED                                         1
  DEL PEAK  6(3P25.3) WILD-TYPE                                       0
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  6(3P25.3) MUTATED                                        2
  DEL PEAK  6(3P25.3) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  6(3P25.3) MUTATED                                         1
  DEL PEAK  6(3P25.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(3P25.3) MUTATED                                                           375
  DEL PEAK  6(3P25.3) WILD-TYPE                                                          95
D36V9, multiclass
                                                             clus
vv                                                            DEL PEAK  6(3P25.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         375
                                                             clus
vv                                                            DEL PEAK  6(3P25.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            95
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P25.3) MUTATED    12 378
  DEL PEAK  6(3P25.3) WILD-TYPE   1 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED     12  378
  DEL PEAK  6(3P25.3) WILD-TYPE    1  102
     clus
vv    DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  NO                           12                             1
  YES                         378                           102
[1] 2 2
[1] FALSE
D36V11, continuous
D36V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(3P25.3) MUTATED   312   8   4  17
  DEL PEAK  6(3P25.3) WILD-TYPE  82   4   0   5
D36V13, multiclass
    clus
vv   DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  R0                         312                            82
  R1                           8                             4
  R2                           4                             0
  RX                          17                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P25.3) MUTATED       6                        26   262
  DEL PEAK  6(3P25.3) WILD-TYPE     3                         5    78
D36V14, multiclass
                           clus
vv                          DEL PEAK  6(3P25.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          26
  WHITE                                             262
                           clus
vv                          DEL PEAK  6(3P25.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V15, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P25.3) MUTATED     6 241
  DEL PEAK  6(3P25.3) WILD-TYPE   2  68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED      6  241
  DEL PEAK  6(3P25.3) WILD-TYPE    2   68
                        clus
vv                       DEL PEAK  6(3P25.3) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         241
                        clus
vv                       DEL PEAK  6(3P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            68
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  7(3P13) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  7(3P13) MUTATED   243 168
  DEL PEAK  7(3P13) WILD-TYPE  38  28
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                        411                          66 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                        168                          28 
$`DEL PEAK  7(3P13) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
       11.34        23.54        92.15        31.99        36.07         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       86.96         6.18         2.79       154.32        49.94       119.54 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 
       46.88        70.16        34.78        31.73       122.43       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
       43.23        31.63        88.11        33.93        10.82        32.19 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 
       21.99         7.33        14.93         4.31        14.10        27.02 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
       48.82        20.48        48.33        24.13        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 
       13.12        32.02        19.30         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       64.93        63.55        14.63        44.25         0.79        54.28 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
       71.34        79.20        11.74        18.84        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
       56.32        16.64        22.06         7.63       133.74        98.01 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
       79.53       103.53       151.27        14.07        54.44         1.55 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       27.02         4.70         0.30        36.62         6.94       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
       44.19       118.36        27.16         2.63        61.61        31.50 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5236 
       28.96        32.88        31.27        65.23        67.79         9.07 
TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       23.24        16.93        30.94        18.15         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       27.19         4.04        26.43        20.91         3.95         0.43 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        6.58         8.12         7.46         7.82         6.81         0.39 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        3.39        47.80        74.07        44.75        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       70.03        60.79         1.71        24.33         1.94        27.39 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
       36.39        15.58        35.64        40.21        22.49        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 
       27.02        33.11        27.91        12.36        21.47        19.59 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
        7.76        66.51        13.38        11.77         2.93        11.61 
TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       12.03         9.99        10.65        13.91         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
       29.95        28.34         5.46        30.35         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 
       28.96         0.10        18.25         2.04         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
        0.99         1.45         1.32         0.85         6.51         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 
       17.49         3.48        26.89        17.00        14.07         1.35 
TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       16.77         1.18        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       20.94        19.23        13.32        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        0.13         0.26         2.76         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L 
       29.95        71.24        16.47        34.78        34.36        56.65 
TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       35.24        21.11         3.58        10.22        96.82        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       92.71        21.93        80.45        49.48        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
        9.01        56.91        42.64        32.32        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI 
       23.57        26.83        11.77       102.67        66.61        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       59.97        45.57        14.99        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       16.37        25.41        36.16        34.59        16.96        43.10 
TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
       21.07         2.01         0.92         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       25.05         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
       23.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        3.98        12.00        24.95         1.97        25.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
       22.98         4.04        22.98         5.03        30.02        10.06 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 
       54.08         4.01         2.73         6.64         6.94         8.02 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       13.35        16.18        14.73        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       23.28        11.18        89.98         0.49        42.28        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
      106.95         0.16        46.78        15.75        86.76        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       37.81        82.92        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       11.54        26.40        27.39         6.97         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
       65.49        35.90         0.33       132.36       117.57        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        5.92        42.41        42.08        30.81        27.62        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
        9.67        11.97        12.99         6.41        36.53        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
       31.30        32.91         1.38         1.15        29.95        18.94 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       19.04        24.13        31.56        14.07        16.87        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
       10.09         0.76        13.22        22.45        16.77         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 
       32.71         2.01         0.72         7.76        14.63         0.10 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ 
       15.62        25.68        19.33        17.72        14.96        18.18 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 
       19.73        16.21        15.85        14.96        12.39         3.65 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        9.50         2.93        14.07        20.22        22.62        10.59 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
        3.48         4.01         5.26         2.30        21.04         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 
       11.70         4.01         5.03        26.63        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
       17.69        49.87        57.07        18.31        17.46        19.36 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        2.76        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       18.15         2.01        18.58        20.71        19.10        12.89 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF 
       13.18        13.41        11.84         0.07        64.08         4.54 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
       51.78        45.37        13.74         4.21         2.89        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR 
       37.22        30.58        24.00        14.73        29.75        83.57 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       65.49         3.65        16.80         3.72        12.72        43.89 
TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        8.58        11.18         0.20 

$`DEL PEAK  7(3P13) WILD-TYPE`
TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 TCGA-21-1081 TCGA-21-5784 
       27.19        99.16        60.89        15.58         9.34        41.69 
TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 TCGA-22-4596 TCGA-33-4566 TCGA-33-6737 
       64.21         1.74        35.08         0.56       174.08        19.76 
TCGA-34-5234 TCGA-34-5240 TCGA-37-3792 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
       56.38        12.00         0.39        35.70        17.88        17.06 
TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U 
       18.38        24.89         5.46         3.81         9.73        14.20 
TCGA-56-6546 TCGA-56-8622 TCGA-56-8623 TCGA-58-A46J TCGA-58-A46N TCGA-60-2697 
        0.62         1.81        22.75        85.12        29.92        12.23 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-63-A5MG TCGA-63-A5MN 
       50.33        35.34        48.49         3.19        70.62        11.34 
TCGA-63-A5MW TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2763 TCGA-66-2800 
       53.88         2.01         0.99         1.02         0.99        49.05 
TCGA-77-7140 TCGA-77-8007 TCGA-77-8131 TCGA-77-A5FZ TCGA-85-8048 TCGA-85-8352 
       20.78         6.51        12.59       126.18        25.15         5.29 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 
       13.94        12.59        24.36        12.56         0.79        24.92 
TCGA-90-7769 TCGA-92-7340 TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53C TCGA-98-A53D 
       11.77         2.70        16.57         8.42        27.02        21.21 
TCGA-98-A53H TCGA-L3-A524 TCGA-NC-A5HH TCGA-NC-A5HT TCGA-NK-A7XE TCGA-O2-A52N 
       20.32        16.11         1.22        22.78         0.43        33.07 

  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                       0.03                        0.39 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                     154.32                      174.08 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                     19.330                      16.815 
[1] "0.0 - 154.3 (19.3)" "0.4 - 174.1 (16.8)"
[1] "hr=" "1.1"
D37V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(3P13) MUTATED         1       77      130        2        53
  DEL PEAK  7(3P13) WILD-TYPE       1       10       21        0        10
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P13) MUTATED          74         3         58         18
  DEL PEAK  7(3P13) WILD-TYPE        18         0          4          3
                             vv
clus                          STAGE IV
  DEL PEAK  7(3P13) MUTATED          7
  DEL PEAK  7(3P13) WILD-TYPE        0
D37V3, multiclass
            clus
vv           DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  STAGE I                            1                           1
  STAGE IA                          77                          10
  STAGE IB                         130                          21
  STAGE II                           2                           0
  STAGE IIA                         53                          10
  STAGE IIB                         74                          18
  STAGE III                          3                           0
  STAGE IIIA                        58                           4
  STAGE IIIB                        18                           3
  STAGE IV                           7                           0
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  7(3P13) MUTATED    98 247  62  19
  DEL PEAK  7(3P13) WILD-TYPE  13  43   7   4
D37V4, multiclass
    clus
vv   DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  T1                        98                          13
  T2                       247                          43
  T3                        62                           7
  T4                        19                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK  7(3P13) MUTATED   270 112  35   5
  DEL PEAK  7(3P13) WILD-TYPE  42  19   4   0
D37V5, multiclass
    clus
vv   DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  N0                       270                          42
  N1                       112                          19
  N2                        35                           4
  N3                         5                           0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                             cls
clus                            0   1
  DEL PEAK  7(3P13) MUTATED   347   7
  DEL PEAK  7(3P13) WILD-TYPE  57   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3P13) MUTATED    347    7
  DEL PEAK  7(3P13) WILD-TYPE   57    0
   clus
vv  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  0                       347                          57
  1                         7                           0
[1] 2 2
[1] FALSE
D37V7, binary
                             cls
clus                            0   1
  DEL PEAK  7(3P13) MUTATED   108 318
  DEL PEAK  7(3P13) WILD-TYPE  19  48
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3P13) MUTATED    108  318
  DEL PEAK  7(3P13) WILD-TYPE   19   48
        clus
vv       DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  FEMALE                       108                          19
  MALE                         318                          48
[1] 2 2
[1] FALSE
D37V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(3P13) MUTATED                                      12
  DEL PEAK  7(3P13) WILD-TYPE                                     3
                             vv
clus                          LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(3P13) MUTATED                                         1
  DEL PEAK  7(3P13) WILD-TYPE                                       0
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  7(3P13) MUTATED                                        3
  DEL PEAK  7(3P13) WILD-TYPE                                      3
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(3P13) MUTATED                                         1
  DEL PEAK  7(3P13) WILD-TYPE                                       0
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(3P13) MUTATED                                                           409
  DEL PEAK  7(3P13) WILD-TYPE                                                          61
D37V9, multiclass
                                                             clus
vv                                                            DEL PEAK  7(3P13) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                              12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                             1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       409
                                                             clus
vv                                                            DEL PEAK  7(3P13) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          61
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, binary
                             cls
clus                            0   1
  DEL PEAK  7(3P13) MUTATED    12 414
  DEL PEAK  7(3P13) WILD-TYPE   1  66
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3P13) MUTATED     12  414
  DEL PEAK  7(3P13) WILD-TYPE    1   66
     clus
vv    DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  NO                         12                           1
  YES                       414                          66
[1] 2 2
[1] FALSE
D37V11, continuous
D37V12, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  7(3P13) MUTATED   342   8   4  18
  DEL PEAK  7(3P13) WILD-TYPE  52   4   0   4
D37V13, multiclass
    clus
vv   DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  R0                       342                          52
  R1                         8                           4
  R2                         4                           0
  RX                        18                           4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P13) MUTATED       6                        30   290
  DEL PEAK  7(3P13) WILD-TYPE     3                         1    50
D37V14, multiclass
                           clus
vv                          DEL PEAK  7(3P13) MUTATED
  ASIAN                                             6
  BLACK OR AFRICAN AMERICAN                        30
  WHITE                                           290
                           clus
vv                          DEL PEAK  7(3P13) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V15, binary
                             cls
clus                            0   1
  DEL PEAK  7(3P13) MUTATED     8 264
  DEL PEAK  7(3P13) WILD-TYPE   0  45
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3P13) MUTATED      8  264
  DEL PEAK  7(3P13) WILD-TYPE    0   45
                        clus
vv                       DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  HISPANIC OR LATINO                             8                           0
  NOT HISPANIC OR LATINO                       264                          45
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  8(3P12.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P12.3) MUTATED   240 164
  DEL PEAK  8(3P12.3) WILD-TYPE  41  32
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          404                            73 
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          164                            32 
$`DEL PEAK  8(3P12.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
       11.34        23.54        92.15        31.99        36.07         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       86.96         6.18         2.79       154.32        49.94       119.54 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
       46.88        70.16        31.73       122.43       119.80        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
       31.63        88.11        33.93        32.19        21.99         7.33 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
       14.93         4.31        14.10        27.02        48.82        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       35.08        48.33        24.13        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
       32.02        19.30         9.57        11.77        31.73        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       63.55        14.63        44.25         0.79        54.28        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       79.20        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
       16.64        22.06         7.63       133.74        98.01        79.53 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 
      103.53       151.27        14.07        54.44         1.55        27.02 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI 
        4.70         0.30        36.62         6.94       110.99        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
      118.36        27.16         2.63        61.61        31.50        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5236 TCGA-34-5239 
       32.88        31.27        65.23        67.79         9.07        23.24 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       16.93        30.94        18.15         4.96         1.12        27.19 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
        4.04        26.43        20.91         3.95         0.43         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        8.12         7.46         7.82         0.39         3.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
       74.07        44.75        68.58        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
        1.71        24.33         1.94        36.39        15.58        35.64 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       40.21        22.49        38.66        27.02        33.11        27.91 
TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       12.36        21.47        19.59         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 
       11.77         2.93        11.61        12.03         9.99        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       13.91         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       30.35         8.75        27.45        28.96         0.10        18.25 
TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
        2.04         0.99         0.43         0.99         1.45         1.32 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 
        0.85         6.51         0.10        17.49         3.48        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 
       17.00        14.07         1.35        16.77         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
        9.93        20.25        15.81        20.94        19.23        13.32 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T 
       17.85        21.04        18.74         0.13         0.26         2.76 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        0.03        13.25        13.55        29.95        71.24        16.47 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 
       34.36        56.65        35.24        21.11         3.58        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       96.82        37.94        92.71        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2719 TCGA-60-2721 
       66.54        41.42         9.01        56.91        42.64        32.32 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB 
       29.85        35.90        23.57        26.83        11.77       102.67 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MP 
       66.61        58.65        59.97        45.57        14.99        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY 
       89.29        78.28        16.37        25.41        36.16        34.59 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
       16.96        43.10        21.07         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       43.99        21.01        25.05         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         7.07        23.01        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
       25.97        40.01        22.98         4.04        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
       30.02        10.06        54.08         4.01        49.05         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        6.64         6.94         8.02        13.35        16.18        14.73 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       29.56        73.12        75.09        23.28        11.18        89.98 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        0.49        42.28        70.13       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
       15.75        86.76        53.95        82.92        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
       17.72       104.09        11.54        27.39         6.97         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 
       54.41        65.49        35.90         0.33       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
       22.29         5.92        42.41        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       38.86         9.67        11.97        12.99         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
       34.95        31.30        32.91         1.38         1.15        29.95 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
       18.94        19.04        24.13        31.56        14.07        16.87 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       34.52        10.09         0.76        13.22        22.45        16.77 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
        3.09        32.71         2.01         0.72         7.76        14.63 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC 
        0.10        15.62        25.68        19.33        17.72        14.96 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 
       18.18        19.73        16.21        15.85        12.39         3.65 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        9.50         2.93        14.07        20.22        22.62        10.59 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
        3.48         4.01         5.26         2.30        21.04         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 
       11.70         4.01         5.03        26.63        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
       17.69        49.87        57.07        18.31        17.46        19.36 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        2.76        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       18.15         2.01        18.58        20.71        19.10        12.89 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF 
       13.18        13.41        11.84         0.07        64.08         4.54 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
       51.78        45.37        13.74         4.21         2.89        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CT 
       37.22        30.58        24.00        14.73        29.75        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W 
        3.65        16.80         3.72        12.72        43.89         8.58 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

$`DEL PEAK  8(3P12.3) WILD-TYPE`
TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 
       27.19        99.16        60.89        34.78        15.58         9.34 
TCGA-21-5784 TCGA-21-5787 TCGA-22-1005 TCGA-22-1011 TCGA-22-4596 TCGA-33-4566 
       41.69        10.82        64.21         1.74         0.56       174.08 
TCGA-33-6737 TCGA-34-5234 TCGA-34-5240 TCGA-37-3792 TCGA-37-4135 TCGA-39-5031 
       19.76        56.38        12.00         0.39         6.81        27.39 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 
       35.70        17.88        17.06        18.38        24.89         5.46 
TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U TCGA-56-6546 TCGA-56-8622 TCGA-56-8623 
        3.81         9.73        14.20         0.62         1.81        22.75 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46N TCGA-60-2697 TCGA-60-2714 TCGA-60-2715 
       34.78        85.12        29.92        12.23        50.33        35.34 
TCGA-60-2716 TCGA-60-2720 TCGA-63-A5MG TCGA-63-A5MN TCGA-63-A5MW TCGA-66-2737 
       48.49         3.19        70.62        11.34        53.88         2.01 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2763 TCGA-77-7140 TCGA-77-8007 TCGA-77-8128 
        0.99         1.02         0.99        20.78         6.51        37.81 
TCGA-77-8131 TCGA-77-8143 TCGA-77-A5FZ TCGA-85-8048 TCGA-85-8352 TCGA-85-8582 
       12.59        26.40       126.18        25.15         5.29        13.94 
TCGA-85-8584 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 
       12.59        24.36        12.56        14.96         0.79        24.92 
TCGA-90-7769 TCGA-92-7340 TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53C TCGA-98-A53D 
       11.77         2.70        16.57         8.42        27.02        21.21 
TCGA-98-A53H TCGA-L3-A524 TCGA-NC-A5HH TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A7XE 
       20.32        16.11         1.22        22.78        83.57         0.43 
TCGA-O2-A52N 
       33.07 

  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                         0.03                          0.39 
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                       154.32                        174.08 
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                       19.315                        17.060 
[1] "0.0 - 154.3 (19.3)" "0.4 - 174.1 (17.1)"
[1] "hr=" "1.1"
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(3P12.3) MUTATED         1       76      128        2        54
  DEL PEAK  8(3P12.3) WILD-TYPE       1       11       23        0         9
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P12.3) MUTATED          72         3         55         18
  DEL PEAK  8(3P12.3) WILD-TYPE        20         0          7          3
                               vv
clus                            STAGE IV
  DEL PEAK  8(3P12.3) MUTATED          7
  DEL PEAK  8(3P12.3) WILD-TYPE        0
D38V3, multiclass
            clus
vv           DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            76                            11
  STAGE IB                           128                            23
  STAGE II                             2                             0
  STAGE IIA                           54                             9
  STAGE IIB                           72                            20
  STAGE III                            3                             0
  STAGE IIIA                          55                             7
  STAGE IIIB                          18                             3
  STAGE IV                             7                             0
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  8(3P12.3) MUTATED    97 240  62  20
  DEL PEAK  8(3P12.3) WILD-TYPE  14  50   7   3
D38V4, multiclass
    clus
vv   DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  T1                          97                            14
  T2                         240                            50
  T3                          62                             7
  T4                          20                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  8(3P12.3) MUTATED   268 110  32   5
  DEL PEAK  8(3P12.3) WILD-TYPE  44  21   7   0
D38V5, multiclass
    clus
vv   DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  N0                         268                            44
  N1                         110                            21
  N2                          32                             7
  N3                           5                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.3) MUTATED   341   7
  DEL PEAK  8(3P12.3) WILD-TYPE  63   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.3) MUTATED    341    7
  DEL PEAK  8(3P12.3) WILD-TYPE   63    0
   clus
vv  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  0                         341                            63
  1                           7                             0
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.3) MUTATED   106 313
  DEL PEAK  8(3P12.3) WILD-TYPE  21  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.3) MUTATED    106  313
  DEL PEAK  8(3P12.3) WILD-TYPE   21   53
        clus
vv       DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  FEMALE                         106                            21
  MALE                           313                            53
[1] 2 2
[1] FALSE
D38V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(3P12.3) MUTATED                                      12
  DEL PEAK  8(3P12.3) WILD-TYPE                                     3
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(3P12.3) MUTATED                                         1
  DEL PEAK  8(3P12.3) WILD-TYPE                                       0
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  8(3P12.3) MUTATED                                        3
  DEL PEAK  8(3P12.3) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  8(3P12.3) MUTATED                                         1
  DEL PEAK  8(3P12.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(3P12.3) MUTATED                                                           402
  DEL PEAK  8(3P12.3) WILD-TYPE                                                          68
D38V9, multiclass
                                                             clus
vv                                                            DEL PEAK  8(3P12.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         402
                                                             clus
vv                                                            DEL PEAK  8(3P12.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            68
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.3) MUTATED    11 408
  DEL PEAK  8(3P12.3) WILD-TYPE   2  72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.3) MUTATED     11  408
  DEL PEAK  8(3P12.3) WILD-TYPE    2   72
     clus
vv    DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  NO                           11                             2
  YES                         408                            72
[1] 2 2
[1] FALSE
D38V11, continuous
D38V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(3P12.3) MUTATED   336   8   4  18
  DEL PEAK  8(3P12.3) WILD-TYPE  58   4   0   4
D38V13, multiclass
    clus
vv   DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  R0                         336                            58
  R1                           8                             4
  R2                           4                             0
  RX                          18                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P12.3) MUTATED       6                        29   287
  DEL PEAK  8(3P12.3) WILD-TYPE     3                         2    53
D38V14, multiclass
                           clus
vv                          DEL PEAK  8(3P12.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          29
  WHITE                                             287
                           clus
vv                          DEL PEAK  8(3P12.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V15, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.3) MUTATED     8 258
  DEL PEAK  8(3P12.3) WILD-TYPE   0  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.3) MUTATED      8  258
  DEL PEAK  8(3P12.3) WILD-TYPE    0   51
                        clus
vv                       DEL PEAK  8(3P12.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         258
                        clus
vv                       DEL PEAK  8(3P12.3) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            51
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK  9(3P12.3) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(3P12.3) MUTATED   235 163
  DEL PEAK  9(3P12.3) WILD-TYPE  46  33
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                          398                            79 
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                          163                            33 
$`DEL PEAK  9(3P12.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
       11.34        23.54        92.15        31.99        36.07         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       86.96         6.18         2.79       154.32        49.94       119.54 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
       46.88        70.16        31.73       122.43       119.80        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
       31.63        88.11        33.93        32.19        21.99         7.33 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
       14.93         4.31        14.10        27.02        48.82        20.48 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       48.33        24.13        38.17        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       14.63        44.25         0.79        54.28        71.34        79.20 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       11.74        18.84        30.12        62.86        56.32        16.64 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
       22.06         7.63       133.74        98.01        79.53       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN 
      151.27        14.07        54.44         1.55        27.02         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        0.30        36.62         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       27.16         2.63        61.61        31.50        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 
       31.27        65.23        67.79         9.07        23.24        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       30.94        18.15         4.96         1.12        27.19         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 
       26.43        20.91         3.95         0.43         6.58         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        7.46         7.82         6.81         0.39         3.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 
       74.07        44.75        68.58        55.20        60.79         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-43-2576 
       24.33         1.94        36.39        15.58        35.64        40.21 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       22.49        38.66        27.02        33.11        27.91        12.36 
TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
       21.47        19.59         7.76        66.51        13.38        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
        2.93        11.61        12.03         9.99        10.65        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
        0.39         0.39        29.95        28.34         5.46        30.35 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        8.75        27.45        28.96         0.10        18.25         2.04 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
        0.99         0.43         0.99         1.45         1.32         0.85 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 
        6.51         0.10        17.49         3.48        26.89        17.00 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       14.07         1.35        16.77         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
       20.25        15.81        20.94        19.23        13.32        17.85 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       21.04        18.74         0.13         0.26         2.76         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K 
       13.25        13.55        29.95        71.24        16.47        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 
       56.65        35.24        21.11         3.58        10.22        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 
       41.42         9.01        56.91        42.64        32.32        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH 
       35.90        23.57        26.83        11.77       102.67        66.61 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MP TCGA-63-A5MR 
       58.65        59.97        45.57        14.99        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 
       78.28        16.37        25.41        36.16        34.59        16.96 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
       43.10        21.07         2.01         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       21.01        25.05         2.01         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
       23.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
       12.00        24.95        25.97        40.01        22.98         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       22.98         5.03        30.02        10.06        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       49.05         2.73         6.64         6.94         8.02        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       16.18        14.73        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       11.18        89.98         0.49        42.28        70.13       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 
        0.16        46.78        15.75        86.76        53.95        82.92 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
       53.92        39.09        17.72       104.09        11.54        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        6.97         9.63        54.41        65.49        35.90         0.33 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
      132.36       117.57        22.29         5.92        42.41        42.08 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       30.81        27.62        38.86         9.67        11.97        12.99 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
        6.41        36.53        34.95        31.30        32.91         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
        1.15        29.95        18.94        19.04        24.13        14.07 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       16.87        34.52        10.09         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       16.77         3.09        32.71         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
       14.63         0.10        15.62        25.68        19.33        17.72 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A53L 
       14.96        18.18        19.73        16.21        15.85        12.39 
TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
        3.65         9.50         2.93        14.07        20.22        22.62 
TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
       10.59         3.48         4.01         5.26         2.30        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        0.16        11.70         4.01         5.03        26.63        14.14 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
       16.14        17.69        49.87        57.07        18.31        17.46 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 
       19.36         2.76        30.81        30.67        21.34         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       18.15         2.01        18.58        20.71        19.10        12.89 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF 
       13.18        13.41        11.84         0.07        64.08         4.54 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
       51.78        45.37        13.74         4.21         2.89        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CT 
       37.22        30.58        24.00        14.73        29.75        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W 
        3.65        16.80         3.72        12.72        43.89         8.58 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

$`DEL PEAK  9(3P12.3) WILD-TYPE`
TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 
       27.19        99.16        60.89        34.78        15.58         9.34 
TCGA-21-5784 TCGA-21-5787 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 TCGA-22-4596 
       41.69        10.82        64.21         1.74        35.08         0.56 
TCGA-33-4566 TCGA-33-6737 TCGA-34-5234 TCGA-34-5240 TCGA-37-3792 TCGA-39-5024 
      174.08        19.76        56.38        12.00         0.39        70.03 
TCGA-39-5031 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-5668 TCGA-43-6647 
       27.39        35.70        17.88        17.06        18.38        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U TCGA-56-6546 TCGA-56-8622 
        5.46         3.81         9.73        14.20         0.62         1.81 
TCGA-56-8623 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46N TCGA-60-2697 TCGA-60-2714 
       22.75        34.78        85.12        29.92        12.23        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-63-A5MG TCGA-63-A5MN TCGA-63-A5MW 
       35.34        48.49         3.19        70.62        11.34        53.88 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2763 TCGA-66-2766 TCGA-66-2781 
        2.01         0.99         1.02         0.99         1.02         3.98 
TCGA-66-2785 TCGA-77-7140 TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 TCGA-77-8143 
        1.97        20.78         6.51        37.81        12.59        26.40 
TCGA-77-A5FZ TCGA-85-8048 TCGA-85-8070 TCGA-85-8352 TCGA-85-8582 TCGA-85-8584 
      126.18        25.15        31.56         5.29        13.94        12.59 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 
       24.36        12.56        14.96         0.79        24.92        11.77 
TCGA-92-7340 TCGA-96-A4JL TCGA-98-7454 TCGA-98-A538 TCGA-98-A53C TCGA-98-A53D 
        2.70        16.57         8.42        27.16        27.02        21.21 
TCGA-98-A53H TCGA-L3-A524 TCGA-NC-A5HH TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A7XE 
       20.32        16.11         1.22        22.78        83.57         0.43 
TCGA-O2-A52N 
       33.07 

  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                         0.03                          0.39 
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                       154.32                        174.08 
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                       19.265                        17.880 
[1] "0.0 - 154.3 (19.3)" "0.4 - 174.1 (17.9)"
[1] "hr=" "1.1"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(3P12.3) MUTATED         1       76      125        2        53
  DEL PEAK  9(3P12.3) WILD-TYPE       1       11       26        0        10
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3P12.3) MUTATED          71         3         53         19
  DEL PEAK  9(3P12.3) WILD-TYPE        21         0          9          2
                               vv
clus                            STAGE IV
  DEL PEAK  9(3P12.3) MUTATED          7
  DEL PEAK  9(3P12.3) WILD-TYPE        0
D39V3, multiclass
            clus
vv           DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            76                            11
  STAGE IB                           125                            26
  STAGE II                             2                             0
  STAGE IIA                           53                            10
  STAGE IIB                           71                            21
  STAGE III                            3                             0
  STAGE IIIA                          53                             9
  STAGE IIIB                          19                             2
  STAGE IV                             7                             0
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  9(3P12.3) MUTATED    97 235  61  20
  DEL PEAK  9(3P12.3) WILD-TYPE  14  55   8   3
D39V4, multiclass
    clus
vv   DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  T1                          97                            14
  T2                         235                            55
  T3                          61                             8
  T4                          20                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK  9(3P12.3) MUTATED   264 110  30   5
  DEL PEAK  9(3P12.3) WILD-TYPE  48  21   9   0
D39V5, multiclass
    clus
vv   DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  N0                         264                            48
  N1                         110                            21
  N2                          30                             9
  N3                           5                             0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P12.3) MUTATED   335   7
  DEL PEAK  9(3P12.3) WILD-TYPE  69   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.3) MUTATED    335    7
  DEL PEAK  9(3P12.3) WILD-TYPE   69    0
   clus
vv  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  0                         335                            69
  1                           7                             0
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P12.3) MUTATED   105 308
  DEL PEAK  9(3P12.3) WILD-TYPE  22  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.3) MUTATED    105  308
  DEL PEAK  9(3P12.3) WILD-TYPE   22   58
        clus
vv       DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  FEMALE                         105                            22
  MALE                           308                            58
[1] 2 2
[1] FALSE
D39V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(3P12.3) MUTATED                                      12
  DEL PEAK  9(3P12.3) WILD-TYPE                                     3
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(3P12.3) MUTATED                                         1
  DEL PEAK  9(3P12.3) WILD-TYPE                                       0
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK  9(3P12.3) MUTATED                                        3
  DEL PEAK  9(3P12.3) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK  9(3P12.3) MUTATED                                         1
  DEL PEAK  9(3P12.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(3P12.3) MUTATED                                                           396
  DEL PEAK  9(3P12.3) WILD-TYPE                                                          74
D39V9, multiclass
                                                             clus
vv                                                            DEL PEAK  9(3P12.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         396
                                                             clus
vv                                                            DEL PEAK  9(3P12.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            74
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P12.3) MUTATED    11 402
  DEL PEAK  9(3P12.3) WILD-TYPE   2  78
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.3) MUTATED     11  402
  DEL PEAK  9(3P12.3) WILD-TYPE    2   78
     clus
vv    DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  NO                           11                             2
  YES                         402                            78
[1] 2 2
[1] FALSE
D39V11, continuous
D39V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(3P12.3) MUTATED   330   8   4  18
  DEL PEAK  9(3P12.3) WILD-TYPE  64   4   0   4
D39V13, multiclass
    clus
vv   DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  R0                         330                            64
  R1                           8                             4
  R2                           4                             0
  RX                          18                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3P12.3) MUTATED       6                        29   284
  DEL PEAK  9(3P12.3) WILD-TYPE     3                         2    56
D39V14, multiclass
                           clus
vv                          DEL PEAK  9(3P12.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          29
  WHITE                                             284
                           clus
vv                          DEL PEAK  9(3P12.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V15, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P12.3) MUTATED     8 256
  DEL PEAK  9(3P12.3) WILD-TYPE   0  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.3) MUTATED      8  256
  DEL PEAK  9(3P12.3) WILD-TYPE    0   53
                        clus
vv                       DEL PEAK  9(3P12.3) MUTATED
  HISPANIC OR LATINO                               8
  NOT HISPANIC OR LATINO                         256
                        clus
vv                       DEL PEAK  9(3P12.3) WILD-TYPE
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            53
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 10(3Q11.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(3Q11.1) MUTATED    50  26
  DEL PEAK 10(3Q11.1) WILD-TYPE 231 170
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                           76                           401 
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                           26                           170 
$`DEL PEAK 10(3Q11.1) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3417 TCGA-18-5592 TCGA-21-1079 
       75.75       117.57        11.34        36.07        49.94        31.73 
TCGA-21-1082 TCGA-22-0940 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-33-4533 
      119.80        21.99        27.02        48.82        48.33       133.74 
TCGA-33-4583 TCGA-33-4589 TCGA-33-6738 TCGA-33-AASJ TCGA-34-5232 TCGA-37-4129 
      151.27         1.55        27.02       118.36        67.79         6.58 
TCGA-37-4132 TCGA-37-5819 TCGA-39-5019 TCGA-43-8115 TCGA-43-A474 TCGA-46-6025 
        7.46         3.39        44.75        13.38        11.61        10.65 
TCGA-46-6026 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-7579 TCGA-56-8308 
       13.91         8.75        27.45        28.96         1.45        17.00 
TCGA-56-8504 TCGA-56-A4BX TCGA-56-A5DS TCGA-60-2711 TCGA-60-2719 TCGA-63-A5MH 
       16.77        13.32         0.26        41.42        42.64        66.61 
TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MY TCGA-66-2754 TCGA-66-2767 
       25.28        16.37        25.41        34.59         2.01         2.01 
TCGA-66-2781 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-8251 TCGA-68-A59J 
        3.98        54.08        49.05         2.73        13.35        14.73 
TCGA-77-6842 TCGA-77-8130 TCGA-77-8138 TCGA-77-A5G1 TCGA-77-A5GB TCGA-77-A5GH 
       29.56        82.92        17.72       132.36        30.81        38.86 
TCGA-85-6175 TCGA-85-7697 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8354 
        9.67        34.95        19.04        14.07        16.87        32.71 
TCGA-85-8481 TCGA-85-8666 TCGA-85-A4CN TCGA-90-A4ED TCGA-92-7341 TCGA-94-A5I4 
        7.76        15.62        19.33        20.22         3.48        16.14 
TCGA-96-7545 TCGA-98-8022 TCGA-98-8023 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HO 
       57.07        30.67        21.34        13.41         4.54        30.58 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-O2-A52S TCGA-O2-A52V 
       83.57        65.49        12.72        43.89 

$`DEL PEAK 10(3Q11.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 
       12.20         7.46        79.46         4.80        23.54        92.15 
TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       31.99         1.64        86.96         6.18         2.79       154.32 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
       27.19       119.54        46.88        99.16        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 
       34.78        15.58       122.43         9.34        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 
       88.11        41.69        33.93        10.82        32.19         7.33 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 
       14.93         4.31        64.21         1.74        14.10        20.48 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       35.08        24.13         0.56        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
       32.02        19.30         9.57        11.77        31.73        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       63.55        14.63        44.25         0.79        54.28        71.34 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       79.20        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       16.64        22.06         7.63        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6737 TCGA-33-A4WN TCGA-33-A5GW 
      103.53        14.07        54.44        19.76         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 
       36.62         6.94       110.99        44.19        27.16         2.63 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
       61.61        31.50        28.96        32.88        31.27        65.23 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       56.38         9.07        23.24        12.00        16.93        30.94 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       18.15         4.96         1.12        27.19         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 
       20.91         3.95         0.43         0.39         8.12         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 
        6.81         0.39        47.80        74.07        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       70.03        60.79         1.71        24.33         1.94        27.39 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
       36.39        15.58        35.64        35.70        17.88        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
       40.21        22.49        38.66        27.02        33.11        18.38 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       27.91        12.36        24.89        21.47         5.46         3.81 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 
       19.59         7.76        66.51        11.77         2.93         9.73 
TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
       14.20        12.03         9.99         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
       28.34         5.46        30.35         0.10        18.25         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 
        0.62         0.99         0.43         0.99         1.32         0.85 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
        6.51         0.10        17.49         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35         1.81        22.75         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ 
       20.25        15.81        20.94        19.23        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       18.74         0.13         2.76         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       29.95        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 
       56.65        35.24        29.92        21.11         3.58        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       10.22        96.82        37.94        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       49.48        66.54         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       48.49         3.19        32.32        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
       26.83        11.77       102.67        70.62        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV 
       45.57        14.99        11.34        89.29        78.28        36.16 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       53.88        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        1.02         0.92         0.99        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
        0.99         2.01         1.02         2.01         7.07        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
       19.00         3.02         2.01        19.00        12.03        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
       24.95         1.97        25.97        40.01        22.98         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-68-7756 
       22.98         5.03        30.02        10.06         4.01         6.64 
TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
        6.94         8.02        16.18        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       11.18        89.98        20.78         0.49        42.28        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
      106.95         0.16        46.78        15.75         6.51        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 
       53.95        37.81        12.59        53.92        39.09       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       11.54        26.40        27.39         6.97         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 
       65.49        35.90         0.33       126.18       117.57        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6560 TCGA-85-6561 
        5.92        42.41        42.08        27.62        11.97        12.99 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
        6.41        36.53        31.30        32.91         1.38         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 
       29.95        18.94        25.15        24.13        31.56        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       10.09         0.76        13.22        22.45        16.77         5.29 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        3.09         2.01         0.72        14.63        13.94        12.59 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
        0.10        25.68        17.72        14.96        24.36        18.18 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       19.73        12.56        16.21        15.85        14.96         0.79 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
       12.39         3.65        24.92         9.50         2.93        11.77 
TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 
       14.07        22.62        10.59         2.70         4.01         5.26 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        2.30        21.04         0.16        11.70         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
       26.63        14.14        17.69        49.87        18.31        17.46 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-A538 
       19.36        16.57         8.42         2.76        30.81        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
        3.88        18.15         2.01        27.02        21.21        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       18.58        20.71        19.10        12.89        16.11        13.18 
TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       11.84         0.07        64.08        51.78         1.22        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP 
       13.74         4.21         2.89        39.85        37.22        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE 
       14.73        29.75        22.78         3.65        16.80         0.43 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07         3.72         8.58        11.18         0.20 

  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                         0.26                          0.03 
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                       151.27                        174.08 
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                       23.635                        18.840 
[1] "0.3 - 151.3 (23.6)" "0.0 - 174.1 (18.8)"
[1] "hr=" "1.6"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(3Q11.1) MUTATED         0       10       26        1         9
  DEL PEAK 10(3Q11.1) WILD-TYPE       2       77      125        1        54
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(3Q11.1) MUTATED          14         1         11          4
  DEL PEAK 10(3Q11.1) WILD-TYPE        78         2         51         17
                               vv
clus                            STAGE IV
  DEL PEAK 10(3Q11.1) MUTATED          2
  DEL PEAK 10(3Q11.1) WILD-TYPE        5
D40V3, multiclass
            clus
vv           DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                            10                            77
  STAGE IB                            26                           125
  STAGE II                             1                             1
  STAGE IIA                            9                            54
  STAGE IIB                           14                            78
  STAGE III                            1                             2
  STAGE IIIA                          11                            51
  STAGE IIIB                           4                            17
  STAGE IV                             2                             5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 10(3Q11.1) MUTATED    16  43  15   4
  DEL PEAK 10(3Q11.1) WILD-TYPE  95 247  54  19
D40V4, multiclass
    clus
vv   DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  T1                          16                            95
  T2                          43                           247
  T3                          15                            54
  T4                           4                            19
[1] 4 2
[1] TRUE
[1] "dimension of 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(3Q11.1) MUTATED    48  20   8   1
  DEL PEAK 10(3Q11.1) WILD-TYPE 264 111  31   4
D40V5, multiclass
    clus
vv   DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  N0                          48                           264
  N1                          20                           111
  N2                           8                            31
  N3                           1                             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"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(3Q11.1) MUTATED    59   2
  DEL PEAK 10(3Q11.1) WILD-TYPE 345   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3Q11.1) MUTATED     59    2
  DEL PEAK 10(3Q11.1) WILD-TYPE  345    5
   clus
vv  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  0                          59                           345
  1                           2                             5
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(3Q11.1) MUTATED    19  59
  DEL PEAK 10(3Q11.1) WILD-TYPE 108 307
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3Q11.1) MUTATED     19   59
  DEL PEAK 10(3Q11.1) WILD-TYPE  108  307
        clus
vv       DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  FEMALE                          19                           108
  MALE                            59                           307
[1] 2 2
[1] FALSE
D40V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(3Q11.1) MUTATED                                       0
  DEL PEAK 10(3Q11.1) WILD-TYPE                                    15
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(3Q11.1) MUTATED                                         0
  DEL PEAK 10(3Q11.1) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 10(3Q11.1) MUTATED                                        2
  DEL PEAK 10(3Q11.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 10(3Q11.1) MUTATED                                         0
  DEL PEAK 10(3Q11.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(3Q11.1) MUTATED                                                            76
  DEL PEAK 10(3Q11.1) WILD-TYPE                                                         394
D40V9, multiclass
                                                             clus
vv                                                            DEL PEAK 10(3Q11.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 0
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          76
                                                             clus
vv                                                            DEL PEAK 10(3Q11.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  15
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           394
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, binary
                               cls
clus                              0   1
  DEL PEAK 10(3Q11.1) MUTATED     1  77
  DEL PEAK 10(3Q11.1) WILD-TYPE  12 403
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3Q11.1) MUTATED      1   77
  DEL PEAK 10(3Q11.1) WILD-TYPE   12  403
     clus
vv    DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  NO                            1                            12
  YES                          77                           403
[1] 2 2
[1] FALSE
D40V11, continuous
D40V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(3Q11.1) MUTATED    62   1   1   2
  DEL PEAK 10(3Q11.1) WILD-TYPE 332  11   3  20
D40V13, multiclass
    clus
vv   DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  R0                          62                           332
  R1                           1                            11
  R2                           1                             3
  RX                           2                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(3Q11.1) MUTATED       1                         5    52
  DEL PEAK 10(3Q11.1) WILD-TYPE     8                        26   288
D40V14, multiclass
                           clus
vv                          DEL PEAK 10(3Q11.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              52
                           clus
vv                          DEL PEAK 10(3Q11.1) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            26
  WHITE                                               288
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V15, binary
                               cls
clus                              0   1
  DEL PEAK 10(3Q11.1) MUTATED     4  51
  DEL PEAK 10(3Q11.1) WILD-TYPE   4 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3Q11.1) MUTATED      4   51
  DEL PEAK 10(3Q11.1) WILD-TYPE    4  258
                        clus
vv                       DEL PEAK 10(3Q11.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          51
                        clus
vv                       DEL PEAK 10(3Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           258
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 11(4P15.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4P15.2) MUTATED   180 120
  DEL PEAK 11(4P15.2) WILD-TYPE 101  76
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          300                           177 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          120                            76 
$`DEL PEAK 11(4P15.2) MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
        7.46       117.57        11.34        92.15        31.99        36.07 
TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 
       86.96         2.79        49.94       119.54        46.88        60.89 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
       34.78        31.73       122.43         9.34       119.80        43.23 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
       31.63        33.93        10.82        21.99         7.33        14.93 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
        1.74        14.10        35.08        48.33        24.13        38.17 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 
       13.12        32.02        19.30         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 
       64.93        63.55        14.63        44.25        54.28        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4532 TCGA-33-4533 
       18.84        30.12        62.86        56.32         7.63       133.74 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       98.01        79.53       103.53       151.27        14.07        54.44 
TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB 
        1.55        19.76        27.02         4.70        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2605 
      110.99        44.19       118.36        27.16        61.61        28.96 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       65.23        67.79         9.07        16.93        30.94        18.15 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 
        4.96         1.12        26.43         3.95         0.43         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        6.81         0.39         3.39        74.07        44.75        68.58 
TCGA-39-5027 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 
       60.79        27.39        15.58        35.70        17.06        22.49 
TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.02        27.91        12.36         5.46         3.81        19.59 
TCGA-43-7657 TCGA-43-8115 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V 
        7.76        13.38         2.93        11.61        14.20        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
        9.99        10.65        13.91        29.95         5.46        30.35 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 
        8.75        27.45        28.96        18.25         2.04         0.99 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 
        0.43         0.99         1.45         0.85         6.51         3.48 
TCGA-56-8308 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK 
       17.00        10.36        20.94        19.23        13.32        18.74 
TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8392 TCGA-58-8393 
        0.13         2.76         0.03        13.25        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 
       85.12        34.36        56.65        35.24        21.11         3.58 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       10.22        96.82        92.71        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 
       66.54        41.42         9.01        56.91        42.64         3.19 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB 
       32.32        29.85        35.90        23.57        11.77       102.67 
TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MY 
       66.61        59.97        45.57        89.29        78.28        34.59 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 
       16.96        43.10         2.01        21.07         1.02         2.01 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2771 
       21.01        25.05         2.01         1.02         2.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 
        3.02         2.01        19.00        12.03         3.98        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
        1.97        25.97         5.03        30.02        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59J TCGA-77-6845 TCGA-77-7139 
       49.05         2.73         6.64        14.73        23.28        89.98 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 
       42.28        70.13       106.95        46.78        15.75        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 
       37.81        82.92        53.92        17.72       104.09        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 
        6.97         9.63        54.41        65.49        35.90       117.57 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
        5.92        42.41        42.08        30.81        27.62        38.86 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       11.97        12.99        36.53        34.95        31.30        32.91 
TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 
        1.15        25.15        19.04        24.13        14.07        16.87 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       34.52        10.09        13.22        22.45        16.77         5.29 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 
        3.09        32.71         7.76        14.63         0.10        15.62 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L 
       25.68        19.33        19.73        15.85        14.96        12.39 
TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        3.65         9.50        14.07        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7557 
        2.70         3.48         4.01         5.26         2.30         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 TCGA-94-A5I6 
       11.70         4.01         5.03        26.63        16.14        17.69 
TCGA-96-A4JK TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-A538 TCGA-98-A539 
       19.36         8.42         2.76        30.81        27.16         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 
       18.15         2.01        18.58        20.71        12.89        16.11 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       13.41        11.84         0.07        64.08         4.54        51.78 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN 
       45.37        13.74         4.21         2.89        39.85        37.22 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CT 
       30.58        24.00        14.73        29.75        83.57        65.49 
TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        3.65        12.72        43.89         8.58        11.18         0.20 

$`DEL PEAK 11(4P15.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3419 
       12.20        75.75        79.46         4.80        23.54         1.64 
TCGA-18-4083 TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 
        6.18       154.32        27.19        99.16        70.16        15.58 
TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 
       88.11        41.69        32.19         4.31        64.21        27.02 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4596 TCGA-22-4601 TCGA-22-5478 TCGA-22-5480 
       48.82        20.48         0.56        34.75         0.79        71.34 
TCGA-22-5481 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4566 TCGA-33-A5GW TCGA-34-2596 
       79.20        16.64        22.06       174.08         0.30         2.63 
TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
       31.50        32.88        31.27        56.38        23.24        12.00 
TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       27.19         4.04        20.91         0.39         6.58         8.12 
TCGA-37-4132 TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
        7.46        47.80        55.20        70.03         1.71        24.33 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 
        1.94        36.39        35.64        17.88        40.21        38.66 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 TCGA-43-6770 TCGA-43-7658 TCGA-43-8116 
       33.11        18.38        24.89        21.47        66.51        11.77 
TCGA-43-A475 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-56-5897 TCGA-56-6546 
        9.73         0.39         0.39        28.34         0.10         0.62 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
        1.32         0.10        17.49        26.89        14.07         1.35 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 
       16.77         1.81        22.75         1.18         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
       15.81        17.85        21.04         0.26        13.55        29.95 
TCGA-58-8391 TCGA-58-A46N TCGA-60-2697 TCGA-60-2704 TCGA-60-2714 TCGA-60-2715 
       71.24        29.92        12.23        37.94        50.33        35.34 
TCGA-60-2716 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN 
       48.49        26.83        70.62        58.65        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2744 
       25.28        16.37        25.41        36.16        53.88         0.99 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 TCGA-66-2768 TCGA-66-2769 
        0.92         0.99        43.99         0.99         2.01         7.07 
TCGA-66-2770 TCGA-66-2782 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
       23.01        12.00        40.01        22.98         4.04        22.98 
TCGA-66-2793 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 
       10.06         6.94         8.02        13.35        16.18        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 TCGA-77-7338 
       73.12        75.09        11.18        20.78         0.49         0.16 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8140 TCGA-77-8143 
        6.51        86.76        12.59        39.09        11.54        26.40 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-85-6175 TCGA-85-6798 
        0.33       126.18       132.36        22.29         9.67         6.41 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8070 TCGA-85-8287 TCGA-85-8355 
        1.38        29.95        18.94        31.56         0.76         2.01 
TCGA-85-8479 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA 
        0.72        13.94        12.59        17.72        14.96        24.36 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A513 TCGA-90-6837 TCGA-90-7767 
       18.18        12.56        16.21         0.79        24.92         2.93 
TCGA-90-7769 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
       11.77        21.04        14.14        49.87        57.07        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-8022 TCGA-98-8023 TCGA-98-A53C TCGA-98-A53D 
       17.46        16.57        30.67        21.34        27.02        21.21 
TCGA-98-A53H TCGA-J1-A4AH TCGA-LA-A446 TCGA-NC-A5HH TCGA-NC-A5HT TCGA-NK-A5D1 
       20.32        19.10        13.18         1.22        22.78        16.80 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
        0.43        33.07         3.72 

  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                         0.03                          0.10 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                       151.27                        174.08 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                       19.315                        18.380 
[1] "0.0 - 151.3 (19.3)" "0.1 - 174.1 (18.4)"
[1] "hr=" "1.2"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(4P15.2) MUTATED         1       50      102        2        44
  DEL PEAK 11(4P15.2) WILD-TYPE       1       37       49        0        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4P15.2) MUTATED          52         2         40         13
  DEL PEAK 11(4P15.2) WILD-TYPE        40         1         22          8
                               vv
clus                            STAGE IV
  DEL PEAK 11(4P15.2) MUTATED          4
  DEL PEAK 11(4P15.2) WILD-TYPE        3
D41V3, multiclass
            clus
vv           DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            50                            37
  STAGE IB                           102                            49
  STAGE II                             2                             0
  STAGE IIA                           44                            19
  STAGE IIB                           52                            40
  STAGE III                            2                             1
  STAGE IIIA                          40                            22
  STAGE IIIB                          13                             8
  STAGE IV                             4                             3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 11(4P15.2) MUTATED    64 193  44  11
  DEL PEAK 11(4P15.2) WILD-TYPE  47  97  25  12
D41V4, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  T1                          64                            47
  T2                         193                            97
  T3                          44                            25
  T4                          11                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 11(4P15.2) MUTATED   193  84  27   4
  DEL PEAK 11(4P15.2) WILD-TYPE 119  47  12   1
D41V5, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  N0                         193                           119
  N1                          84                            47
  N2                          27                            12
  N3                           4                             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"
D41V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P15.2) MUTATED   255   4
  DEL PEAK 11(4P15.2) WILD-TYPE 149   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED    255    4
  DEL PEAK 11(4P15.2) WILD-TYPE  149    3
   clus
vv  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  0                         255                           149
  1                           4                             3
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P15.2) MUTATED    76 236
  DEL PEAK 11(4P15.2) WILD-TYPE  51 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     76  236
  DEL PEAK 11(4P15.2) WILD-TYPE   51  130
        clus
vv       DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  FEMALE                          76                            51
  MALE                           236                           130
[1] 2 2
[1] FALSE
D41V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(4P15.2) MUTATED                                       8
  DEL PEAK 11(4P15.2) WILD-TYPE                                     7
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(4P15.2) MUTATED                                         0
  DEL PEAK 11(4P15.2) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 11(4P15.2) MUTATED                                        2
  DEL PEAK 11(4P15.2) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 11(4P15.2) MUTATED                                         1
  DEL PEAK 11(4P15.2) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(4P15.2) MUTATED                                                           301
  DEL PEAK 11(4P15.2) WILD-TYPE                                                         169
D41V9, multiclass
                                                             clus
vv                                                            DEL PEAK 11(4P15.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         301
                                                             clus
vv                                                            DEL PEAK 11(4P15.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           169
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P15.2) MUTATED    11 301
  DEL PEAK 11(4P15.2) WILD-TYPE   2 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     11  301
  DEL PEAK 11(4P15.2) WILD-TYPE    2  179
     clus
vv    DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  NO                           11                             2
  YES                         301                           179
[1] 2 2
[1] FALSE
D41V11, continuous
D41V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4P15.2) MUTATED   248   7   4  15
  DEL PEAK 11(4P15.2) WILD-TYPE 146   5   0   7
D41V13, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  R0                         248                           146
  R1                           7                             5
  R2                           4                             0
  RX                          15                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4P15.2) MUTATED       3                        23   215
  DEL PEAK 11(4P15.2) WILD-TYPE     6                         8   125
D41V14, multiclass
                           clus
vv                          DEL PEAK 11(4P15.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          23
  WHITE                                             215
                           clus
vv                          DEL PEAK 11(4P15.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               125
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V15, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P15.2) MUTATED     5 189
  DEL PEAK 11(4P15.2) WILD-TYPE   3 120
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED      5  189
  DEL PEAK 11(4P15.2) WILD-TYPE    3  120
                        clus
vv                       DEL PEAK 11(4P15.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         189
                        clus
vv                       DEL PEAK 11(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           120
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 12(4Q22.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(4Q22.1) MUTATED   162 108
  DEL PEAK 12(4Q22.1) WILD-TYPE 119  88
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          270                           207 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          108                            88 
$`DEL PEAK 12(4Q22.1) MUTATED`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-4083 TCGA-18-4086 
        7.46       117.57        11.34        92.15         6.18         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
      154.32        49.94       119.54        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
       60.89        34.78        31.73       122.43       119.80        43.23 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1000 TCGA-22-1011 TCGA-22-1012 
       33.93        10.82         7.33        14.93         1.74        14.10 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       48.33        24.13        38.17        13.12        32.02        19.30 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 
       11.77        31.73        64.93        63.55        14.63        54.28 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4532 TCGA-33-4533 
       11.74        18.84        30.12        62.86         7.63       133.74 
TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       98.01       174.08       103.53       151.27        14.07        54.44 
TCGA-33-4589 TCGA-33-6737 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASJ TCGA-33-AASL 
        1.55        19.76         4.70        36.62       118.36        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-2609 TCGA-34-5236 TCGA-34-5241 
        2.63        61.61        28.96        31.27         9.07        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-37-3783 TCGA-37-3789 
       30.94        18.15         4.96         1.12         3.95         0.43 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 
        7.82         6.81         0.39         3.39        44.75        68.58 
TCGA-39-5027 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 
       60.79        27.39        36.39        15.58        35.64        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 
       40.21        22.49        27.02        33.11        12.36        21.47 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-A474 
        5.46        19.59         7.76        66.51        13.38        11.61 
TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 
       14.20        12.03         9.99        13.91         0.39        29.95 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 
        5.46        30.35         8.75        28.96        18.25         2.04 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 
        0.99         0.43         0.99         0.85         6.51         3.48 
TCGA-56-8308 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR 
       17.00        10.36        20.94        13.32        21.04         0.13 
TCGA-56-A62T TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
        2.76        29.95        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 TCGA-60-2706 TCGA-60-2707 
       56.65        35.24        21.11         3.58        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
       80.45        49.48        66.54         9.01        56.91        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB 
       42.64         3.19        35.90        23.57        11.77       102.67 
TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       70.62        59.97        45.57        89.29        78.28        16.37 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
       53.88        16.96        43.10         2.01        21.07         1.02 
TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2771 
        2.01        43.99        21.01         0.99         2.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 
        3.02         2.01        19.00        12.03         3.98         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 
       25.97        40.01         5.03        30.02        10.06         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J 
       49.05         2.73         6.64         6.94        16.18        14.73 
TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       73.12        89.98         0.49        42.28        70.13       106.95 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       46.78        15.75         6.51        53.95        37.81        82.92 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 
       53.92        39.09        17.72        27.39         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
       65.49        35.90        22.29         5.92        42.41        42.08 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
       30.81        27.62        38.86        11.97         6.41        36.53 
TCGA-85-7699 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8276 TCGA-85-8277 
       32.91        25.15        19.04        24.13        34.52        10.09 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 
        0.76        22.45         5.29         3.09         0.72        14.63 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 
        0.10        15.62        19.33        18.18        19.73        15.85 
TCGA-85-A53L TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       12.39        11.77        14.07        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7557 
        2.70         3.48         4.01         5.26         2.30         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-A5I6 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8020 
       11.70         4.01        17.69        19.36         8.42         2.76 
TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53B TCGA-98-A53I 
       30.81        30.67        27.16         3.88         2.01        18.58 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
       20.71        19.10        16.11        13.41        11.84         0.07 
TCGA-NC-A5HF TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HP 
        4.54        45.37         4.21         2.89        39.85        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX 
       14.73        29.75        22.78        83.57        65.49         3.65 
TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       16.80         3.72        12.72        43.89         8.58         0.20 

$`DEL PEAK 12(4Q22.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
       12.20        75.75        79.46         4.80        23.54        31.99 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-5595 TCGA-21-1078 TCGA-21-1081 
       36.07         1.64        86.96        27.19        15.58         9.34 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1002 
       31.63        88.11        41.69        32.19        21.99         4.31 
TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 
       64.21        27.02        48.82        20.48        35.08         0.56 
TCGA-22-4601 TCGA-22-4609 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
       34.75         9.57        44.25         0.79        71.34        79.20 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4547 TCGA-33-6738 TCGA-33-A5GW 
       56.32        16.64        22.06        79.53        27.02         0.30 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 
        6.94       110.99        44.19        31.50        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 TCGA-34-8455 
       67.79        56.38        23.24        12.00        27.19         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       26.43        20.91         0.39         6.58         8.12         7.46 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
       47.80        74.07        55.20        70.03         1.71        24.33 
TCGA-39-5030 TCGA-39-5037 TCGA-39-5039 TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 
        1.94        35.70        17.88        38.66        18.38        27.91 
TCGA-43-6647 TCGA-43-6773 TCGA-43-8116 TCGA-43-8118 TCGA-43-A475 TCGA-46-6025 
       24.89         3.81        11.77         2.93         9.73        10.65 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 TCGA-56-6546 TCGA-56-7579 
        0.39        28.34        27.45         0.10         0.62         1.45 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
        1.32         0.10        17.49        26.89        14.07         1.35 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 
       16.77         1.81        22.75         1.18         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 
       15.81        19.23        17.85        18.74         0.26         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 
       13.25        13.55        71.24        29.92        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2711 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 
       96.82        37.94        41.42        35.34        48.49        32.32 
TCGA-60-2722 TCGA-60-2725 TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN 
       29.85        26.83        66.61        58.65        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2744 TCGA-66-2755 
       25.28        25.41        36.16        34.59         0.99         0.92 
TCGA-66-2756 TCGA-66-2759 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
        0.99        25.05         1.02         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2782 TCGA-66-2783 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
       23.01        12.00        24.95        22.98         4.04        22.98 
TCGA-66-2794 TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 
       54.08         8.02        13.35        29.56        75.09        23.28 
TCGA-77-7138 TCGA-77-7140 TCGA-77-7338 TCGA-77-8008 TCGA-77-8131 TCGA-77-8139 
       11.18        20.78         0.16        86.76        12.59       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       11.54        26.40         6.97         0.33       126.18       132.36 
TCGA-77-A5G3 TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
      117.57         9.67        12.99        34.95        31.30         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
        1.15        29.95        18.94        31.56        14.07        16.87 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 
       13.22        16.77        32.71         2.01         7.76        13.94 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50M 
       12.59        25.68        17.72        14.96        24.36        12.56 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
       16.21        14.96         0.79         3.65        24.92         9.50 
TCGA-90-7767 TCGA-94-7033 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 
        2.93        21.04         5.03        26.63        14.14        16.14 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8023 
       49.87        57.07        18.31        17.46        16.57        21.34 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A446 
       18.15        27.02        21.21        20.32        12.89        13.18 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HN TCGA-NC-A5HO 
       64.08        51.78         1.22        13.74        37.22        30.58 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A5IB 
        0.43        33.07        11.18 

  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                       174.08                        132.36 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                        19.07                         19.23 
[1] "0.1 - 174.1 (19.1)" "0.0 - 132.4 (19.2)"
[1] "hr=" "1.2"
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(4Q22.1) MUTATED         1       43      102        2        33
  DEL PEAK 12(4Q22.1) WILD-TYPE       1       44       49        0        30
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q22.1) MUTATED          44         2         39         10
  DEL PEAK 12(4Q22.1) WILD-TYPE        48         1         23         11
                               vv
clus                            STAGE IV
  DEL PEAK 12(4Q22.1) MUTATED          2
  DEL PEAK 12(4Q22.1) WILD-TYPE        5
D42V3, multiclass
            clus
vv           DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            43                            44
  STAGE IB                           102                            49
  STAGE II                             2                             0
  STAGE IIA                           33                            30
  STAGE IIB                           44                            48
  STAGE III                            2                             1
  STAGE IIIA                          39                            23
  STAGE IIIB                          10                            11
  STAGE IV                             2                             5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 12(4Q22.1) MUTATED    53 177  40  10
  DEL PEAK 12(4Q22.1) WILD-TYPE  58 113  29  13
D42V4, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  T1                          53                            58
  T2                         177                           113
  T3                          40                            29
  T4                          10                            13
[1] 4 2
[1] TRUE
[1] "dimension of 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(4Q22.1) MUTATED   184  69  23   2
  DEL PEAK 12(4Q22.1) WILD-TYPE 128  62  16   3
D42V5, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  N0                         184                           128
  N1                          69                            62
  N2                          23                            16
  N3                           2                             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"
D42V6, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED   227   2
  DEL PEAK 12(4Q22.1) WILD-TYPE 177   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED    227    2
  DEL PEAK 12(4Q22.1) WILD-TYPE  177    5
   clus
vv  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  0                         227                           177
  1                           2                             5
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED    77 203
  DEL PEAK 12(4Q22.1) WILD-TYPE  50 163
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     77  203
  DEL PEAK 12(4Q22.1) WILD-TYPE   50  163
        clus
vv       DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  FEMALE                          77                            50
  MALE                           203                           163
[1] 2 2
[1] FALSE
D42V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(4Q22.1) MUTATED                                       7
  DEL PEAK 12(4Q22.1) WILD-TYPE                                     8
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(4Q22.1) MUTATED                                         0
  DEL PEAK 12(4Q22.1) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 12(4Q22.1) MUTATED                                        2
  DEL PEAK 12(4Q22.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 12(4Q22.1) MUTATED                                         1
  DEL PEAK 12(4Q22.1) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(4Q22.1) MUTATED                                                           270
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                         200
D42V9, multiclass
                                                             clus
vv                                                            DEL PEAK 12(4Q22.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         270
                                                             clus
vv                                                            DEL PEAK 12(4Q22.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           200
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED    11 269
  DEL PEAK 12(4Q22.1) WILD-TYPE   2 211
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     11  269
  DEL PEAK 12(4Q22.1) WILD-TYPE    2  211
     clus
vv    DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  NO                           11                             2
  YES                         269                           211
[1] 2 2
[1] FALSE
D42V11, continuous
D42V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(4Q22.1) MUTATED   224   5   3  14
  DEL PEAK 12(4Q22.1) WILD-TYPE 170   7   1   8
D42V13, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  R0                         224                           170
  R1                           5                             7
  R2                           3                             1
  RX                          14                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(4Q22.1) MUTATED       4                        22   188
  DEL PEAK 12(4Q22.1) WILD-TYPE     5                         9   152
D42V14, multiclass
                           clus
vv                          DEL PEAK 12(4Q22.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          22
  WHITE                                             188
                           clus
vv                          DEL PEAK 12(4Q22.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                               152
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V15, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED     4 173
  DEL PEAK 12(4Q22.1) WILD-TYPE   4 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED      4  173
  DEL PEAK 12(4Q22.1) WILD-TYPE    4  136
                        clus
vv                       DEL PEAK 12(4Q22.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         173
                        clus
vv                       DEL PEAK 12(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           136
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 13(4Q32.3) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(4Q32.3) MUTATED   188 124
  DEL PEAK 13(4Q32.3) WILD-TYPE  93  72
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                          312                           165 
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                          124                            72 
$`DEL PEAK 13(4Q32.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 
       12.20         7.46       117.57        11.34        92.15        36.07 
TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        6.18         2.79        49.94       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 
       70.16        60.89        34.78        31.73       122.43       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1000 
       43.23        31.63        33.93        10.82         7.33        14.93 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
        1.74        14.10        27.02        48.33        24.13        38.17 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 
       13.12        32.02        19.30        11.77        64.93        63.55 
TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
       14.63        54.28        11.74        18.84        30.12        62.86 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 
       56.32        22.06         7.63       133.74        98.01       174.08 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
      103.53       151.27        14.07        54.44         1.55        19.76 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL 
        4.70         0.30        36.62         6.94       118.36        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-5236 TCGA-34-5241 
        2.63        61.61        31.50        28.96         9.07        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-A5IX TCGA-37-4129 
       30.94        18.15         4.96         1.12        20.91         6.58 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        8.12         7.82         6.81         0.39         3.39        47.80 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       44.75        68.58        60.79        36.39        15.58        35.64 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 
       35.70        17.06        40.21        22.49        27.02        33.11 
TCGA-43-6143 TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       12.36         5.46         3.81         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
       11.77         2.93        11.61        14.20        12.03         9.99 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       10.65        13.91         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 
       30.35         8.75        28.96        18.25         2.04         0.99 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 TCGA-56-8308 
        0.43         0.99         0.85         6.51         3.48        17.00 
TCGA-56-8503 TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ 
        1.35        10.36        15.81        20.94        13.32        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       18.74         0.13        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 
       85.12        34.36        56.65        35.24        21.11         3.58 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       10.22        96.82        37.94        21.93        80.45        49.48 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
       41.42         9.01        56.91        50.33        42.64         3.19 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-63-A5MB TCGA-63-A5MG 
       32.32        29.85        35.90        23.57       102.67        70.62 
TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       66.61        59.97        45.57        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       16.37        25.41        53.88        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 
        2.01        21.07         1.02         2.01         0.99        43.99 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2771 TCGA-66-2773 
       21.01         0.99         2.01         1.02        19.00         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 
        2.01        19.00        12.03         3.98         1.97        25.97 
TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       40.01         5.03        30.02        10.06        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I 
       49.05         2.73         6.64         6.94         8.02        16.18 
TCGA-68-A59J TCGA-77-6843 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
       14.73        73.12        89.98        20.78         0.49        42.28 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        0.16        46.78        15.75         6.51        86.76        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 
       37.81        82.92        53.92        39.09        17.72        11.54 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
       27.39         9.63        54.41        65.49        35.90         0.33 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
      117.57        22.29         5.92        42.41        42.08        30.81 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       27.62        38.86        11.97        12.99         6.41        36.53 
TCGA-85-7699 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
       32.91        25.15        19.04        24.13        31.56        16.87 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 
       10.09         0.76        22.45         5.29         3.09         0.72 
TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
       14.63         0.10        15.62        25.68        19.33        17.72 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L 
       18.18        19.73        16.21        15.85        14.96        12.39 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
        2.93        11.77        14.07        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 
        2.70         4.01         5.26         2.30        21.04         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
       11.70         4.01         5.03        14.14        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 
       49.87        57.07        19.36         8.42         2.76        30.81 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I 
       30.67        27.16         3.88        18.15         2.01        18.58 
TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
       20.71        16.11        13.18        13.41        11.84         0.07 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
       64.08         4.54        45.37         4.21         2.89        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR 
       37.22        30.58        24.00        14.73        29.75        83.57 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       65.49         3.65        12.72        43.89         8.58         0.20 

$`DEL PEAK 13(4Q32.3) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 TCGA-18-3419 
       75.75        79.46         4.80        23.54        31.99         1.64 
TCGA-18-3421 TCGA-18-4721 TCGA-18-5595 TCGA-21-1078 TCGA-21-1081 TCGA-21-5783 
       86.96       154.32        27.19        15.58         9.34        88.11 
TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1017 
       41.69        32.19        21.99         4.31        64.21        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-4609 TCGA-22-5471 
       20.48        35.08         0.56        34.75         9.57        31.73 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 TCGA-33-4547 
       44.25         0.79        71.34        79.20        16.64        79.53 
TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
       27.02       110.99        44.19        32.88        31.27        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 TCGA-34-8455 
       67.79        56.38        23.24        12.00        27.19         4.04 
TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4132 TCGA-39-5016 
       26.43         3.95         0.43         0.39         7.46        74.07 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       55.20        70.03         1.71        24.33         1.94        27.39 
TCGA-39-5039 TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
       17.88        38.66        18.38        27.91        24.89        21.47 
TCGA-43-7656 TCGA-43-A475 TCGA-51-4080 TCGA-52-7812 TCGA-56-5897 TCGA-56-6546 
       19.59         9.73         0.39        27.45         0.10         0.62 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8309 
        1.45         1.32         0.10        17.49        26.89        14.07 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 
       16.77         1.81        22.75         1.18         9.93        20.25 
TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       19.23        17.85         0.26         2.76         0.03        13.25 
TCGA-58-8388 TCGA-58-A46N TCGA-60-2697 TCGA-60-2706 TCGA-60-2710 TCGA-60-2715 
       13.55        29.92        12.23        92.71        66.54        35.34 
TCGA-60-2716 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN 
       48.49        26.83        11.77        58.65        14.99        11.34 
TCGA-63-A5MV TCGA-66-2744 TCGA-66-2755 TCGA-66-2759 TCGA-66-2767 TCGA-66-2768 
       36.16         0.99         0.92        25.05         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2782 TCGA-66-2783 TCGA-66-2788 TCGA-66-2789 
        7.07        23.01        12.00        24.95        22.98         4.04 
TCGA-66-2790 TCGA-68-8251 TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       22.98        13.35        29.56        75.09        23.28        11.18 
TCGA-77-7335 TCGA-77-7337 TCGA-77-8131 TCGA-77-8139 TCGA-77-8143 TCGA-77-8145 
       70.13       106.95        12.59       104.09        26.40         6.97 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-85-6175 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
      126.18       132.36         9.67        34.95        31.30         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8071 TCGA-85-8276 TCGA-85-8288 
        1.15        29.95        18.94        14.07        34.52        13.22 
TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 
       16.77        32.71         2.01         7.76        13.94        12.59 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50M TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 
       14.96        24.36        12.56         0.79         3.65        24.92 
TCGA-90-7766 TCGA-92-7341 TCGA-94-8491 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
        9.50         3.48        26.63        18.31        17.46        16.57 
TCGA-98-8023 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH TCGA-L3-A4E7 
       21.34        27.02        21.21        20.32        19.10        12.89 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HT TCGA-NK-A5D1 TCGA-NK-A7XE 
       51.78         1.22        13.74        22.78        16.80         0.43 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A5IB 
       33.07         3.72        11.18 

  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                       174.08                        154.32 
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                        19.00                         19.59 
[1] "0.1 - 174.1 (19.0)" "0.0 - 154.3 (19.6)"
[1] "hr=" "1.1"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(4Q32.3) MUTATED         1       53      114        2        32
  DEL PEAK 13(4Q32.3) WILD-TYPE       1       34       37        0        31
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(4Q32.3) MUTATED          62         1         40         11
  DEL PEAK 13(4Q32.3) WILD-TYPE        30         2         22         10
                               vv
clus                            STAGE IV
  DEL PEAK 13(4Q32.3) MUTATED          3
  DEL PEAK 13(4Q32.3) WILD-TYPE        4
D43V3, multiclass
            clus
vv           DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            53                            34
  STAGE IB                           114                            37
  STAGE II                             2                             0
  STAGE IIA                           32                            31
  STAGE IIB                           62                            30
  STAGE III                            1                             2
  STAGE IIIA                          40                            22
  STAGE IIIB                          11                            10
  STAGE IV                             3                             4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 13(4Q32.3) MUTATED    64 204  42  11
  DEL PEAK 13(4Q32.3) WILD-TYPE  47  86  27  12
D43V4, multiclass
    clus
vv   DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  T1                          64                            47
  T2                         204                            86
  T3                          42                            27
  T4                          11                            12
[1] 4 2
[1] TRUE
[1] "dimension of 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(4Q32.3) MUTATED   210  82  24   2
  DEL PEAK 13(4Q32.3) WILD-TYPE 102  49  15   3
D43V5, multiclass
    clus
vv   DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  N0                         210                           102
  N1                          82                            49
  N2                          24                            15
  N3                           2                             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"
D43V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q32.3) MUTATED   263   3
  DEL PEAK 13(4Q32.3) WILD-TYPE 141   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q32.3) MUTATED    263    3
  DEL PEAK 13(4Q32.3) WILD-TYPE  141    4
   clus
vv  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  0                         263                           141
  1                           3                             4
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q32.3) MUTATED    87 234
  DEL PEAK 13(4Q32.3) WILD-TYPE  40 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q32.3) MUTATED     87  234
  DEL PEAK 13(4Q32.3) WILD-TYPE   40  132
        clus
vv       DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  FEMALE                          87                            40
  MALE                           234                           132
[1] 2 2
[1] FALSE
D43V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(4Q32.3) MUTATED                                       6
  DEL PEAK 13(4Q32.3) WILD-TYPE                                     9
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(4Q32.3) MUTATED                                         0
  DEL PEAK 13(4Q32.3) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 13(4Q32.3) MUTATED                                        2
  DEL PEAK 13(4Q32.3) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 13(4Q32.3) MUTATED                                         1
  DEL PEAK 13(4Q32.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(4Q32.3) MUTATED                                                           312
  DEL PEAK 13(4Q32.3) WILD-TYPE                                                         158
D43V9, multiclass
                                                             clus
vv                                                            DEL PEAK 13(4Q32.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         312
                                                             clus
vv                                                            DEL PEAK 13(4Q32.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           158
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q32.3) MUTATED    11 310
  DEL PEAK 13(4Q32.3) WILD-TYPE   2 170
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q32.3) MUTATED     11  310
  DEL PEAK 13(4Q32.3) WILD-TYPE    2  170
     clus
vv    DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  NO                           11                             2
  YES                         310                           170
[1] 2 2
[1] FALSE
D43V11, continuous
D43V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(4Q32.3) MUTATED   260   6   2  15
  DEL PEAK 13(4Q32.3) WILD-TYPE 134   6   2   7
D43V13, multiclass
    clus
vv   DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  R0                         260                           134
  R1                           6                             6
  R2                           2                             2
  RX                          15                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(4Q32.3) MUTATED       4                        22   219
  DEL PEAK 13(4Q32.3) WILD-TYPE     5                         9   121
D43V14, multiclass
                           clus
vv                          DEL PEAK 13(4Q32.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          22
  WHITE                                             219
                           clus
vv                          DEL PEAK 13(4Q32.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                               121
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V15, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q32.3) MUTATED     5 199
  DEL PEAK 13(4Q32.3) WILD-TYPE   3 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q32.3) MUTATED      5  199
  DEL PEAK 13(4Q32.3) WILD-TYPE    3  110
                        clus
vv                       DEL PEAK 13(4Q32.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         199
                        clus
vv                       DEL PEAK 13(4Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           110
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 14(4Q35.2) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(4Q35.2) MUTATED   186 129
  DEL PEAK 14(4Q35.2) WILD-TYPE  95  67
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          315                           162 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          129                            67 
$`DEL PEAK 14(4Q35.2) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3411 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
       12.20         7.46       117.57        92.15        31.99        36.07 
TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        6.18         2.79        49.94       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 
       70.16        60.89        34.78        31.73       122.43       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1000 
       43.23        31.63        33.93        10.82         7.33        14.93 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
        1.74        14.10        27.02        48.33        24.13        38.17 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 
       13.12        32.02        19.30        11.77        64.93        63.55 
TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
       14.63        54.28        11.74        18.84        30.12        62.86 
TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
       56.32        22.06         7.63       133.74        98.01        79.53 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
      174.08       103.53       151.27        14.07        54.44         1.55 
TCGA-33-6737 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI 
       19.76         4.70         0.30        36.62         6.94        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
      118.36        27.16         2.63        61.61        31.50        28.96 
TCGA-34-2608 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 
       32.88         9.07        16.93        30.94         4.96         1.12 
TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 
       20.91         0.43         0.39         6.58         8.12         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
        6.81         0.39         3.39        47.80        44.75        68.58 
TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
       60.79        36.39        15.58        35.64        35.70        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 
       40.21        22.49        27.02        33.11        12.36        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       21.47         5.46         3.81         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
       11.77         2.93        11.61         9.73        14.20        12.03 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       10.65        13.91         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 
       30.35         8.75        28.96        18.25         0.99         0.43 
TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 TCGA-56-8308 TCGA-56-8503 
        0.99         0.85         6.51         3.48        17.00         1.35 
TCGA-56-8622 TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ 
        1.81        10.36        15.81        20.94        13.32        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       18.74         0.13        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 
       85.12        34.36        56.65        35.24        21.11         3.58 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       10.22        96.82        37.94        21.93        80.45        49.48 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
        9.01        56.91        50.33        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH 
       35.90        23.57        11.77       102.67        70.62        66.61 
TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW 
       45.57        25.28        89.29        78.28        16.37        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
       34.59        16.96        43.10         2.01        21.07         1.02 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 
        2.01         0.99        43.99        21.01         0.99         2.01 
TCGA-66-2766 TCGA-66-2769 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        1.02         7.07         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2785 TCGA-66-2787 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 
        3.98         1.97        40.01         4.04         5.03        30.02 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       10.06        54.08         4.01        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 
        6.94         8.02        16.18        14.73        73.12        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
       11.18        89.98        20.78         0.49        42.28         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
       46.78        15.75         6.51        86.76        53.95        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       82.92        53.92        39.09        17.72       104.09        11.54 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
       27.39         9.63        54.41        65.49        35.90         0.33 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
       22.29         5.92        42.41        42.08        30.81        27.62 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 
       11.97        12.99         6.41        36.53        31.30        32.91 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 
       25.15        19.04        24.13        31.56        16.87        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 
       10.09         0.76        22.45         5.29         3.09         0.72 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
        7.76        14.63         0.10        15.62        25.68        19.33 
TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       17.72        18.18        19.73        12.56        16.21        15.85 
TCGA-85-A511 TCGA-85-A53L TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE 
       14.96        12.39        11.77        14.07        20.22        22.62 
TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       10.59         4.01         2.30        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 
        4.01         5.03        14.14        16.14        17.69        49.87 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 
       57.07        19.36         8.42        30.81        30.67        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 
        3.88        18.15         2.01        18.58        20.71        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF 
       13.18        13.41        11.84         0.07        64.08         4.54 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO 
       45.37         4.21         2.89        39.85        37.22        30.58 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-O2-A52S 
       24.00        14.73        29.75        65.49         3.65        12.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       43.89         8.58         0.20 

$`DEL PEAK 14(4Q35.2) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 TCGA-18-3419 
       75.75        79.46         4.80        11.34        23.54         1.64 
TCGA-18-3421 TCGA-18-4721 TCGA-18-5595 TCGA-21-1078 TCGA-21-1081 TCGA-21-5783 
       86.96       154.32        27.19        15.58         9.34        88.11 
TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1017 
       41.69        32.19        21.99         4.31        64.21        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-4609 TCGA-22-5471 
       20.48        35.08         0.56        34.75         9.57        31.73 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 TCGA-33-6738 
       44.25         0.79        71.34        79.20        16.64        27.02 
TCGA-33-AASD TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
      110.99        31.27        65.23        67.79        56.38        23.24 
TCGA-34-5240 TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 
       12.00        18.15        27.19         4.04        26.43         3.95 
TCGA-37-4132 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
        7.46        74.07        55.20        70.03         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5039 TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 
        1.94        27.39        17.88        38.66        18.38        27.91 
TCGA-43-7656 TCGA-46-3768 TCGA-51-4080 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 
       19.59         9.99         0.39        27.45         0.10         2.04 
TCGA-56-6546 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 
        0.62         1.45         1.32         0.10        17.49        26.89 
TCGA-56-8309 TCGA-56-8504 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 
       14.07        16.77        22.75         1.18         9.93        20.25 
TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       19.23        17.85         0.26         2.76         0.03        13.25 
TCGA-58-8388 TCGA-58-A46N TCGA-60-2697 TCGA-60-2706 TCGA-60-2710 TCGA-60-2711 
       13.55        29.92        12.23        92.71        66.54        41.42 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 TCGA-60-2725 TCGA-63-A5MI TCGA-63-A5MJ 
       35.34        48.49        32.32        26.83        58.65        59.97 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MU TCGA-63-A5MV TCGA-66-2744 TCGA-66-2755 
       14.99        11.34        25.41        36.16         0.99         0.92 
TCGA-66-2759 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2782 
       25.05         2.01         2.01        23.01        19.00        12.00 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2790 TCGA-68-8251 TCGA-77-6842 
       24.95        25.97        22.98        22.98        13.35        29.56 
TCGA-77-6844 TCGA-77-7335 TCGA-77-7337 TCGA-77-8131 TCGA-77-8143 TCGA-77-8145 
       75.09        70.13       106.95        12.59        26.40         6.97 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5GH TCGA-85-6175 TCGA-85-7697 
      126.18       132.36       117.57        38.86         9.67        34.95 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8071 TCGA-85-8288 
        1.38         1.15        29.95        18.94        14.07        13.22 
TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JC 
       16.77        32.71         2.01        13.94        12.59        14.96 
TCGA-85-A4PA TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 
       24.36         0.79         3.65        24.92         9.50         2.93 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-8491 TCGA-96-8169 TCGA-96-8170 
        2.70         3.48         5.26        26.63        18.31        17.46 
TCGA-96-A4JL TCGA-98-8020 TCGA-98-8023 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       16.57         2.76        21.34        27.02        21.21        20.32 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HT 
       19.10        12.89        51.78         1.22        13.74        22.78 
TCGA-NK-A5CR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A5IB 
       83.57        16.80         0.43        33.07         3.72        11.18 

  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                       174.08                        154.32 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                        19.00                         19.41 
[1] "0.1 - 174.1 (19.0)" "0.0 - 154.3 (19.4)"
[1] "hr=" "1"  
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(4Q35.2) MUTATED         1       53      114        2        34
  DEL PEAK 14(4Q35.2) WILD-TYPE       1       34       37        0        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(4Q35.2) MUTATED          63         1         37         13
  DEL PEAK 14(4Q35.2) WILD-TYPE        29         2         25          8
                               vv
clus                            STAGE IV
  DEL PEAK 14(4Q35.2) MUTATED          3
  DEL PEAK 14(4Q35.2) WILD-TYPE        4
D44V3, multiclass
            clus
vv           DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            53                            34
  STAGE IB                           114                            37
  STAGE II                             2                             0
  STAGE IIA                           34                            29
  STAGE IIB                           63                            29
  STAGE III                            1                             2
  STAGE IIIA                          37                            25
  STAGE IIIB                          13                             8
  STAGE IV                             3                             4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 14(4Q35.2) MUTATED    66 201  44  12
  DEL PEAK 14(4Q35.2) WILD-TYPE  45  89  25  11
D44V4, multiclass
    clus
vv   DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  T1                          66                            45
  T2                         201                            89
  T3                          44                            25
  T4                          12                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 14(4Q35.2) MUTATED   216  78  23   3
  DEL PEAK 14(4Q35.2) WILD-TYPE  96  53  16   2
D44V5, multiclass
    clus
vv   DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  N0                         216                            96
  N1                          78                            53
  N2                          23                            16
  N3                           3                             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"
D44V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q35.2) MUTATED   265   3
  DEL PEAK 14(4Q35.2) WILD-TYPE 139   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED    265    3
  DEL PEAK 14(4Q35.2) WILD-TYPE  139    4
   clus
vv  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  0                         265                           139
  1                           3                             4
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q35.2) MUTATED    85 238
  DEL PEAK 14(4Q35.2) WILD-TYPE  42 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED     85  238
  DEL PEAK 14(4Q35.2) WILD-TYPE   42  128
        clus
vv       DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  FEMALE                          85                            42
  MALE                           238                           128
[1] 2 2
[1] FALSE
D44V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(4Q35.2) MUTATED                                       6
  DEL PEAK 14(4Q35.2) WILD-TYPE                                     9
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(4Q35.2) MUTATED                                         0
  DEL PEAK 14(4Q35.2) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 14(4Q35.2) MUTATED                                        3
  DEL PEAK 14(4Q35.2) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 14(4Q35.2) MUTATED                                         1
  DEL PEAK 14(4Q35.2) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(4Q35.2) MUTATED                                                           313
  DEL PEAK 14(4Q35.2) WILD-TYPE                                                         157
D44V9, multiclass
                                                             clus
vv                                                            DEL PEAK 14(4Q35.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         313
                                                             clus
vv                                                            DEL PEAK 14(4Q35.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           157
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q35.2) MUTATED    11 312
  DEL PEAK 14(4Q35.2) WILD-TYPE   2 168
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED     11  312
  DEL PEAK 14(4Q35.2) WILD-TYPE    2  168
     clus
vv    DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  NO                           11                             2
  YES                         312                           168
[1] 2 2
[1] FALSE
D44V11, continuous
D44V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(4Q35.2) MUTATED   262   7   2  16
  DEL PEAK 14(4Q35.2) WILD-TYPE 132   5   2   6
D44V13, multiclass
    clus
vv   DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  R0                         262                           132
  R1                           7                             5
  R2                           2                             2
  RX                          16                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(4Q35.2) MUTATED       4                        23   222
  DEL PEAK 14(4Q35.2) WILD-TYPE     5                         8   118
D44V14, multiclass
                           clus
vv                          DEL PEAK 14(4Q35.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          23
  WHITE                                             222
                           clus
vv                          DEL PEAK 14(4Q35.2) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               118
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V15, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q35.2) MUTATED     5 202
  DEL PEAK 14(4Q35.2) WILD-TYPE   3 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED      5  202
  DEL PEAK 14(4Q35.2) WILD-TYPE    3  107
                        clus
vv                       DEL PEAK 14(4Q35.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         202
                        clus
vv                       DEL PEAK 14(4Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           107
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 15(5Q12.1) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(5Q12.1) MUTATED   210 140
  DEL PEAK 15(5Q12.1) WILD-TYPE  71  56
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          350                           127 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          140                            56 
$`DEL PEAK 15(5Q12.1) MUTATED`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 
       75.75        79.46         4.80        23.54        92.15        31.99 
TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       36.07         6.18         2.79       154.32        49.94       119.54 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
       99.16        70.16        31.73       122.43       119.80        43.23 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
       31.63        41.69        33.93        10.82        32.19        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
        7.33         4.31         1.74        14.10        27.02        20.48 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       35.08        24.13        38.17        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       19.30         9.57        11.77        31.73        64.93        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 
       14.63        44.25         0.79        54.28        11.74        18.84 
TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
       30.12        56.32        16.64        22.06         7.63       133.74 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN 
       98.01        79.53       103.53        14.07        27.02         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        0.30        36.62         6.94       110.99        44.19       118.36 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
        2.63        61.61        31.50        28.96        32.88        31.27 
TCGA-34-5231 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 
       65.23         9.07        23.24        16.93        30.94         4.96 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3789 TCGA-37-4130 
        1.12         4.04        26.43        20.91         0.43         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 
        7.46         7.82         6.81         0.39         3.39        74.07 
TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       68.58        70.03        60.79        24.33         1.94        27.39 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
       35.64        35.70        17.88        40.21        22.49        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
       27.02        33.11        18.38        27.91        24.89        21.47 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 
        3.81        19.59         7.76        66.51        11.77         2.93 
TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       11.61        14.20        12.03         9.99        10.65        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
        0.39         0.39        29.95        28.34         5.46        30.35 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 
        8.75        28.96         0.10         2.04         0.62         0.99 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
        0.43         0.99         1.45         1.32         0.85         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 
        0.10        17.49         3.48        17.00        14.07         1.35 
TCGA-56-8622 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.81        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
       19.23        13.32        17.85        21.04        18.74         0.13 
TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        0.26         0.03        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 
       16.47        85.12        34.36        56.65        35.24        21.11 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
        3.58        10.22        96.82        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
       49.48        66.54        41.42        56.91        50.33        42.64 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MB 
        3.19        29.85        35.90        23.57        26.83       102.67 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MS 
       66.61        58.65        59.97        45.57        25.28        78.28 
TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 
       16.37        25.41        36.16        53.88        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
        2.01        21.07         1.02         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2768 
       43.99        21.01        25.05         0.99         1.02         2.01 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2785 
        7.07        19.00         3.02         2.01         3.98         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
       25.97        40.01        22.98         4.04        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       30.02        10.06        54.08        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 
        6.94         8.02        13.35        16.18        29.56        75.09 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 
       23.28        89.98        20.78         0.49        42.28       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        0.16        46.78        15.75         6.51        86.76        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       37.81        82.92        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       11.54        26.40         6.97         9.63        54.41        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GF 
       35.90         0.33       117.57         5.92        42.08        27.62 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       38.86        11.97        12.99         6.41        36.53        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 
       31.30        32.91         1.15        29.95        24.13        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       14.07        16.87        34.52         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       16.77         3.09        32.71         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ 
       14.63        15.62        19.33        17.72        14.96        18.18 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 
       19.73        12.56        16.21        15.85        14.96         3.65 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 
        9.50         2.93        11.77        14.07        10.59         2.70 
TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 
        4.01         5.26        21.04         0.16        11.70         4.01 
TCGA-94-8490 TCGA-94-A5I4 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK 
        5.03        16.14        49.87        57.07        18.31        19.36 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        2.76        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       18.15         2.01        18.58        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       13.41        11.84         0.07         4.54        51.78        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP 
       13.74         4.21         2.89        39.85        37.22        24.00 
TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52S 
       29.75        22.78        83.57        65.49        16.80        12.72 
TCGA-O2-A52W TCGA-XC-AA0X 
        8.58         0.20 

$`DEL PEAK 15(5Q12.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3411 TCGA-18-3412 TCGA-18-3419 TCGA-18-3421 
       12.20         7.46       117.57        11.34         1.64        86.96 
TCGA-18-5595 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 
       27.19        46.88        60.89        34.78        15.58         9.34 
TCGA-21-5783 TCGA-22-1000 TCGA-22-1005 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 
       88.11        14.93        64.21        48.82        48.33         0.56 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5489 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 
       71.34        79.20        62.86       174.08       151.27        54.44 
TCGA-33-4589 TCGA-33-6737 TCGA-33-AASL TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 
        1.55        19.76        27.16        67.79        56.38        12.00 
TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-39-5011 
       18.15        27.19         3.95         0.39         6.58        47.80 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5028 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 
       44.75        55.20         1.71        36.39        15.58        17.06 
TCGA-43-6143 TCGA-43-6771 TCGA-43-8115 TCGA-43-A475 TCGA-52-7812 TCGA-56-5898 
       12.36         5.46        13.38         9.73        27.45        18.25 
TCGA-56-8307 TCGA-56-8504 TCGA-56-8623 TCGA-56-8624 TCGA-56-A62T TCGA-58-8393 
       26.89        16.77        22.75         1.18         2.76        34.78 
TCGA-58-A46N TCGA-60-2697 TCGA-60-2704 TCGA-60-2712 TCGA-60-2715 TCGA-60-2716 
       29.92        12.23        37.94         9.01        35.34        48.49 
TCGA-60-2721 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR 
       32.32        11.77        70.62        14.99        11.34        89.29 
TCGA-63-A5MY TCGA-66-2744 TCGA-66-2765 TCGA-66-2767 TCGA-66-2770 TCGA-66-2778 
       34.59         0.99         2.01         2.01        23.01        19.00 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2795 TCGA-68-A59J TCGA-77-6843 
       12.03        12.00        24.95         4.01        14.73        73.12 
TCGA-77-7138 TCGA-77-7335 TCGA-77-8131 TCGA-77-8144 TCGA-77-A5FZ TCGA-77-A5G1 
       11.18        70.13        12.59        27.39       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GB TCGA-85-6175 TCGA-85-7710 TCGA-85-7950 
       22.29        42.41        30.81         9.67         1.38        18.94 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8277 TCGA-85-8352 TCGA-85-8582 TCGA-85-8584 
       25.15        19.04        10.09         5.29        13.94        12.59 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
        0.10        25.68        24.36         0.79        12.39        24.92 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8065 TCGA-94-8491 TCGA-94-A4VJ 
       20.22        22.62         3.48         2.30        26.63        14.14 
TCGA-94-A5I6 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53C TCGA-98-A53D 
       17.69        17.46        16.57         8.42        27.02        21.21 
TCGA-98-A53H TCGA-98-A53J TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HO 
       20.32        20.71        19.10        64.08         1.22        30.58 
TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V 
       14.73         3.65         0.43        33.07         3.72        43.89 
TCGA-O2-A5IB 
       11.18 

  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                         0.03                          0.10 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                       154.32                        174.08 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                       19.265                        19.040 
[1] "0.0 - 154.3 (19.3)" "0.1 - 174.1 (19.0)"
[1] "hr=" "1"  
D45V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(5Q12.1) MUTATED         1       64      111        1        47
  DEL PEAK 15(5Q12.1) WILD-TYPE       1       23       40        1        16
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(5Q12.1) MUTATED          66         1         47         14
  DEL PEAK 15(5Q12.1) WILD-TYPE        26         2         15          7
                               vv
clus                            STAGE IV
  DEL PEAK 15(5Q12.1) MUTATED          7
  DEL PEAK 15(5Q12.1) WILD-TYPE        0
D45V3, multiclass
            clus
vv           DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            64                            23
  STAGE IB                           111                            40
  STAGE II                             1                             1
  STAGE IIA                           47                            16
  STAGE IIB                           66                            26
  STAGE III                            1                             2
  STAGE IIIA                          47                            15
  STAGE IIIB                          14                             7
  STAGE IV                             7                             0
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 15(5Q12.1) MUTATED    83 217  44  18
  DEL PEAK 15(5Q12.1) WILD-TYPE  28  73  25   5
D45V4, multiclass
    clus
vv   DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  T1                          83                            28
  T2                         217                            73
  T3                          44                            25
  T4                          18                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 15(5Q12.1) MUTATED   232  97  28   2
  DEL PEAK 15(5Q12.1) WILD-TYPE  80  34  11   3
D45V5, multiclass
    clus
vv   DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  N0                         232                            80
  N1                          97                            34
  N2                          28                            11
  N3                           2                             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"
D45V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED   293   7
  DEL PEAK 15(5Q12.1) WILD-TYPE 111   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED    293    7
  DEL PEAK 15(5Q12.1) WILD-TYPE  111    0
   clus
vv  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  0                         293                           111
  1                           7                             0
[1] 2 2
[1] FALSE
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED    85 277
  DEL PEAK 15(5Q12.1) WILD-TYPE  42  89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED     85  277
  DEL PEAK 15(5Q12.1) WILD-TYPE   42   89
        clus
vv       DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  FEMALE                          85                            42
  MALE                           277                            89
[1] 2 2
[1] FALSE
D45V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(5Q12.1) MUTATED                                      11
  DEL PEAK 15(5Q12.1) WILD-TYPE                                     4
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(5Q12.1) MUTATED                                         1
  DEL PEAK 15(5Q12.1) WILD-TYPE                                       0
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 15(5Q12.1) MUTATED                                        3
  DEL PEAK 15(5Q12.1) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 15(5Q12.1) MUTATED                                         0
  DEL PEAK 15(5Q12.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(5Q12.1) MUTATED                                                           347
  DEL PEAK 15(5Q12.1) WILD-TYPE                                                         123
D45V9, multiclass
                                                             clus
vv                                                            DEL PEAK 15(5Q12.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         347
                                                             clus
vv                                                            DEL PEAK 15(5Q12.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           123
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED    12 350
  DEL PEAK 15(5Q12.1) WILD-TYPE   1 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED     12  350
  DEL PEAK 15(5Q12.1) WILD-TYPE    1  130
     clus
vv    DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  NO                           12                             1
  YES                         350                           130
[1] 2 2
[1] FALSE
D45V11, continuous
D45V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(5Q12.1) MUTATED   294   9   2  14
  DEL PEAK 15(5Q12.1) WILD-TYPE 100   3   2   8
D45V13, multiclass
    clus
vv   DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  R0                         294                           100
  R1                           9                             3
  R2                           2                             2
  RX                          14                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(5Q12.1) MUTATED       4                        26   249
  DEL PEAK 15(5Q12.1) WILD-TYPE     5                         5    91
D45V14, multiclass
                           clus
vv                          DEL PEAK 15(5Q12.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          26
  WHITE                                             249
                           clus
vv                          DEL PEAK 15(5Q12.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED     6 222
  DEL PEAK 15(5Q12.1) WILD-TYPE   2  87
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED      6  222
  DEL PEAK 15(5Q12.1) WILD-TYPE    2   87
                        clus
vv                       DEL PEAK 15(5Q12.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         222
                        clus
vv                       DEL PEAK 15(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            87
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 16(5Q31.1) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(5Q31.1) MUTATED   220 146
  DEL PEAK 16(5Q31.1) WILD-TYPE  61  50
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                          366                           111 
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                          146                            50 
$`DEL PEAK 16(5Q31.1) MUTATED`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       75.75        79.46         4.80       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       92.15        31.99        36.07         6.18         2.79       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 
       49.94       119.54        99.16        70.16        60.89        31.73 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
      119.80        31.63        41.69        33.93        10.82        32.19 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       21.99         7.33         4.31         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
       20.48        35.08        48.33        24.13        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 
       13.12        32.02        19.30         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       64.93        63.55        14.63        44.25         0.79        54.28 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       11.74        18.84        30.12        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 
        7.63       133.74        98.01        79.53       103.53        14.07 
TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       54.44        19.76        27.02         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 
        6.94       110.99        44.19       118.36         2.63        61.61 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 
       31.50        28.96        32.88        31.27        65.23        56.38 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 
        9.07        23.24        16.93        30.94         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4130 TCGA-37-4132 
       27.19         4.04        26.43        20.91         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
        7.82         6.81         0.39         3.39        47.80        74.07 
TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       68.58        70.03        60.79        24.33         1.94        27.39 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
       35.64        35.70        17.88        40.21        22.49        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 
       27.02        33.11        18.38        27.91        24.89        21.47 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 
        3.81        19.59         7.76        66.51        11.77         2.93 
TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       11.61        14.20        12.03         9.99        10.65        13.91 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
        0.39        29.95        28.34         5.46        30.35         8.75 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
       28.96         0.10        18.25         0.62         0.99         0.43 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
        1.45         1.32         0.85         6.51         0.10        17.49 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        3.48        26.89        17.00        14.07         1.35         1.81 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW 
       10.36         9.93        20.25        15.81        20.94        19.23 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS 
       13.32        17.85        21.04        18.74         0.13         0.26 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        0.03        13.25        13.55        29.95        71.24        16.47 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2696 
       85.12        34.36        56.65        35.24        21.11         3.58 
TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       96.82        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
       41.42        56.91        50.33        42.64         3.19        32.32 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MH 
       29.85        35.90        23.57        26.83       102.67        66.61 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT 
       58.65        59.97        45.57        25.28        78.28        16.37 
TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       25.41        36.16        53.88        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
        2.01        21.07         1.02         0.92         0.99        43.99 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 
       25.05         0.99         2.01         1.02         2.01         7.07 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
       19.00         3.02         2.01        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
       12.00         1.97        25.97        40.01        22.98         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
       22.98         5.03        30.02        10.06        54.08        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 
        2.73         6.64         6.94         8.02        13.35        29.56 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
       75.09        23.28        89.98        20.78         0.49        42.28 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
      106.95         0.16        46.78        15.75         6.51        86.76 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       37.81        82.92        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       11.54        26.40         6.97         9.63        54.41        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
       35.90         0.33       117.57        22.29         5.92        42.41 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       27.62        38.86        11.97        12.99         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 
       34.95        31.30        32.91         1.38         1.15        18.94 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       24.13        31.56        14.07        16.87        34.52        10.09 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
        0.76        13.22        22.45        16.77         5.29         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       32.71         2.01         0.72         7.76        14.63        13.94 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ 
        0.10        15.62        19.33        17.72        14.96        18.18 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7766 
       19.73        12.56        15.85        14.96         3.65         9.50 
TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
        2.93        11.77        14.07        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 
        3.48         4.01         5.26         0.16        11.70         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7544 TCGA-96-7545 
        5.03        26.63        14.14        16.14        49.87        57.07 
TCGA-96-8169 TCGA-96-A4JK TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       18.31        19.36         2.76        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-J1-A4AH 
       27.16         3.88        18.15         2.01        18.58        19.10 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
       12.89        16.11        13.18        13.41        11.84         0.07 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54        51.78        45.37        13.74         4.21         2.89 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
       39.85        37.22        24.00        29.75        22.78        83.57 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52S TCGA-O2-A52W TCGA-XC-AA0X 
       65.49         3.65        16.80        12.72         8.58         0.20 

$`DEL PEAK 16(5Q31.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3419 TCGA-18-3421 TCGA-18-5595 TCGA-21-1071 
       12.20         7.46         1.64        86.96        27.19        46.88 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5783 
       34.78        15.58       122.43         9.34        43.23        88.11 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1017 TCGA-22-4596 TCGA-22-5480 TCGA-22-5481 
       14.93        64.21        48.82         0.56        71.34        79.20 
TCGA-22-5489 TCGA-33-4566 TCGA-33-4583 TCGA-33-4589 TCGA-33-AASL TCGA-34-5232 
       62.86       174.08       151.27         1.55        27.16        67.79 
TCGA-34-5240 TCGA-34-5928 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       12.00        18.15         3.95         0.43         0.39         6.58 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5028 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 
       44.75        55.20         1.71        36.39        15.58        17.06 
TCGA-43-6143 TCGA-43-6771 TCGA-43-8115 TCGA-43-A475 TCGA-51-4080 TCGA-52-7812 
       12.36         5.46        13.38         9.73         0.39        27.45 
TCGA-56-6545 TCGA-56-7223 TCGA-56-8504 TCGA-56-8623 TCGA-56-8624 TCGA-56-A62T 
        2.04         0.99        16.77        22.75         1.18         2.76 
TCGA-58-8393 TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2712 
       34.78        29.92        12.23        10.22        37.94         9.01 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN 
       35.34        48.49        11.77        70.62        14.99        11.34 
TCGA-63-A5MR TCGA-66-2744 TCGA-66-2754 TCGA-66-2758 TCGA-66-2767 TCGA-66-2770 
       89.29         0.99         2.01        21.01         2.01        23.01 
TCGA-66-2783 TCGA-66-2795 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-7138 
       24.95         4.01        16.18        14.73        73.12        11.18 
TCGA-77-7335 TCGA-77-8009 TCGA-77-8131 TCGA-77-8144 TCGA-77-A5FZ TCGA-77-A5G1 
       70.13        53.95        12.59        27.39       126.18       132.36 
TCGA-77-A5GA TCGA-77-A5GB TCGA-85-6175 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 
       42.08        30.81         9.67        29.95        25.15        19.04 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A513 TCGA-85-A53L 
       12.59        25.68        24.36        16.21         0.79        12.39 
TCGA-90-6837 TCGA-90-A4ED TCGA-92-8065 TCGA-94-7033 TCGA-94-A5I6 TCGA-96-8170 
       24.92        20.22         2.30        21.04        17.69        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J 
       16.57         8.42        27.02        21.21        20.32        20.71 
TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NK-A7XE TCGA-O2-A52N 
       64.08         1.22        30.58        14.73         0.43        33.07 
TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB 
        3.72        43.89        11.18 

  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                         0.03                          0.39 
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                       154.32                        174.08 
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                       19.265                        18.150 
[1] "0.0 - 154.3 (19.3)" "0.4 - 174.1 (18.1)"
[1] "hr=" "1"  
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(5Q31.1) MUTATED         1       69      112        1        51
  DEL PEAK 16(5Q31.1) WILD-TYPE       1       18       39        1        12
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(5Q31.1) MUTATED          68         1         52         14
  DEL PEAK 16(5Q31.1) WILD-TYPE        24         2         10          7
                               vv
clus                            STAGE IV
  DEL PEAK 16(5Q31.1) MUTATED          7
  DEL PEAK 16(5Q31.1) WILD-TYPE        0
D46V3, multiclass
            clus
vv           DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            69                            18
  STAGE IB                           112                            39
  STAGE II                             1                             1
  STAGE IIA                           51                            12
  STAGE IIB                           68                            24
  STAGE III                            1                             2
  STAGE IIIA                          52                            10
  STAGE IIIB                          14                             7
  STAGE IV                             7                             0
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 16(5Q31.1) MUTATED    88 224  50  17
  DEL PEAK 16(5Q31.1) WILD-TYPE  23  66  19   6
D46V4, multiclass
    clus
vv   DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  T1                          88                            23
  T2                         224                            66
  T3                          50                            19
  T4                          17                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 16(5Q31.1) MUTATED   243  99  31   3
  DEL PEAK 16(5Q31.1) WILD-TYPE  69  32   8   2
D46V5, multiclass
    clus
vv   DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  N0                         243                            69
  N1                          99                            32
  N2                          31                             8
  N3                           3                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                               cls
clus                              0   1
  DEL PEAK 16(5Q31.1) MUTATED   309   7
  DEL PEAK 16(5Q31.1) WILD-TYPE  95   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q31.1) MUTATED    309    7
  DEL PEAK 16(5Q31.1) WILD-TYPE   95    0
   clus
vv  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  0                         309                            95
  1                           7                             0
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(5Q31.1) MUTATED    94 285
  DEL PEAK 16(5Q31.1) WILD-TYPE  33  81
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q31.1) MUTATED     94  285
  DEL PEAK 16(5Q31.1) WILD-TYPE   33   81
        clus
vv       DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  FEMALE                          94                            33
  MALE                           285                            81
[1] 2 2
[1] FALSE
D46V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 16(5Q31.1) MUTATED                                      10
  DEL PEAK 16(5Q31.1) WILD-TYPE                                     5
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 16(5Q31.1) MUTATED                                         1
  DEL PEAK 16(5Q31.1) WILD-TYPE                                       0
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 16(5Q31.1) MUTATED                                        3
  DEL PEAK 16(5Q31.1) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 16(5Q31.1) MUTATED                                         1
  DEL PEAK 16(5Q31.1) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(5Q31.1) MUTATED                                                           364
  DEL PEAK 16(5Q31.1) WILD-TYPE                                                         106
D46V9, multiclass
                                                             clus
vv                                                            DEL PEAK 16(5Q31.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         364
                                                             clus
vv                                                            DEL PEAK 16(5Q31.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           106
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, binary
                               cls
clus                              0   1
  DEL PEAK 16(5Q31.1) MUTATED    12 367
  DEL PEAK 16(5Q31.1) WILD-TYPE   1 113
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q31.1) MUTATED     12  367
  DEL PEAK 16(5Q31.1) WILD-TYPE    1  113
     clus
vv    DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  NO                           12                             1
  YES                         367                           113
[1] 2 2
[1] FALSE
D46V11, continuous
D46V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(5Q31.1) MUTATED   305   9   3  14
  DEL PEAK 16(5Q31.1) WILD-TYPE  89   3   1   8
D46V13, multiclass
    clus
vv   DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  R0                         305                            89
  R1                           9                             3
  R2                           3                             1
  RX                          14                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(5Q31.1) MUTATED       4                        24   261
  DEL PEAK 16(5Q31.1) WILD-TYPE     5                         7    79
D46V14, multiclass
                           clus
vv                          DEL PEAK 16(5Q31.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          24
  WHITE                                             261
                           clus
vv                          DEL PEAK 16(5Q31.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V15, binary
                               cls
clus                              0   1
  DEL PEAK 16(5Q31.1) MUTATED     6 232
  DEL PEAK 16(5Q31.1) WILD-TYPE   2  77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q31.1) MUTATED      6  232
  DEL PEAK 16(5Q31.1) WILD-TYPE    2   77
                        clus
vv                       DEL PEAK 16(5Q31.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         232
                        clus
vv                       DEL PEAK 16(5Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            77
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 17(6P25.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(6P25.3) MUTATED    70  56
  DEL PEAK 17(6P25.3) WILD-TYPE 211 140
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                          126                           351 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                           56                           140 
$`DEL PEAK 17(6P25.3) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3416 TCGA-18-4083 
       12.20        75.75       117.57        11.34        31.99         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-21-1076 TCGA-21-5783 TCGA-22-0940 TCGA-22-1012 
        2.79       154.32        60.89        88.11        21.99        14.10 
TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4609 TCGA-22-5473 
       35.08         0.56        38.17        13.12         9.57        63.55 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 
       44.25         0.79        54.28        11.74        18.84        56.32 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4589 TCGA-33-AASD TCGA-33-AASL 
       79.53       103.53       151.27         1.55       110.99        27.16 
TCGA-34-2596 TCGA-34-2604 TCGA-34-5232 TCGA-34-7107 TCGA-34-8455 TCGA-37-3789 
        2.63        31.50        67.79         1.12         4.04         0.43 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5027 TCGA-39-5029 TCGA-39-5035 
        3.39        47.80        74.07        60.79        24.33        15.58 
TCGA-39-5037 TCGA-39-5039 TCGA-43-6143 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
       35.70        17.88        12.36         2.93        11.61         9.73 
TCGA-43-A56V TCGA-46-3768 TCGA-51-4081 TCGA-52-7622 TCGA-56-7579 TCGA-56-7582 
       12.03         9.99        29.95        28.34         1.45         0.85 
TCGA-56-7822 TCGA-56-8309 TCGA-56-8624 TCGA-56-8626 TCGA-56-A4ZK TCGA-58-8386 
       17.49        14.07         1.18         9.93        18.74         0.03 
TCGA-58-8391 TCGA-58-A46M TCGA-60-2698 TCGA-60-2707 TCGA-60-2725 TCGA-60-2726 
       71.24        35.24        10.22        21.93        26.83        11.77 
TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5MP TCGA-63-A5MR TCGA-66-2782 TCGA-66-2786 
      102.67        59.97        25.28        89.29        12.00        25.97 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-68-7755 
       22.98         4.04         5.03        30.02        54.08         2.73 
TCGA-68-7756 TCGA-68-A59I TCGA-77-7140 TCGA-77-7141 TCGA-77-7337 TCGA-77-7338 
        6.64        16.18        20.78         0.49       106.95         0.16 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8138 TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5G8 
       37.81        12.59        17.72        54.41       117.57        42.41 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7843 TCGA-85-7950 TCGA-85-8049 
       36.53        34.95        31.30         1.15        18.94        19.04 
TCGA-85-8070 TCGA-85-8277 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC 
       31.56        10.09        15.62        25.68        19.33        14.96 
TCGA-85-A4QQ TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 
       18.18         3.65         2.93        10.59         3.48         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8491 TCGA-94-A5I4 TCGA-96-7544 TCGA-96-A4JK 
        5.26         2.30        26.63        16.14        49.87        19.36 
TCGA-98-8020 TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-LA-A7SW TCGA-NC-A5HL 
        2.76        18.58        20.71        19.10        13.41         2.89 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5D1 TCGA-O2-A52V TCGA-XC-AA0X 
       24.00        14.73        83.57        16.80        43.89         0.20 

$`DEL PEAK 17(6P25.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
        7.46        79.46         4.80        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 
        1.64        86.96        49.94        27.19       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       99.16        70.16        34.78        15.58        31.73       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
        9.34       119.80        43.23        31.63        41.69        33.93 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       10.82        32.19         7.33        14.93         4.31        64.21 
TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
        1.74        27.02        48.82        20.48        48.33        24.13 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
       34.75        32.02        19.30        11.77        31.73        64.93 
TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 
       14.63        71.34        79.20        30.12        62.86        16.64 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 TCGA-33-4586 
       22.06         7.63       133.74        98.01       174.08        14.07 
TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       54.44        19.76        27.02         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 
        6.94        44.19       118.36        61.61        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       31.27        65.23        56.38         9.07        23.24        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 
       16.93        30.94        18.15         4.96        27.19        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       20.91         3.95         0.39         6.58         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        7.82         6.81         0.39        44.75        68.58        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
       70.03         1.71         1.94        27.39        36.39        35.64 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       17.06        40.21        22.49        38.66        27.02        33.11 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       18.38        27.91        24.89        21.47         5.46         3.81 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U 
       19.59         7.76        66.51        13.38        11.77        14.20 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 
       10.65        13.91         0.39         0.39         5.46        30.35 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        8.75        27.45        28.96         0.10        18.25         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 
        0.62         0.99         0.43         0.99         1.32         6.51 
TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8503 TCGA-56-8504 
        0.10         3.48        26.89        17.00         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.81        22.75        10.36        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
       19.23        13.32        17.85        21.04         0.13         0.26 
TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 
        2.76        13.25        13.55        29.95        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 
       85.12        34.36        56.65        29.92        21.11         3.58 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
       12.23        96.82        37.94        92.71        80.45        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       66.54        41.42         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
       48.49        42.64         3.19        32.32        29.85        35.90 
TCGA-60-2724 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MM 
       23.57        70.62        66.61        58.65        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       11.34        78.28        16.37        25.41        36.16        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       34.59        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        1.02         2.01         0.92         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
       25.05         0.99         2.01         1.02         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 
        7.07        23.01        19.00         3.02         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2790 
       12.03         3.98        24.95         1.97        40.01        22.98 
TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       10.06         4.01        49.05         6.94         8.02        13.35 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       14.73        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       89.98        42.28        70.13        46.78        15.75         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 
       86.76        53.95        82.92        53.92        39.09       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 
       11.54        26.40        27.39         6.97         9.63        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
       35.90         0.33       126.18       132.36        22.29         5.92 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       42.08        30.81        27.62        38.86         9.67        11.97 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 
       12.99         6.41        32.91         1.38        29.95        25.15 
TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
       24.13        14.07        16.87        34.52         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       22.45        16.77         5.29         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
        0.72         7.76        14.63        13.94        12.59         0.10 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       17.72        24.36        19.73        12.56        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 
       14.96         0.79        12.39        24.92         9.50        11.77 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-94-7033 TCGA-94-7557 
       14.07        20.22        22.62         2.70        21.04         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7545 
       11.70         4.01         5.03        14.14        17.69        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       18.31        17.46        16.57         8.42        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       21.34        27.16         3.88        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
       21.21        20.32        12.89        16.11        13.18        11.84 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
        0.07        64.08         4.54        51.78         1.22        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HR 
       13.74         4.21        39.85        37.22        30.58        29.75 
TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       22.78        65.49         3.65         0.43        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52W TCGA-O2-A5IB 
       12.72         8.58        11.18 

  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                         0.03                          0.07 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                       154.32                        174.08 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                        18.66                         19.76 
[1] "0.0 - 154.3 (18.7)" "0.1 - 174.1 (19.8)"
[1] "hr=" "1.1"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(6P25.3) MUTATED         0       23       37        2        23
  DEL PEAK 17(6P25.3) WILD-TYPE       2       64      114        0        40
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6P25.3) MUTATED          24         0         17          3
  DEL PEAK 17(6P25.3) WILD-TYPE        68         3         45         18
                               vv
clus                            STAGE IV
  DEL PEAK 17(6P25.3) MUTATED          3
  DEL PEAK 17(6P25.3) WILD-TYPE        4
D47V3, multiclass
            clus
vv           DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                            23                            64
  STAGE IB                            37                           114
  STAGE II                             2                             0
  STAGE IIA                           23                            40
  STAGE IIB                           24                            68
  STAGE III                            0                             3
  STAGE IIIA                          17                            45
  STAGE IIIB                           3                            18
  STAGE IV                             3                             4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 17(6P25.3) MUTATED    32  78  18   4
  DEL PEAK 17(6P25.3) WILD-TYPE  79 212  51  19
D47V4, multiclass
    clus
vv   DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  T1                          32                            79
  T2                          78                           212
  T3                          18                            51
  T4                           4                            19
[1] 4 2
[1] TRUE
[1] "dimension of 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(6P25.3) MUTATED    77  41  10   2
  DEL PEAK 17(6P25.3) WILD-TYPE 235  90  29   3
D47V5, multiclass
    clus
vv   DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  N0                          77                           235
  N1                          41                            90
  N2                          10                            29
  N3                           2                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                               cls
clus                              0   1
  DEL PEAK 17(6P25.3) MUTATED   110   3
  DEL PEAK 17(6P25.3) WILD-TYPE 294   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED    110    3
  DEL PEAK 17(6P25.3) WILD-TYPE  294    4
   clus
vv  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  0                         110                           294
  1                           3                             4
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(6P25.3) MUTATED    28 104
  DEL PEAK 17(6P25.3) WILD-TYPE  99 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED     28  104
  DEL PEAK 17(6P25.3) WILD-TYPE   99  262
        clus
vv       DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  FEMALE                          28                            99
  MALE                           104                           262
[1] 2 2
[1] FALSE
D47V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(6P25.3) MUTATED                                       3
  DEL PEAK 17(6P25.3) WILD-TYPE                                    12
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(6P25.3) MUTATED                                         0
  DEL PEAK 17(6P25.3) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 17(6P25.3) MUTATED                                        1
  DEL PEAK 17(6P25.3) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 17(6P25.3) MUTATED                                         0
  DEL PEAK 17(6P25.3) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(6P25.3) MUTATED                                                           128
  DEL PEAK 17(6P25.3) WILD-TYPE                                                         342
D47V9, multiclass
                                                             clus
vv                                                            DEL PEAK 17(6P25.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         128
                                                             clus
vv                                                            DEL PEAK 17(6P25.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           342
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, binary
                               cls
clus                              0   1
  DEL PEAK 17(6P25.3) MUTATED     2 130
  DEL PEAK 17(6P25.3) WILD-TYPE  11 350
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED      2  130
  DEL PEAK 17(6P25.3) WILD-TYPE   11  350
     clus
vv    DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  NO                            2                            11
  YES                         130                           350
[1] 2 2
[1] FALSE
D47V11, continuous
D47V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(6P25.3) MUTATED   105   5   0   9
  DEL PEAK 17(6P25.3) WILD-TYPE 289   7   4  13
D47V13, multiclass
    clus
vv   DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  R0                         105                           289
  R1                           5                             7
  R2                           0                             4
  RX                           9                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(6P25.3) MUTATED       1                        10    94
  DEL PEAK 17(6P25.3) WILD-TYPE     8                        21   246
D47V14, multiclass
                           clus
vv                          DEL PEAK 17(6P25.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              94
                           clus
vv                          DEL PEAK 17(6P25.3) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V15, binary
                               cls
clus                              0   1
  DEL PEAK 17(6P25.3) MUTATED     4  82
  DEL PEAK 17(6P25.3) WILD-TYPE   4 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED      4   82
  DEL PEAK 17(6P25.3) WILD-TYPE    4  227
                        clus
vv                       DEL PEAK 17(6P25.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          82
                        clus
vv                       DEL PEAK 17(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           227
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 18(6Q22.31) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(6Q22.31) MUTATED    73  43
  DEL PEAK 18(6Q22.31) WILD-TYPE 208 153
  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                           116                            361 
  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                            43                            153 
$`DEL PEAK 18(6Q22.31) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3421 TCGA-18-4083 
       75.75       117.57        11.34        92.15        86.96         6.18 
TCGA-18-5592 TCGA-21-1072 TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 
       49.94        99.16        43.23        88.11        33.93        10.82 
TCGA-22-0940 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 
       21.99        24.13         0.56        38.17        34.75        19.30 
TCGA-22-5471 TCGA-22-5478 TCGA-22-5479 TCGA-22-5492 TCGA-33-4582 TCGA-33-4583 
       31.73         0.79        54.28        16.64       103.53       151.27 
TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2604 TCGA-34-5231 
        6.94        44.19        27.16         2.63        31.50        65.23 
TCGA-34-5928 TCGA-34-8455 TCGA-34-8456 TCGA-37-4133 TCGA-39-5016 TCGA-39-5021 
       18.15         4.04        26.43         7.82        74.07        68.58 
TCGA-39-5027 TCGA-39-5034 TCGA-39-5037 TCGA-39-5039 TCGA-43-2581 TCGA-43-6143 
       60.79        36.39        35.70        17.88        38.66        12.36 
TCGA-43-6770 TCGA-43-8115 TCGA-46-6025 TCGA-51-4081 TCGA-52-7812 TCGA-56-6545 
       21.47        13.38        10.65        29.95        27.45         2.04 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8624 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BY 
        0.85         6.51         1.18        10.36        20.94        17.85 
TCGA-56-A4ZK TCGA-58-8393 TCGA-58-A46M TCGA-60-2707 TCGA-60-2711 TCGA-60-2722 
       18.74        34.78        35.24        21.93        41.42        29.85 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MR TCGA-63-A5MY TCGA-66-2758 
       11.77       102.67        58.65        89.29        34.59        21.01 
TCGA-66-2763 TCGA-66-2773 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2788 
        0.99         3.02        12.03        12.00        24.95        22.98 
TCGA-66-2792 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I 
       30.02         4.01         2.73         6.64         6.94        16.18 
TCGA-77-7141 TCGA-77-8007 TCGA-77-8009 TCGA-77-8150 TCGA-77-A5G8 TCGA-85-7696 
        0.49         6.51        53.95        54.41        42.41        36.53 
TCGA-85-7698 TCGA-85-7710 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 
       31.30         1.38        24.13        31.56        16.87        10.09 
TCGA-85-8354 TCGA-85-8479 TCGA-85-8584 TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR 
       32.71         0.72        12.59        14.96        18.18        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7767 TCGA-92-7341 
       12.56        16.21        15.85         3.65         2.93         3.48 
TCGA-94-7033 TCGA-94-8491 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53I TCGA-J1-A4AH 
       21.04        26.63        21.34        27.16        18.58        19.10 
TCGA-L3-A524 TCGA-NC-A5HG TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5D1 
       16.11        51.78        37.22        14.73        29.75        16.80 
TCGA-O2-A52Q TCGA-O2-A52S 
        3.72        12.72 

$`DEL PEAK 18(6Q22.31) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 
       12.20         7.46        79.46         4.80        23.54        31.99 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 
       36.07         1.64         2.79       154.32        27.19       119.54 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       46.88        70.16        60.89        34.78        15.58        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI 
      122.43         9.34       119.80        31.63        41.69        32.19 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
        7.33        14.93         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4604 
       27.02        48.82        20.48        35.08        48.33        13.12 
TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
       32.02         9.57        11.77        64.93        63.55        14.63 
TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       44.25        71.34        79.20        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
       62.86        56.32        22.06         7.63       133.74        98.01 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
       79.53       174.08        14.07        54.44         1.55        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ 
       27.02         4.70         0.30        36.62       110.99       118.36 
TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 
       61.61        28.96        32.88        31.27        67.79        56.38 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 
        9.07        23.24        12.00        16.93        30.94         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
        1.12        27.19        20.91         3.95         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        6.58         8.12         7.46         6.81         0.39         3.39 
TCGA-39-5011 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
       47.80        44.75        55.20        70.03         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 
        1.94        27.39        15.58        35.64        17.06        40.21 
TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 
       22.49        27.02        33.11        18.38        27.91        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 
        5.46         3.81        19.59         7.76        66.51        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
        2.93        11.61         9.73        14.20        12.03         9.99 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
       13.91         0.39         0.39        28.34         5.46        30.35 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 
        8.75        28.96         0.10        18.25         0.62         0.99 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 
        0.43         0.99         1.45         1.32         0.10        17.49 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
        3.48        26.89        17.00        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
        1.81        22.75         9.93        20.25        15.81        19.23 
TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       13.32        21.04         0.13         0.26         2.76         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J 
       13.25        13.55        29.95        71.24        16.47        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 
       34.36        56.65        29.92        21.11         3.58        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
       10.22        96.82        37.94        92.71        80.45        49.48 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       66.54         9.01        56.91        50.33        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       42.64         3.19        32.32        35.90        23.57        26.83 
TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
       70.62        66.61        59.97        45.57        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       25.28        78.28        16.37        25.41        36.16        53.88 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 
       16.96        43.10         2.01        21.07         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 
        2.01         0.92         0.99        43.99        25.05         2.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
        1.02         2.01         2.01         7.07        23.01        19.00 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
        2.01        19.00         3.98         1.97        25.97        40.01 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
        4.04        22.98         5.03        10.06        54.08        49.05 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
        8.02        13.35        14.73        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7142 TCGA-77-7335 
       23.28        11.18        89.98        20.78        42.28        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8128 
      106.95         0.16        46.78        15.75        86.76        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       82.92        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 
       11.54        26.40        27.39         6.97         9.63        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
       35.90         0.33       126.18       132.36       117.57        22.29 
TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
        5.92        42.08        30.81        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 TCGA-85-7843 
       11.97        12.99         6.41        34.95        32.91         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8276 
       29.95        18.94        25.15        19.04        14.07        34.52 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
        0.76        13.22        22.45        16.77         5.29         3.09 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
        2.01         7.76        14.63        13.94         0.10        15.62 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A511 TCGA-85-A513 
       25.68        19.33        17.72        24.36        14.96         0.79 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
       12.39        24.92         9.50        11.77        14.07        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       22.62        10.59         2.70         4.01         5.26         2.30 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 
        0.16        11.70         4.01         5.03        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
       17.69        49.87        57.07        18.31        17.46        19.36 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-A539 
       16.57         8.42         2.76        30.81        30.67         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J 
       18.15         2.01        27.02        21.21        20.32        20.71 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       12.89        13.18        13.41        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54         1.22        45.37        13.74         4.21         2.89 
TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
       39.85        30.58        24.00        22.78        83.57        65.49 
TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
        3.65         0.43        33.07        43.89         8.58        11.18 
TCGA-XC-AA0X 
        0.20 

  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                          0.49                           0.03 
  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                        151.27                         174.08 
  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE 
                        21.025                         18.840 
[1] "0.5 - 151.3 (21.0)" "0.0 - 174.1 (18.8)"
[1] "hr=" "1.2"
D48V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(6Q22.31) MUTATED         0       14       42        0        22
  DEL PEAK 18(6Q22.31) WILD-TYPE       2       73      109        2        41
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(6Q22.31) MUTATED          21         2         16          3
  DEL PEAK 18(6Q22.31) WILD-TYPE        71         1         46         18
                                vv
clus                             STAGE IV
  DEL PEAK 18(6Q22.31) MUTATED          1
  DEL PEAK 18(6Q22.31) WILD-TYPE        6
D48V3, multiclass
            clus
vv           DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                             14                             73
  STAGE IB                             42                            109
  STAGE II                              0                              2
  STAGE IIA                            22                             41
  STAGE IIB                            21                             71
  STAGE III                             2                              1
  STAGE IIIA                           16                             46
  STAGE IIIB                            3                             18
  STAGE IV                              1                              6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 18(6Q22.31) MUTATED    18  79  18   6
  DEL PEAK 18(6Q22.31) WILD-TYPE  93 211  51  17
D48V4, multiclass
    clus
vv   DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  T1                           18                             93
  T2                           79                            211
  T3                           18                             51
  T4                            6                             17
[1] 4 2
[1] TRUE
[1] "dimension of 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(6Q22.31) MUTATED    75  35  10   1
  DEL PEAK 18(6Q22.31) WILD-TYPE 237  96  29   4
D48V5, multiclass
    clus
vv   DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  N0                           75                            237
  N1                           35                             96
  N2                           10                             29
  N3                            1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                                cls
clus                               0   1
  DEL PEAK 18(6Q22.31) MUTATED   101   1
  DEL PEAK 18(6Q22.31) WILD-TYPE 303   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(6Q22.31) MUTATED    101    1
  DEL PEAK 18(6Q22.31) WILD-TYPE  303    6
   clus
vv  DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  0                          101                            303
  1                            1                              6
[1] 2 2
[1] FALSE
D48V7, binary
                                cls
clus                               0   1
  DEL PEAK 18(6Q22.31) MUTATED    31  90
  DEL PEAK 18(6Q22.31) WILD-TYPE  96 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(6Q22.31) MUTATED     31   90
  DEL PEAK 18(6Q22.31) WILD-TYPE   96  276
        clus
vv       DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  FEMALE                           31                             96
  MALE                             90                            276
[1] 2 2
[1] FALSE
D48V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(6Q22.31) MUTATED                                       5
  DEL PEAK 18(6Q22.31) WILD-TYPE                                    10
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(6Q22.31) MUTATED                                         0
  DEL PEAK 18(6Q22.31) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 18(6Q22.31) MUTATED                                        3
  DEL PEAK 18(6Q22.31) WILD-TYPE                                      3
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(6Q22.31) MUTATED                                         0
  DEL PEAK 18(6Q22.31) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(6Q22.31) MUTATED                                                           113
  DEL PEAK 18(6Q22.31) WILD-TYPE                                                         357
D48V9, multiclass
                                                             clus
vv                                                            DEL PEAK 18(6Q22.31) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          113
                                                             clus
vv                                                            DEL PEAK 18(6Q22.31) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            357
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, binary
                                cls
clus                               0   1
  DEL PEAK 18(6Q22.31) MUTATED     4 117
  DEL PEAK 18(6Q22.31) WILD-TYPE   9 363
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(6Q22.31) MUTATED      4  117
  DEL PEAK 18(6Q22.31) WILD-TYPE    9  363
     clus
vv    DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  NO                             4                              9
  YES                          117                            363
[1] 2 2
[1] FALSE
D48V11, continuous
D48V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 18(6Q22.31) MUTATED    98   2   2   8
  DEL PEAK 18(6Q22.31) WILD-TYPE 296  10   2  14
D48V13, multiclass
    clus
vv   DEL PEAK 18(6Q22.31) MUTATED DEL PEAK 18(6Q22.31) WILD-TYPE
  R0                           98                            296
  R1                            2                             10
  R2                            2                              2
  RX                            8                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(6Q22.31) MUTATED       2                         7    86
  DEL PEAK 18(6Q22.31) WILD-TYPE     7                        24   254
D48V14, multiclass
                           clus
vv                          DEL PEAK 18(6Q22.31) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               86
                           clus
vv                          DEL PEAK 18(6Q22.31) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             24
  WHITE                                                254
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, binary
                                cls
clus                               0   1
  DEL PEAK 18(6Q22.31) MUTATED     2  77
  DEL PEAK 18(6Q22.31) WILD-TYPE   6 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(6Q22.31) MUTATED      2   77
  DEL PEAK 18(6Q22.31) WILD-TYPE    6  232
                        clus
vv                       DEL PEAK 18(6Q22.31) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           77
                        clus
vv                       DEL PEAK 18(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            232
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 19(6Q26) MUTATION ANALYSIS
D49V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 19(6Q26) MUTATED    71  55
  DEL PEAK 19(6Q26) WILD-TYPE 210 141
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                        126                         351 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                         55                         141 
$`DEL PEAK 19(6Q26) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-5592 
       75.75       117.57        92.15         1.64         6.18        49.94 
TCGA-21-1072 TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
       99.16        43.23        88.11        33.93        10.82        21.99 
TCGA-22-1011 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 
        1.74        24.13         0.56        38.17        34.75        19.30 
TCGA-22-5471 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5489 TCGA-22-5492 
       31.73         0.79        54.28        79.20        62.86        16.64 
TCGA-33-4582 TCGA-33-4583 TCGA-33-6737 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL 
      103.53       151.27        19.76         6.94        44.19        27.16 
TCGA-34-2596 TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 TCGA-34-5927 TCGA-34-5928 
        2.63        31.50        32.88        65.23        30.94        18.15 
TCGA-34-5929 TCGA-34-8455 TCGA-37-4133 TCGA-39-5016 TCGA-39-5021 TCGA-39-5027 
        4.96         4.04         7.82        74.07        68.58        60.79 
TCGA-39-5028 TCGA-39-5034 TCGA-39-5037 TCGA-39-5039 TCGA-43-2581 TCGA-43-5668 
        1.71        36.39        35.70        17.88        38.66        18.38 
TCGA-43-6143 TCGA-43-6770 TCGA-43-8118 TCGA-46-6025 TCGA-51-4081 TCGA-52-7812 
       12.36        21.47         2.93        10.65        29.95        27.45 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-8624 
        2.04         0.43         0.99         0.85         6.51         1.18 
TCGA-56-8625 TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M 
       10.36        17.85        18.74        34.78        34.36        35.24 
TCGA-60-2707 TCGA-60-2722 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5ML TCGA-63-A5MR 
       21.93        29.85        11.77       102.67        45.57        89.29 
TCGA-63-A5MU TCGA-63-A5MY TCGA-66-2727 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
       25.41        34.59        16.96        21.01        25.05         0.99 
TCGA-66-2773 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2791 TCGA-66-2795 
        3.02        12.03        12.00        24.95         5.03         4.01 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-77-7141 TCGA-77-8007 TCGA-77-8009 
        2.73         6.64         6.94         0.49         6.51        53.95 
TCGA-77-8144 TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-85-7696 TCGA-85-7698 
       27.39        54.41       117.57        42.41        36.53        31.30 
TCGA-85-7710 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8354 
        1.38        24.13        31.56        16.87        10.09        32.71 
TCGA-85-8479 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
        0.72        25.68        14.96        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A5B5 TCGA-92-7341 TCGA-94-7557 TCGA-98-A538 
       16.21        15.85         3.65         3.48         0.16        27.16 
TCGA-98-A53B TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HD 
        2.01        18.58        19.10        16.11        13.18         0.07 
TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5D1 
        1.22         4.21        37.22        14.73        29.75        16.80 

$`DEL PEAK 19(6Q26) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 
       12.20         7.46        79.46         4.80        11.34        23.54 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
       31.99        36.07        86.96         2.79       154.32        27.19 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
      119.54        46.88        70.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 
       31.73       122.43         9.34       119.80        31.63        41.69 
TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 
       32.19         7.33        14.93         4.31        64.21        14.10 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4604 
       27.02        48.82        20.48        35.08        48.33        13.12 
TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
       32.02         9.57        11.77        64.93        63.55        14.63 
TCGA-22-5477 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 
       44.25        71.34        11.74        18.84        30.12        56.32 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       22.06         7.63       133.74        98.01        79.53       174.08 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       14.07        54.44         1.55        27.02         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ TCGA-34-2600 TCGA-34-2605 TCGA-34-2609 
       36.62       110.99       118.36        61.61        28.96        31.27 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       67.79        56.38         9.07        23.24        12.00        16.93 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
        1.12        27.19        26.43        20.91         3.95         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 
        0.39         6.58         8.12         7.46         6.81         0.39 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 
        3.39        47.80        44.75        55.20        70.03        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 
        1.94        27.39        15.58        35.64        17.06        40.21 
TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 
       22.49        27.02        33.11        27.91        24.89         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        3.81        19.59         7.76        66.51        13.38        11.77 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 
       11.61         9.73        14.20        12.03         9.99        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
        0.39         0.39        28.34         5.46        30.35         8.75 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 TCGA-56-7579 
       28.96         0.10        18.25         0.62         0.99         1.45 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 
        1.32         0.10        17.49         3.48        26.89        17.00 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8626 
       14.07         1.35        16.77         1.81        22.75         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ 
       20.25        15.81        20.94        19.23        13.32        21.04 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        0.13         0.26         2.76         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N 
       29.95        71.24        16.47        85.12        56.65        29.92 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       21.11         3.58        12.23        10.22        96.82        37.94 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 
       92.71        80.45        49.48        66.54        41.42         9.01 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       56.91        50.33        35.34        48.49        42.64         3.19 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MH 
       32.32        35.90        23.57        26.83        70.62        66.61 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS 
       58.65        59.97        14.99        11.34        25.28        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       16.37        36.16        53.88        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
        0.99         1.02         2.01         0.92         0.99        43.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
        2.01         1.02         2.01         2.01         7.07        23.01 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 
       19.00         2.01        19.00         3.98         1.97        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 
       40.01        22.98         4.04        22.98        30.02        10.06 
TCGA-66-2794 TCGA-66-2800 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
       54.08        49.05         8.02        13.35        16.18        14.73 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       29.56        73.12        75.09        23.28        11.18        89.98 
TCGA-77-7140 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
       20.78        42.28        70.13       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
       15.75        86.76        37.81        82.92        12.59        53.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 
       39.09        17.72       104.09        11.54        26.40         6.97 
TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
        9.63        65.49        35.90         0.33       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH 
       22.29         5.92        42.08        30.81        27.62        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 
        9.67        11.97        12.99         6.41        34.95        32.91 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 
        1.15        29.95        18.94        25.15        19.04        14.07 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       34.52         0.76        13.22        22.45        16.77         5.29 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        3.09         2.01         7.76        14.63        13.94        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A511 
        0.10        15.62        19.33        17.72        24.36        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
        0.79        12.39        24.92         9.50         2.93        11.77 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
       14.07        20.22        22.62        10.59         2.70         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        5.26         2.30        21.04        11.70         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
       26.63        14.14        16.14        17.69        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       18.31        17.46        19.36        16.57         8.42         2.76 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C 
       30.81        30.67        21.34         3.88        18.15        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 
       21.21        20.32        20.71        12.89        13.41        11.84 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL 
       64.08         4.54        51.78        45.37        13.74         2.89 
TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
       39.85        30.58        24.00        22.78        83.57        65.49 
TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
        3.65         0.43        33.07         3.72        12.72        43.89 
TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        8.58        11.18         0.20 

  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                       0.07                        0.03 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                     151.27                      174.08 
  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE 
                      19.20                       19.04 
[1] "0.1 - 151.3 (19.2)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1.1"
D49V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(6Q26) MUTATED         0       21       45        0        19
  DEL PEAK 19(6Q26) WILD-TYPE       2       66      106        2        44
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(6Q26) MUTATED          25         0         16          4
  DEL PEAK 19(6Q26) WILD-TYPE        67         3         46         17
                             vv
clus                          STAGE IV
  DEL PEAK 19(6Q26) MUTATED          1
  DEL PEAK 19(6Q26) WILD-TYPE        6
D49V3, multiclass
            clus
vv           DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                          21                          66
  STAGE IB                          45                         106
  STAGE II                           0                           2
  STAGE IIA                         19                          44
  STAGE IIB                         25                          67
  STAGE III                          0                           3
  STAGE IIIA                        16                          46
  STAGE IIIB                         4                          17
  STAGE IV                           1                           6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 19(6Q26) MUTATED    26  82  18   6
  DEL PEAK 19(6Q26) WILD-TYPE  85 208  51  17
D49V4, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  T1                        26                          85
  T2                        82                         208
  T3                        18                          51
  T4                         6                          17
[1] 4 2
[1] TRUE
[1] "dimension of 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(6Q26) MUTATED    88  33   9   2
  DEL PEAK 19(6Q26) WILD-TYPE 224  98  30   3
D49V5, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  N0                        88                         224
  N1                        33                          98
  N2                         9                          30
  N3                         2                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED   115   1
  DEL PEAK 19(6Q26) WILD-TYPE 289   6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED    115    1
  DEL PEAK 19(6Q26) WILD-TYPE  289    6
   clus
vv  DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  0                       115                         289
  1                         1                           6
[1] 2 2
[1] FALSE
D49V7, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED    32 100
  DEL PEAK 19(6Q26) WILD-TYPE  95 266
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED     32  100
  DEL PEAK 19(6Q26) WILD-TYPE   95  266
        clus
vv       DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  FEMALE                        32                          95
  MALE                         100                         266
[1] 2 2
[1] FALSE
D49V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(6Q26) MUTATED                                       6
  DEL PEAK 19(6Q26) WILD-TYPE                                     9
                             vv
clus                          LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(6Q26) MUTATED                                         0
  DEL PEAK 19(6Q26) WILD-TYPE                                       1
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 19(6Q26) MUTATED                                        2
  DEL PEAK 19(6Q26) WILD-TYPE                                      4
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(6Q26) MUTATED                                         0
  DEL PEAK 19(6Q26) WILD-TYPE                                       1
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(6Q26) MUTATED                                                           124
  DEL PEAK 19(6Q26) WILD-TYPE                                                         346
D49V9, multiclass
                                                             clus
vv                                                            DEL PEAK 19(6Q26) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       124
                                                             clus
vv                                                            DEL PEAK 19(6Q26) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         346
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED     4 128
  DEL PEAK 19(6Q26) WILD-TYPE   9 352
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED      4  128
  DEL PEAK 19(6Q26) WILD-TYPE    9  352
     clus
vv    DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  NO                          4                           9
  YES                       128                         352
[1] 2 2
[1] FALSE
D49V11, continuous
D49V12, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 19(6Q26) MUTATED   105   3   2   8
  DEL PEAK 19(6Q26) WILD-TYPE 289   9   2  14
D49V13, multiclass
    clus
vv   DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  R0                       105                         289
  R1                         3                           9
  R2                         2                           2
  RX                         8                          14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(6Q26) MUTATED       2                         7    92
  DEL PEAK 19(6Q26) WILD-TYPE     7                        24   248
D49V14, multiclass
                           clus
vv                          DEL PEAK 19(6Q26) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         7
  WHITE                                            92
                           clus
vv                          DEL PEAK 19(6Q26) WILD-TYPE
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          24
  WHITE                                             248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, binary
                             cls
clus                            0   1
  DEL PEAK 19(6Q26) MUTATED     2  79
  DEL PEAK 19(6Q26) WILD-TYPE   6 230
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(6Q26) MUTATED      2   79
  DEL PEAK 19(6Q26) WILD-TYPE    6  230
                        clus
vv                       DEL PEAK 19(6Q26) MUTATED DEL PEAK 19(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             2                           6
  NOT HISPANIC OR LATINO                        79                         230
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 20(7Q11.22) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(7Q11.22) MUTATED    28  17
  DEL PEAK 20(7Q11.22) WILD-TYPE 253 179
  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                            45                            432 
  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                            17                            179 
$`DEL PEAK 20(7Q11.22) MUTATED`
TCGA-18-3421 TCGA-21-1082 TCGA-21-5787 TCGA-22-1016 TCGA-22-5477 TCGA-22-5481 
       86.96       119.80        10.82        27.02        44.25        79.20 
TCGA-33-AASI TCGA-37-5819 TCGA-43-2578 TCGA-43-2581 TCGA-43-6770 TCGA-43-6771 
       44.19         3.39        22.49        38.66        21.47         5.46 
TCGA-43-7656 TCGA-46-6026 TCGA-56-6545 TCGA-56-6546 TCGA-56-7580 TCGA-56-8629 
       19.59        13.91         2.04         0.62         1.32        15.81 
TCGA-56-A4BW TCGA-60-2695 TCGA-60-2703 TCGA-60-2719 TCGA-63-A5MH TCGA-63-A5MT 
       19.23        21.11        96.82        42.64        66.61        16.37 
TCGA-66-2727 TCGA-66-2754 TCGA-66-2773 TCGA-66-2788 TCGA-77-7465 TCGA-77-8139 
       16.96         2.01         3.02        22.98        15.75       104.09 
TCGA-77-8144 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 
       27.39        38.86        11.97        32.91         1.15        25.15 
TCGA-85-8072 TCGA-85-8350 TCGA-85-8353 TCGA-85-A510 TCGA-98-A53B TCGA-NC-A5HK 
       16.87        22.45         3.09        15.85         2.01         4.21 
TCGA-NC-A5HL TCGA-O2-A52N TCGA-O2-A52S 
        2.89        33.07        12.72 

$`DEL PEAK 20(7Q11.22) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
       11.34        23.54        92.15        31.99        36.07         1.64 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
        6.18         2.79       154.32        49.94        27.19       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       46.88        99.16        70.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       31.73       122.43         9.34        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 
       41.69        33.93        32.19        21.99         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 
        4.31        64.21         1.74        14.10        48.82        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       35.08        48.33        24.13         0.56        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 
       13.12        32.02        19.30         9.57        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       64.93        63.55        14.63         0.79        54.28        71.34 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       11.74        18.84        30.12        62.86        56.32        16.64 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       22.06         7.63       133.74        98.01        79.53       174.08 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
      103.53       151.27        14.07        54.44         1.55        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       27.02         4.70         0.30        36.62         6.94       110.99 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
      118.36        27.16         2.63        61.61        31.50        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       32.88        31.27        65.23        67.79        56.38         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       23.24        12.00        16.93        30.94        18.15         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        1.12        27.19         4.04        26.43        20.91         3.95 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        0.43         0.39         6.58         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        6.81         0.39        47.80        74.07        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        70.03        60.79         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
       27.39        36.39        15.58        35.64        35.70        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
       17.06        40.21        27.02        33.11        18.38        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       12.36        24.89         3.81         7.76        66.51        13.38 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V 
       11.77         2.93        11.61         9.73        14.20        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        9.99        10.65         0.39         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
        5.46        30.35         8.75        27.45        28.96         0.10 
TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
       18.25         0.99         0.43         0.99         1.45         0.85 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 
        6.51         0.10        17.49         3.48        26.89        17.00 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       14.07         1.35        16.77         1.81        22.75         1.18 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY 
       10.36         9.93        20.25        20.94        13.32        17.85 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       21.04        18.74         0.13         0.26         2.76         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       13.25        13.55        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 
       85.12        34.36        56.65        35.24        29.92         3.58 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       12.23        10.22        37.94        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
       49.48        66.54        41.42         9.01        56.91        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
       35.34        48.49         3.19        32.32        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       23.57        26.83        11.77       102.67        70.62        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       59.97        45.57        14.99        11.34        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 
       78.28        25.41        36.16        53.88        34.59        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 
        2.01        21.07         0.99         1.02         0.92         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
       43.99        21.01        25.05         0.99         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 
        2.01         2.01         7.07        23.01        19.00         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
       25.97        40.01         4.04        22.98         5.03        30.02 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       10.06        54.08         4.01        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
        6.94         8.02        13.35        16.18        14.73        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 
       73.12        75.09        23.28        11.18        89.98        20.78 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        0.49        42.28        70.13       106.95         0.16        46.78 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        6.51        86.76        53.95        37.81        82.92        12.59 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 
       53.92        39.09        17.72        11.54        26.40         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
        9.63        54.41        65.49        35.90         0.33       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
      132.36       117.57        22.29         5.92        42.41        42.08 
TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       30.81        27.62         9.67        12.99         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
       34.95        31.30         1.38        29.95        18.94        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       24.13        31.56        14.07        34.52        10.09         0.76 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       13.22        16.77         5.29        32.71         2.01         0.72 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        7.76        14.63        13.94        12.59         0.10        15.62 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       25.68        19.33        17.72        14.96        24.36        18.18 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       19.73        12.56        16.21        14.96         0.79        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
        3.65        24.92         9.50         2.93        11.77        14.07 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       20.22        22.62        10.59         2.70         3.48         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 
        5.26         2.30        21.04         0.16        11.70         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 
        5.03        26.63        14.14        16.14        17.69        49.87 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
       57.07        18.31        17.46        19.36        16.57         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        2.76        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
       18.15        27.02        21.21        20.32        18.58        20.71 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       19.10        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
        0.07        64.08         4.54        51.78         1.22        45.37 
TCGA-NC-A5HJ TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
       13.74        39.85        37.22        30.58        24.00        14.73 
TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       29.75        22.78        83.57        65.49         3.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        0.43         3.72        43.89         8.58        11.18         0.20 

  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                          0.62                           0.03 
  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                        119.80                         174.08 
  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE 
                         19.23                          19.07 
[1] "0.6 - 119.8 (19.2)" "0.0 - 174.1 (19.1)"
[1] "hr=" "1.1"
D50V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(7Q11.22) MUTATED         1        8       15        0         7
  DEL PEAK 20(7Q11.22) WILD-TYPE       1       79      136        2        56
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(7Q11.22) MUTATED           8         1          6          0
  DEL PEAK 20(7Q11.22) WILD-TYPE        84         2         56         21
                                vv
clus                             STAGE IV
  DEL PEAK 20(7Q11.22) MUTATED          0
  DEL PEAK 20(7Q11.22) WILD-TYPE        7
D50V3, multiclass
            clus
vv           DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              8                             79
  STAGE IB                             15                            136
  STAGE II                              0                              2
  STAGE IIA                             7                             56
  STAGE IIB                             8                             84
  STAGE III                             1                              2
  STAGE IIIA                            6                             56
  STAGE IIIB                            0                             21
  STAGE IV                              0                              7
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 20(7Q11.22) MUTATED    10  29   5   2
  DEL PEAK 20(7Q11.22) WILD-TYPE 101 261  64  21
D50V4, multiclass
    clus
vv   DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  T1                           10                            101
  T2                           29                            261
  T3                            5                             64
  T4                            2                             21
[1] 4 2
[1] TRUE
[1] "dimension of 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(7Q11.22) MUTATED    31  11   4   0
  DEL PEAK 20(7Q11.22) WILD-TYPE 281 120  35   5
D50V5, multiclass
    clus
vv   DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  N0                           31                            281
  N1                           11                            120
  N2                            4                             35
  N3                            0                              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"
D50V6, binary
                                cls
clus                               0   1
  DEL PEAK 20(7Q11.22) MUTATED    38   0
  DEL PEAK 20(7Q11.22) WILD-TYPE 366   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(7Q11.22) MUTATED     38    0
  DEL PEAK 20(7Q11.22) WILD-TYPE  366    7
   clus
vv  DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  0                           38                            366
  1                            0                              7
[1] 2 2
[1] FALSE
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(7Q11.22) MUTATED    13  33
  DEL PEAK 20(7Q11.22) WILD-TYPE 114 333
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(7Q11.22) MUTATED     13   33
  DEL PEAK 20(7Q11.22) WILD-TYPE  114  333
        clus
vv       DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  FEMALE                           13                            114
  MALE                             33                            333
[1] 2 2
[1] FALSE
D50V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(7Q11.22) MUTATED                                       1
  DEL PEAK 20(7Q11.22) WILD-TYPE                                    14
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(7Q11.22) MUTATED                                         0
  DEL PEAK 20(7Q11.22) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 20(7Q11.22) MUTATED                                        0
  DEL PEAK 20(7Q11.22) WILD-TYPE                                      6
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(7Q11.22) MUTATED                                         0
  DEL PEAK 20(7Q11.22) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(7Q11.22) MUTATED                                                            45
  DEL PEAK 20(7Q11.22) WILD-TYPE                                                         425
D50V9, multiclass
                                                             clus
vv                                                            DEL PEAK 20(7Q11.22) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  1
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           45
                                                             clus
vv                                                            DEL PEAK 20(7Q11.22) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   14
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            425
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, binary
                                cls
clus                               0   1
  DEL PEAK 20(7Q11.22) MUTATED     2  44
  DEL PEAK 20(7Q11.22) WILD-TYPE  11 436
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(7Q11.22) MUTATED      2   44
  DEL PEAK 20(7Q11.22) WILD-TYPE   11  436
     clus
vv    DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  NO                             2                             11
  YES                           44                            436
[1] 2 2
[1] FALSE
D50V11, continuous
D50V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 20(7Q11.22) MUTATED    38   0   1   3
  DEL PEAK 20(7Q11.22) WILD-TYPE 356  12   3  19
D50V13, multiclass
    clus
vv   DEL PEAK 20(7Q11.22) MUTATED DEL PEAK 20(7Q11.22) WILD-TYPE
  R0                           38                            356
  R1                            0                             12
  R2                            1                              3
  RX                            3                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(7Q11.22) MUTATED       0                         3    34
  DEL PEAK 20(7Q11.22) WILD-TYPE     9                        28   306
D50V14, multiclass
                           clus
vv                          DEL PEAK 20(7Q11.22) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               34
                           clus
vv                          DEL PEAK 20(7Q11.22) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                             28
  WHITE                                                306
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V15, binary
                                cls
clus                               0   1
  DEL PEAK 20(7Q11.22) MUTATED     0  30
  DEL PEAK 20(7Q11.22) WILD-TYPE   8 279
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(7Q11.22) MUTATED      0   30
  DEL PEAK 20(7Q11.22) WILD-TYPE    8  279
                        clus
vv                       DEL PEAK 20(7Q11.22) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           30
                        clus
vv                       DEL PEAK 20(7Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            279
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 21(7Q36.3) MUTATION ANALYSIS
D51V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(7Q36.3) MUTATED    55  42
  DEL PEAK 21(7Q36.3) WILD-TYPE 226 154
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           97                           380 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                           42                           154 
$`DEL PEAK 21(7Q36.3) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3415 TCGA-18-4721 TCGA-18-5595 TCGA-21-1072 
       12.20        75.75        92.15       154.32        27.19        99.16 
TCGA-21-1082 TCGA-21-5786 TCGA-22-1002 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 
      119.80        33.93         4.31         1.74        27.02        48.82 
TCGA-22-4595 TCGA-22-4601 TCGA-22-5481 TCGA-22-5482 TCGA-33-4589 TCGA-33-A5GW 
       24.13        34.75        79.20        11.74         1.55         0.30 
TCGA-34-5241 TCGA-37-3789 TCGA-37-3792 TCGA-37-4135 TCGA-37-5819 TCGA-39-5024 
       16.93         0.43         0.39         6.81         3.39        70.03 
TCGA-39-5031 TCGA-39-5034 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 
       27.39        36.39        22.49        38.66        33.11        18.38 
TCGA-43-5670 TCGA-43-6771 TCGA-43-7658 TCGA-43-A475 TCGA-46-6026 TCGA-52-7809 
       27.91         5.46        66.51         9.73        13.91         5.46 
TCGA-56-1622 TCGA-56-6545 TCGA-56-7580 TCGA-56-8503 TCGA-56-8626 TCGA-56-8629 
       28.96         2.04         1.32         1.35         9.93        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 
       20.94        19.23        17.85        56.65        21.11         3.58 
TCGA-60-2703 TCGA-60-2707 TCGA-60-2712 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH 
       96.82        21.93         9.01        11.77       102.67        66.61 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2753 
       89.29        78.28        36.16        53.88        34.59         1.02 
TCGA-66-2773 TCGA-66-2788 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 TCGA-77-6843 
        3.02        22.98         2.73         6.94         8.02        73.12 
TCGA-77-6844 TCGA-77-7138 TCGA-77-7337 TCGA-77-7465 TCGA-77-8131 TCGA-77-8136 
       75.09        11.18       106.95        15.75        12.59        39.09 
TCGA-77-8139 TCGA-77-8144 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 
      104.09        27.39        30.81        38.86        11.97        32.91 
TCGA-85-8048 TCGA-85-8070 TCGA-85-8287 TCGA-85-8353 TCGA-85-A4JB TCGA-85-A4QQ 
       25.15        31.56         0.76         3.09        17.72        18.18 
TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-90-7767 TCGA-92-8065 TCGA-94-A4VJ 
       15.85         0.79        12.39         2.93         2.30        14.14 
TCGA-94-A5I4 TCGA-98-8022 TCGA-98-A53A TCGA-LA-A7SW TCGA-NC-A5HK TCGA-NC-A5HM 
       16.14        30.67        18.15        13.41         4.21        39.85 
TCGA-NC-A5HQ 
       14.73 

$`DEL PEAK 21(7Q36.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        7.46        79.46         4.80       117.57        11.34        23.54 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       31.99        36.07         1.64        86.96         6.18         2.79 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
       49.94       119.54        46.88        70.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 
       15.58        31.73       122.43         9.34        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
       88.11        41.69        10.82        32.19        21.99         7.33 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
       14.93        64.21        14.10        20.48        35.08        48.33 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
        0.56        38.17        13.12        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       11.77        31.73        64.93        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
        0.79        54.28        71.34        18.84        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
       56.32        16.64        22.06         7.63       133.74        98.01 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       79.53       174.08       103.53       151.27        14.07        54.44 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       19.76        27.02         4.70        36.62         6.94       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
       44.19       118.36        27.16         2.63        61.61        31.50 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       28.96        32.88        31.27        65.23        67.79        56.38 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
        9.07        23.24        12.00        30.94        18.15         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        1.12        27.19         4.04        26.43        20.91         3.95 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-39-5011 
        6.58         8.12         7.46         7.82         0.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 
       74.07        44.75        68.58        55.20        60.79         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
       24.33         1.94        15.58        35.64        35.70        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       17.06        40.21        27.02        12.36        24.89        21.47 
TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
        3.81        19.59         7.76        13.38        11.77         2.93 
TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 
       11.61        14.20        12.03         9.99        10.65         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
        0.39        29.95        28.34        30.35         8.75        27.45 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
        0.10        18.25         0.62         0.99         0.43         0.99 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        1.45         0.85         6.51         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 
       26.89        17.00        14.07        16.77         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK 
        1.18        10.36        20.25        13.32        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        0.13         0.26         2.76         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       29.95        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 
       35.24        29.92        12.23        10.22        37.94        92.71 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
       80.45        49.48        66.54        41.42        56.91        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
       35.34        48.49        42.64         3.19        32.32        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
       35.90        23.57        26.83        70.62        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MU 
       45.57        14.99        11.34        25.28        16.37        25.41 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
       16.96        43.10         2.01        21.07         0.99         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        0.92         0.99        43.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
        2.01         1.02         2.01         2.01         7.07        23.01 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
       19.00         2.01        19.00        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 
       24.95         1.97        25.97        40.01         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        5.03        30.02        10.06        54.08         4.01        49.05 
TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 
        6.64        13.35        16.18        14.73        29.56        23.28 
TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 
       89.98        20.78         0.49        42.28        70.13         0.16 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       46.78         6.51        86.76        53.95        37.81        82.92 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 
       53.92        17.72        11.54        26.40         6.97         9.63 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       54.41        65.49        35.90         0.33       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF 
      117.57        22.29         5.92        42.41        42.08        27.62 
TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
        9.67        12.99         6.41        36.53        34.95        31.30 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 
        1.38         1.15        29.95        18.94        19.04        24.13 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 
       14.07        16.87        34.52        10.09        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       16.77         5.29        32.71         2.01         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       14.63        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       19.33        14.96        24.36        19.73        12.56        16.21 
TCGA-85-A511 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 
       14.96         3.65        24.92         9.50        11.77        14.07 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       20.22        22.62        10.59         2.70         3.48         4.01 
TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        5.26        21.04         0.16        11.70         4.01         5.03 
TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
       26.63        17.69        49.87        57.07        18.31        17.46 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8023 
       19.36        16.57         8.42         2.76        30.81        21.34 
TCGA-98-A538 TCGA-98-A539 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       27.16         3.88         2.01        27.02        21.21        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       18.58        20.71        19.10        12.89        16.11        13.18 
TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       11.84         0.07        64.08         4.54        51.78         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       45.37        13.74         2.89        37.22        30.58        24.00 
TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       29.75        22.78        83.57        65.49         3.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W 
        0.43        33.07         3.72        12.72        43.89         8.58 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                         0.30                          0.03 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                       154.32                        174.08 
  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE 
                        18.38                         19.20 
[1] "0.3 - 154.3 (18.4)" "0.0 - 174.1 (19.2)"
[1] "hr=" "1"  
D51V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(7Q36.3) MUTATED         0       19       37        0        15
  DEL PEAK 21(7Q36.3) WILD-TYPE       2       68      114        2        48
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(7Q36.3) MUTATED          17         0         12          1
  DEL PEAK 21(7Q36.3) WILD-TYPE        75         3         50         20
                               vv
clus                            STAGE IV
  DEL PEAK 21(7Q36.3) MUTATED          0
  DEL PEAK 21(7Q36.3) WILD-TYPE        7
D51V3, multiclass
            clus
vv           DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                            19                            68
  STAGE IB                            37                           114
  STAGE II                             0                             2
  STAGE IIA                           15                            48
  STAGE IIB                           17                            75
  STAGE III                            0                             3
  STAGE IIIA                          12                            50
  STAGE IIIB                           1                            20
  STAGE IV                             0                             7
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 21(7Q36.3) MUTATED    25  61  13   2
  DEL PEAK 21(7Q36.3) WILD-TYPE  86 229  56  21
D51V4, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  T1                          25                            86
  T2                          61                           229
  T3                          13                            56
  T4                           2                            21
[1] 4 2
[1] TRUE
[1] "dimension of 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(7Q36.3) MUTATED    68  24   6   0
  DEL PEAK 21(7Q36.3) WILD-TYPE 244 107  33   5
D51V5, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  N0                          68                           244
  N1                          24                           107
  N2                           6                            33
  N3                           0                             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 21(7Q36.3) MUTATED    87   0
  DEL PEAK 21(7Q36.3) WILD-TYPE 317   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED     87    0
  DEL PEAK 21(7Q36.3) WILD-TYPE  317    7
   clus
vv  DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  0                          87                           317
  1                           0                             7
[1] 2 2
[1] FALSE
D51V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.3) MUTATED    26  75
  DEL PEAK 21(7Q36.3) WILD-TYPE 101 291
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED     26   75
  DEL PEAK 21(7Q36.3) WILD-TYPE  101  291
        clus
vv       DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  FEMALE                          26                           101
  MALE                            75                           291
[1] 2 2
[1] FALSE
D51V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(7Q36.3) MUTATED                                       3
  DEL PEAK 21(7Q36.3) WILD-TYPE                                    12
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(7Q36.3) MUTATED                                         1
  DEL PEAK 21(7Q36.3) WILD-TYPE                                       0
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 21(7Q36.3) MUTATED                                        0
  DEL PEAK 21(7Q36.3) WILD-TYPE                                      6
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(7Q36.3) MUTATED                                         0
  DEL PEAK 21(7Q36.3) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(7Q36.3) MUTATED                                                            97
  DEL PEAK 21(7Q36.3) WILD-TYPE                                                         373
D51V9, multiclass
                                                             clus
vv                                                            DEL PEAK 21(7Q36.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          97
                                                             clus
vv                                                            DEL PEAK 21(7Q36.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           373
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.3) MUTATED     3  98
  DEL PEAK 21(7Q36.3) WILD-TYPE  10 382
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED      3   98
  DEL PEAK 21(7Q36.3) WILD-TYPE   10  382
     clus
vv    DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  NO                            3                            10
  YES                          98                           382
[1] 2 2
[1] FALSE
D51V11, continuous
D51V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(7Q36.3) MUTATED    84   1   1   6
  DEL PEAK 21(7Q36.3) WILD-TYPE 310  11   3  16
D51V13, multiclass
    clus
vv   DEL PEAK 21(7Q36.3) MUTATED DEL PEAK 21(7Q36.3) WILD-TYPE
  R0                          84                           310
  R1                           1                            11
  R2                           1                             3
  RX                           6                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(7Q36.3) MUTATED       2                         4    72
  DEL PEAK 21(7Q36.3) WILD-TYPE     7                        27   268
D51V14, multiclass
                           clus
vv                          DEL PEAK 21(7Q36.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              72
                           clus
vv                          DEL PEAK 21(7Q36.3) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            27
  WHITE                                               268
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                               cls
clus                              0   1
  DEL PEAK 21(7Q36.3) MUTATED     2  62
  DEL PEAK 21(7Q36.3) WILD-TYPE   6 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(7Q36.3) MUTATED      2   62
  DEL PEAK 21(7Q36.3) WILD-TYPE    6  247
                        clus
vv                       DEL PEAK 21(7Q36.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          62
                        clus
vv                       DEL PEAK 21(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           247
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 22(8P23.2) MUTATION ANALYSIS
D52V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(8P23.2) MUTATED   188 136
  DEL PEAK 22(8P23.2) WILD-TYPE  93  60
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          324                           153 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                          136                            60 
$`DEL PEAK 22(8P23.2) MUTATED`
TCGA-18-3406 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 
       12.20       117.57        11.34        92.15        31.99         1.64 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 
        6.18         2.79       154.32        49.94        27.19       119.54 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 
       99.16        70.16        60.89        34.78       122.43         9.34 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-1000 
       43.23        31.63        88.11        33.93        10.82        14.93 
TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 
        4.31        14.10        27.02        48.82        20.48        48.33 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 
        0.56        38.17        34.75        13.12        32.02         9.57 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 
       11.77        31.73        63.55        44.25         0.79        71.34 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       79.20        18.84        30.12        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 
        7.63        79.53       174.08       103.53        14.07         1.55 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD 
       19.76        27.02         4.70         0.30        36.62       110.99 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 
       44.19        27.16         2.63        61.61        31.50        28.96 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5236 TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 
       31.27        65.23         9.07        16.93        18.15        27.19 
TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4132 TCGA-37-4135 
        4.04         3.95         0.43         0.39         7.46         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 
        0.39        47.80        74.07        44.75        68.58        70.03 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 TCGA-39-5039 
       60.79         1.71        24.33        27.39        35.70        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       17.06        40.21        22.49        38.66        27.02        33.11 
TCGA-43-5668 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7657 
       18.38        12.36        24.89        21.47         5.46         7.76 
TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 
       66.51        11.77         2.93        11.61        12.03         9.99 
TCGA-46-6025 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
       10.65         0.39        29.95        28.34         5.46        30.35 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 
       27.45        28.96         0.10        18.25         0.43         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-8504 TCGA-56-8626 TCGA-56-8628 
        1.45         1.32         0.85        16.77         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK 
       15.81        20.94        19.23        13.32        17.85        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8387 TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 
        0.13         0.26        13.25        29.95        16.47        34.78 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       34.36        56.65        35.24        10.22        96.82        37.94 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
       92.71        80.45        66.54        41.42         9.01        56.91 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
       50.33        42.64         3.19        32.32        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML 
       26.83        11.77       102.67        58.65        59.97        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       14.99        11.34        25.28        78.28        16.37        25.41 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
       36.16        53.88        34.59        16.96        43.10         2.01 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
        0.99         1.02         2.01         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 
       21.01        25.05         0.99         1.02         2.01         7.07 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
       12.03         3.98        12.00        24.95         1.97        40.01 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 
        4.04        22.98         5.03        30.02        10.06         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
       49.05         2.73         8.02        13.35        16.18        14.73 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       29.56        73.12        75.09        23.28        11.18        89.98 
TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
       20.78         0.49        42.28       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       15.75         6.51        86.76        53.95        37.81        82.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       39.09        17.72       104.09        11.54        26.40        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5G8 
        6.97         9.63        35.90         0.33        22.29        42.41 
TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       42.08        27.62        38.86         9.67        11.97        12.99 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 
        6.41        36.53        34.95        31.30         1.38         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       29.95        18.94        25.15        24.13        31.56        14.07 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 
       16.87        34.52        10.09        22.45         5.29         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
       32.71         2.01         7.76        13.94        12.59         0.10 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       19.33        17.72        14.96        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 
       16.21        14.96         0.79        12.39         3.65         9.50 
TCGA-90-7767 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-94-7557 TCGA-94-7943 
        2.93        20.22         3.48         4.01         0.16        11.70 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
       26.63        14.14        16.14        17.69        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       18.31        17.46        19.36         2.76        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J 
       21.34        27.16         3.88        18.15         2.01        20.71 
TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       19.10        16.11        13.18        11.84         0.07        64.08 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HM 
       51.78         1.22        45.37        13.74         2.89        39.85 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
       37.22        24.00        14.73        29.75        22.78        83.57 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       33.07         3.72        12.72        43.89         8.58         0.20 

$`DEL PEAK 22(8P23.2) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3414 TCGA-18-3417 
        7.46        75.75        79.46         4.80        23.54        36.07 
TCGA-18-3421 TCGA-21-1071 TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 TCGA-21-5784 
       86.96        46.88        15.58        31.73       119.80        41.69 
TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 
       32.19        21.99         7.33        64.21         1.74        35.08 
TCGA-22-4595 TCGA-22-4607 TCGA-22-5472 TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 
       24.13        19.30        64.93        14.63        54.28        11.74 
TCGA-22-5489 TCGA-33-4533 TCGA-33-4538 TCGA-33-4583 TCGA-33-4587 TCGA-33-AASB 
       62.86       133.74        98.01       151.27        54.44         6.94 
TCGA-33-AASJ TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 
      118.36        32.88        67.79        56.38        23.24        12.00 
TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4129 
       30.94         4.96         1.12        26.43        20.91         6.58 
TCGA-37-4130 TCGA-37-4133 TCGA-37-5819 TCGA-39-5022 TCGA-39-5030 TCGA-39-5034 
        8.12         7.82         3.39        55.20         1.94        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-43-5670 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       15.58        35.64        27.91         3.81        19.59        13.38 
TCGA-43-A475 TCGA-43-A56U TCGA-46-6026 TCGA-51-4079 TCGA-52-7811 TCGA-56-6545 
        9.73        14.20        13.91         0.39         8.75         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        0.62         0.99         6.51         0.10        17.49         3.48 
TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
       26.89        17.00        14.07         1.35         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-A4ZJ TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 
        1.18        10.36        21.04         2.76         0.03        13.55 
TCGA-58-8391 TCGA-58-A46J TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 
       71.24        85.12        29.92        21.11         3.58        12.23 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2715 TCGA-60-2716 TCGA-60-2722 TCGA-63-A5MG 
       21.93        49.48        35.34        48.49        29.85        70.62 
TCGA-63-A5MH TCGA-63-A5MR TCGA-66-2742 TCGA-66-2765 TCGA-66-2767 TCGA-66-2770 
       66.61        89.29        21.07         2.01         2.01        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2786 TCGA-66-2788 
       19.00         3.02         2.01        19.00        25.97        22.98 
TCGA-66-2794 TCGA-68-7756 TCGA-68-7757 TCGA-77-7335 TCGA-77-8131 TCGA-77-8133 
       54.08         6.64         6.94        70.13        12.59        53.92 
TCGA-77-8150 TCGA-77-8153 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 
       54.41        65.49       126.18       132.36       117.57         5.92 
TCGA-77-A5GB TCGA-85-7699 TCGA-85-8049 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
       30.81        32.91        19.04         0.76        13.22        16.77 
TCGA-85-8479 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A510 
        0.72        14.63        15.62        25.68        24.36        15.85 
TCGA-90-6837 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       24.92        11.77        14.07        22.62        10.59         2.70 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 TCGA-94-8490 TCGA-96-A4JL 
        5.26         2.30        21.04         4.01         5.03        16.57 
TCGA-98-7454 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 
        8.42        27.02        21.21        20.32        18.58        12.89 
TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NK-A5CT TCGA-NK-A5CX 
       13.41         4.54         4.21        30.58        65.49         3.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A5IB 
       16.80         0.43        11.18 

  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                       174.08                        151.27 
  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE 
                       19.345                        19.000 
[1] "0.1 - 174.1 (19.3)" "0.0 - 151.3 (19.0)"
[1] "hr=" "1.1"
D52V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(8P23.2) MUTATED         2       62       96        1        41
  DEL PEAK 22(8P23.2) WILD-TYPE       0       25       55        1        22
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(8P23.2) MUTATED          68         2         48         12
  DEL PEAK 22(8P23.2) WILD-TYPE        24         1         14          9
                               vv
clus                            STAGE IV
  DEL PEAK 22(8P23.2) MUTATED          3
  DEL PEAK 22(8P23.2) WILD-TYPE        4
D52V3, multiclass
            clus
vv           DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                            62                            25
  STAGE IB                            96                            55
  STAGE II                             1                             1
  STAGE IIA                           41                            22
  STAGE IIB                           68                            24
  STAGE III                            2                             1
  STAGE IIIA                          48                            14
  STAGE IIIB                          12                             9
  STAGE IV                             3                             4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 22(8P23.2) MUTATED    78 199  46  13
  DEL PEAK 22(8P23.2) WILD-TYPE  33  91  23  10
D52V4, multiclass
    clus
vv   DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  T1                          78                            33
  T2                         199                            91
  T3                          46                            23
  T4                          13                            10
[1] 4 2
[1] TRUE
[1] "dimension of 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   204  96  30   3
  DEL PEAK 22(8P23.2) WILD-TYPE 108  35   9   2
D52V5, multiclass
    clus
vv   DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  N0                         204                           108
  N1                          96                            35
  N2                          30                             9
  N3                           3                             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"
D52V6, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.2) MUTATED   287   3
  DEL PEAK 22(8P23.2) WILD-TYPE 117   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED    287    3
  DEL PEAK 22(8P23.2) WILD-TYPE  117    4
   clus
vv  DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  0                         287                           117
  1                           3                             4
[1] 2 2
[1] FALSE
D52V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.2) MUTATED    82 254
  DEL PEAK 22(8P23.2) WILD-TYPE  45 112
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED     82  254
  DEL PEAK 22(8P23.2) WILD-TYPE   45  112
        clus
vv       DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  FEMALE                          82                            45
  MALE                           254                           112
[1] 2 2
[1] FALSE
D52V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(8P23.2) MUTATED                                       9
  DEL PEAK 22(8P23.2) WILD-TYPE                                     6
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(8P23.2) MUTATED                                         1
  DEL PEAK 22(8P23.2) WILD-TYPE                                       0
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 22(8P23.2) MUTATED                                        3
  DEL PEAK 22(8P23.2) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(8P23.2) MUTATED                                         0
  DEL PEAK 22(8P23.2) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(8P23.2) MUTATED                                                           323
  DEL PEAK 22(8P23.2) WILD-TYPE                                                         147
D52V9, multiclass
                                                             clus
vv                                                            DEL PEAK 22(8P23.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         323
                                                             clus
vv                                                            DEL PEAK 22(8P23.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           147
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.2) MUTATED    10 326
  DEL PEAK 22(8P23.2) WILD-TYPE   3 154
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED     10  326
  DEL PEAK 22(8P23.2) WILD-TYPE    3  154
     clus
vv    DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  NO                           10                             3
  YES                         326                           154
[1] 2 2
[1] FALSE
D52V11, continuous
D52V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(8P23.2) MUTATED   274   7   2  14
  DEL PEAK 22(8P23.2) WILD-TYPE 120   5   2   8
D52V13, multiclass
    clus
vv   DEL PEAK 22(8P23.2) MUTATED DEL PEAK 22(8P23.2) WILD-TYPE
  R0                         274                           120
  R1                           7                             5
  R2                           2                             2
  RX                          14                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(8P23.2) MUTATED       5                        20   230
  DEL PEAK 22(8P23.2) WILD-TYPE     4                        11   110
D52V14, multiclass
                           clus
vv                          DEL PEAK 22(8P23.2) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                          20
  WHITE                                             230
                           clus
vv                          DEL PEAK 22(8P23.2) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V15, binary
                               cls
clus                              0   1
  DEL PEAK 22(8P23.2) MUTATED     5 203
  DEL PEAK 22(8P23.2) WILD-TYPE   3 106
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(8P23.2) MUTATED      5  203
  DEL PEAK 22(8P23.2) WILD-TYPE    3  106
                        clus
vv                       DEL PEAK 22(8P23.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         203
                        clus
vv                       DEL PEAK 22(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           106
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 23(9P23) MUTATION ANALYSIS
D53V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 23(9P23) MUTATED   188 124
  DEL PEAK 23(9P23) WILD-TYPE  93  72
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        312                         165 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                        124                          72 
$`DEL PEAK 23(9P23) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       12.20        79.46       117.57        11.34        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 
       36.07         1.64         2.79       154.32        49.94        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 
       99.16        70.16        34.78        31.73       122.43       119.80 
TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 
       43.23        88.11        33.93        10.82        32.19        21.99 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
       14.93        64.21         1.74        14.10        27.02        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 
       35.08        48.33        24.13        38.17        34.75        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5477 TCGA-22-5478 
        9.57        11.77        31.73        64.93        44.25         0.79 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-A5C4 
       54.28        11.74        18.84        30.12        56.32        22.06 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
       98.01        79.53       103.53        19.76        27.02         4.70 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
       36.62         6.94       110.99        44.19       118.36        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
        2.63        61.61        31.50        28.96        32.88        31.27 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 
       65.23        67.79        16.93        30.94         4.96        27.19 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 
        4.04        26.43        20.91         3.95         0.43         8.12 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5027 
        6.81         0.39         3.39        47.80        74.07        60.79 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5040 
        1.71        24.33         1.94        27.39        35.64        17.06 
TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6770 
       22.49        27.02        33.11        18.38        27.91        21.47 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 
        5.46        19.59         7.76        13.38        11.77         2.93 
TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 
       11.61        12.03         9.99        13.91         0.39        29.95 
TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        5.46        30.35        28.96         0.10        18.25         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
        0.62         0.99         0.43         0.99         1.45         1.32 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 
        0.85         6.51         0.10        17.49        26.89        17.00 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35        16.77         1.81         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
        9.93        20.25        15.81        20.94        19.23        13.32 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 
       21.04         0.13         0.26         0.03        13.25        29.95 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 
       16.47        34.78        85.12        56.65         3.58        10.22 
TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 
       96.82        92.71        21.93        80.45        66.54        41.42 
TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2726 
       56.91        42.64         3.19        32.32        23.57        11.77 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MP 
      102.67        70.62        66.61        58.65        59.97        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 
       89.29        78.28        16.37        53.88        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 
        2.01        21.07         0.99         1.02         2.01         0.99 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2777 
       25.05         2.01         2.01         7.07        19.00         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 
       19.00        12.03         3.98        12.00         1.97        25.97 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-66-2800 TCGA-68-7757 
       22.98         4.04        22.98        10.06        49.05         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       13.35        16.18        73.12        75.09        23.28        11.18 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 
       42.28        70.13       106.95         0.16        15.75        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 
       53.95        37.81        82.92        53.92        17.72        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 
       26.40        27.39         6.97         9.63        65.49        35.90 
TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH 
        0.33       132.36        22.29         5.92        42.41        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 
        9.67        11.97        36.53        34.95        32.91         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8276 
        1.15        29.95        18.94        25.15        14.07        34.52 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 
        0.76        13.22        22.45        16.77         5.29        32.71 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
        0.72         7.76        14.63         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       19.33        17.72        14.96        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       16.21        15.85        14.96         0.79        12.39         3.65 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
        9.50         2.93        14.07        10.59         2.70         3.48 
TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 
        4.01         2.30        21.04         0.16        11.70         4.01 
TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8169 
        5.03        14.14        16.14        17.69        57.07        18.31 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8020 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 
       19.36        16.57         2.76        30.81        21.34        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 
        3.88        18.15         2.01        18.58        20.71        16.11 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       13.41        11.84         0.07         4.54        51.78        45.37 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
       37.22        30.58        24.00        22.78        83.57        65.49 
TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       16.80         3.72        12.72        43.89         8.58         0.20 

$`DEL PEAK 23(9P23) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3416 TCGA-18-3421 TCGA-18-4083 
        7.46        75.75         4.80        31.99        86.96         6.18 
TCGA-18-5595 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 
       27.19       119.54        60.89        15.58         9.34        31.63 
TCGA-21-5784 TCGA-22-0944 TCGA-22-1002 TCGA-22-1017 TCGA-22-4596 TCGA-22-4604 
       41.69         7.33         4.31        48.82         0.56        13.12 
TCGA-22-4605 TCGA-22-5473 TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-22-5489 
       32.02        63.55        14.63        71.34        79.20        62.86 
TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 
       16.64         7.63       133.74       174.08       151.27        14.07 
TCGA-33-4587 TCGA-33-4589 TCGA-33-A5GW TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       54.44         1.55         0.30        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
       12.00        18.15         1.12         0.39         6.58         7.46 
TCGA-37-4133 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5034 
        7.82        44.75        68.58        55.20        70.03        36.39 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-6143 
       15.58        35.70        17.88        40.21        38.66        12.36 
TCGA-43-6647 TCGA-43-6773 TCGA-43-7658 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 
       24.89         3.81        66.51         9.73        14.20        10.65 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-8304 TCGA-56-8623 
        0.39        28.34         8.75        27.45         3.48        22.75 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8388 TCGA-58-8391 TCGA-58-A46K 
       17.85        18.74         2.76        13.55        71.24        34.36 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2704 TCGA-60-2709 
       35.24        29.92        21.11        12.23        37.94        49.48 
TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2722 TCGA-60-2723 
        9.01        50.33        35.34        48.49        29.85        35.90 
TCGA-60-2725 TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MU TCGA-63-A5MV 
       26.83        45.57        14.99        11.34        25.41        36.16 
TCGA-63-A5MY TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 
       34.59         0.92        43.99        21.01         0.99         1.02 
TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 
        2.01        23.01         3.02        24.95        40.01         5.03 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 
       30.02        54.08         4.01         2.73         6.64         8.02 
TCGA-68-A59J TCGA-77-6842 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7463 
       14.73        29.56        89.98        20.78         0.49        46.78 
TCGA-77-8007 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8150 TCGA-77-A5FZ 
        6.51        12.59        39.09       104.09        54.41       126.18 
TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 
      117.57        42.08        30.81        27.62        12.99         6.41 
TCGA-85-7698 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 
       31.30        19.04        24.13        31.56        16.87        10.09 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4PA TCGA-90-6837 
        3.09         2.01        13.94        12.59        24.36        24.92 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-8064 TCGA-94-8491 TCGA-96-7544 
       11.77        20.22        22.62         5.26        26.63        49.87 
TCGA-96-8170 TCGA-98-7454 TCGA-98-8022 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       17.46         8.42        30.67        27.02        21.21        20.32 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HJ 
       19.10        12.89        13.18        64.08         1.22        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CX 
        4.21         2.89        39.85        14.73        29.75         3.65 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A5IB 
        0.43        33.07        11.18 

  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                       0.03                        0.30 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                     154.32                      174.08 
  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE 
                      18.71                       21.01 
[1] "0.0 - 154.3 (18.7)" "0.3 - 174.1 (21.0)"
[1] "hr=" "1"  
D53V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(9P23) MUTATED         1       61       97        1        44
  DEL PEAK 23(9P23) WILD-TYPE       1       26       54        1        19
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(9P23) MUTATED          54         2         45         11
  DEL PEAK 23(9P23) WILD-TYPE        38         1         17         10
                             vv
clus                          STAGE IV
  DEL PEAK 23(9P23) MUTATED          6
  DEL PEAK 23(9P23) WILD-TYPE        1
D53V3, multiclass
            clus
vv           DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  STAGE I                            1                           1
  STAGE IA                          61                          26
  STAGE IB                          97                          54
  STAGE II                           1                           1
  STAGE IIA                         44                          19
  STAGE IIB                         54                          38
  STAGE III                          2                           1
  STAGE IIIA                        45                          17
  STAGE IIIB                        11                          10
  STAGE IV                           6                           1
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 23(9P23) MUTATED    78 184  48  15
  DEL PEAK 23(9P23) WILD-TYPE  33 106  21   8
D53V4, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  T1                        78                          33
  T2                       184                         106
  T3                        48                          21
  T4                        15                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2  N3
  DEL PEAK 23(9P23) MUTATED   211  82  27   2
  DEL PEAK 23(9P23) WILD-TYPE 101  49  12   3
D53V5, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  N0                       211                         101
  N1                        82                          49
  N2                        27                          12
  N3                         2                           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"
D53V6, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED   262   6
  DEL PEAK 23(9P23) WILD-TYPE 142   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED    262    6
  DEL PEAK 23(9P23) WILD-TYPE  142    1
   clus
vv  DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  0                       262                         142
  1                         6                           1
[1] 2 2
[1] FALSE
D53V7, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED    78 247
  DEL PEAK 23(9P23) WILD-TYPE  49 119
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED     78  247
  DEL PEAK 23(9P23) WILD-TYPE   49  119
        clus
vv       DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  FEMALE                        78                          49
  MALE                         247                         119
[1] 2 2
[1] FALSE
D53V8, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(9P23) MUTATED                                       6
  DEL PEAK 23(9P23) WILD-TYPE                                     9
                             vv
clus                          LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(9P23) MUTATED                                         0
  DEL PEAK 23(9P23) WILD-TYPE                                       1
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 23(9P23) MUTATED                                        3
  DEL PEAK 23(9P23) WILD-TYPE                                      3
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(9P23) MUTATED                                         0
  DEL PEAK 23(9P23) WILD-TYPE                                       1
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(9P23) MUTATED                                                           316
  DEL PEAK 23(9P23) WILD-TYPE                                                         154
D53V9, multiclass
                                                             clus
vv                                                            DEL PEAK 23(9P23) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       316
                                                             clus
vv                                                            DEL PEAK 23(9P23) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         154
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED     8 317
  DEL PEAK 23(9P23) WILD-TYPE   5 163
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED      8  317
  DEL PEAK 23(9P23) WILD-TYPE    5  163
     clus
vv    DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  NO                          8                           5
  YES                       317                         163
[1] 2 2
[1] FALSE
D53V11, continuous
D53V12, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 23(9P23) MUTATED   260   7   3  15
  DEL PEAK 23(9P23) WILD-TYPE 134   5   1   7
D53V13, multiclass
    clus
vv   DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  R0                       260                         134
  R1                         7                           5
  R2                         3                           1
  RX                        15                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(9P23) MUTATED       7                        24   218
  DEL PEAK 23(9P23) WILD-TYPE     2                         7   122
D53V14, multiclass
                           clus
vv                          DEL PEAK 23(9P23) MUTATED
  ASIAN                                             7
  BLACK OR AFRICAN AMERICAN                        24
  WHITE                                           218
                           clus
vv                          DEL PEAK 23(9P23) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V15, binary
                             cls
clus                            0   1
  DEL PEAK 23(9P23) MUTATED     4 205
  DEL PEAK 23(9P23) WILD-TYPE   4 104
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 23(9P23) MUTATED      4  205
  DEL PEAK 23(9P23) WILD-TYPE    4  104
                        clus
vv                       DEL PEAK 23(9P23) MUTATED DEL PEAK 23(9P23) WILD-TYPE
  HISPANIC OR LATINO                             4                           4
  NOT HISPANIC OR LATINO                       205                         104
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 24(9P21.3) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 24(9P21.3) MUTATED   220 145
  DEL PEAK 24(9P21.3) WILD-TYPE  61  51
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          365                           112 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                          145                            51 
$`DEL PEAK 24(9P21.3) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       12.20        79.46         4.80       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
       92.15        36.07         1.64         6.18         2.79       154.32 
TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1080 
       49.94        46.88        99.16        70.16        34.78       122.43 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 
      119.80        43.23        31.63        88.11        33.93        10.82 
TCGA-21-A5DI TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       32.19         7.33        64.21         1.74        14.10        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
       20.48        35.08        48.33        24.13        38.17        34.75 
TCGA-22-4604 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
       13.12        19.30         9.57        11.77        31.73        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 
       63.55        14.63        44.25         0.79        54.28        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4538 
       18.84        30.12        62.86        56.32        22.06        98.01 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-6737 TCGA-33-6738 
       79.53       174.08       103.53        14.07        19.76        27.02 
TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        4.70        36.62         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       27.16         2.63        61.61        31.50        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 
       31.27        65.23        67.79        16.93        30.94         4.96 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       27.19         4.04        26.43        20.91         3.95         0.43 
TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
        8.12         6.81         0.39         3.39        47.80        74.07 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       44.75        68.58        70.03        60.79         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
        1.94        27.39        35.64        35.70        17.06        40.21 
TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 
       22.49        27.02        33.11        18.38        27.91        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 
       21.47         5.46        19.59         7.76        13.38        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 
        2.93        11.61        12.03         9.99        13.91         0.39 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
       29.95         5.46        30.35        27.45        28.96         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
       18.25         2.04         0.62         0.99         0.43         0.99 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
        1.45         1.32         0.85         6.51         0.10        17.49 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
        3.48        26.89        17.00        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
        1.81         1.18        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8386 
       20.94        19.23        13.32        21.04         0.26         0.03 
TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
       13.25        29.95        71.24        16.47        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 
       34.36        56.65        35.24         3.58        10.22        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 
       37.94        92.71        21.93        80.45        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
        9.01        56.91        50.33        42.64         3.19        32.32 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB 
       29.85        35.90        23.57        26.83        11.77       102.67 
TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MP 
       70.62        66.61        58.65        59.97        14.99        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       89.29        78.28        16.37        36.16        53.88        34.59 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 
       16.96        43.10         2.01        21.07         1.02         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
        0.92         0.99        21.01        25.05         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
        2.01         2.01         7.07        23.01        19.00         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 
        2.01        19.00        12.03         3.98        12.00         1.97 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-66-2794 
       25.97        22.98         4.04        22.98        10.06        54.08 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 
       49.05         2.73         6.94        13.35        16.18        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 
       73.12        75.09        23.28        11.18         0.49        42.28 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 
       70.13       106.95         0.16        46.78        15.75        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 
       53.95        37.81        82.92        12.59        53.92        17.72 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 
       11.54        26.40        27.39         6.97         9.63        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       35.90         0.33       132.36       117.57        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 
       42.41        42.08        38.86         9.67        11.97        36.53 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
       34.95        32.91         1.38         1.15        29.95        18.94 
TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
       25.15        14.07        16.87        34.52         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8481 
       22.45        16.77         5.29        32.71         0.72         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       14.63        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       19.33        17.72        14.96        18.18        19.73        12.56 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       16.21        15.85        14.96         0.79        12.39         3.65 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
        9.50         2.93        14.07        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        3.48         4.01         2.30        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
        4.01         5.03        26.63        14.14        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       49.87        57.07        18.31        17.46        19.36        16.57 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        2.76        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 
       18.15         2.01        18.58        20.71        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       13.41        11.84         0.07         4.54        51.78        45.37 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
        4.21         2.89        37.22        30.58        24.00        14.73 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE 
       22.78        83.57        65.49         3.65        16.80         0.43 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
        3.72        12.72        43.89         8.58         0.20 

$`DEL PEAK 24(9P21.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3416 TCGA-18-3421 TCGA-18-5595 TCGA-21-1070 
        7.46        75.75        31.99        86.96        27.19       119.54 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-5784 TCGA-22-0940 
       60.89        15.58        31.73         9.34        41.69        21.99 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1017 TCGA-22-4596 TCGA-22-4605 TCGA-22-5480 
       14.93         4.31        48.82         0.56        32.02        71.34 
TCGA-22-5481 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4583 TCGA-33-4587 
       79.20        16.64         7.63       133.74       151.27        54.44 
TCGA-33-4589 TCGA-33-A5GW TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
        1.55         0.30        56.38         9.07        23.24        12.00 
TCGA-34-5928 TCGA-34-7107 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
       18.15         1.12         0.39         6.58         7.46         7.82 
TCGA-39-5022 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 TCGA-43-2581 TCGA-43-6143 
       55.20        36.39        15.58        17.88        38.66        12.36 
TCGA-43-6773 TCGA-43-7658 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-51-4080 
        3.81        66.51         9.73        14.20        10.65         0.39 
TCGA-52-7622 TCGA-52-7811 TCGA-56-8623 TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR 
       28.34         8.75        22.75        17.85        18.74         0.13 
TCGA-56-A62T TCGA-58-8388 TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2709 
        2.76        13.55        29.92        21.11        12.23        49.48 
TCGA-60-2715 TCGA-60-2716 TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MU TCGA-66-2744 
       35.34        48.49        45.57        11.34        25.41         0.99 
TCGA-66-2757 TCGA-66-2763 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 
       43.99         0.99        24.95        40.01         5.03        30.02 
TCGA-66-2795 TCGA-68-7756 TCGA-68-8250 TCGA-68-A59J TCGA-77-7139 TCGA-77-7140 
        4.01         6.64         8.02        14.73        89.98        20.78 
TCGA-77-8007 TCGA-77-8136 TCGA-77-8139 TCGA-77-8150 TCGA-77-A5FZ TCGA-77-A5GB 
        6.51        39.09       104.09        54.41       126.18        30.81 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-8049 TCGA-85-8052 
       27.62        12.99         6.41        31.30        19.04        24.13 
TCGA-85-8070 TCGA-85-8277 TCGA-85-8353 TCGA-85-8355 TCGA-85-A4PA TCGA-90-6837 
       31.56        10.09         3.09         2.01        24.36        24.92 
TCGA-90-7769 TCGA-90-A4ED TCGA-92-8064 TCGA-98-7454 TCGA-98-A53C TCGA-98-A53D 
       11.77        20.22         5.26         8.42        27.02        21.21 
TCGA-98-A53H TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HJ 
       20.32        19.10        12.89        64.08         1.22        13.74 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-O2-A52N TCGA-O2-A5IB 
       39.85        29.75        33.07        11.18 

  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                         0.03                          0.13 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                       174.08                        151.27 
  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE 
                        19.00                         19.66 
[1] "0.0 - 174.1 (19.0)" "0.1 - 151.3 (19.7)"
[1] "hr=" "1.1"
D54V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(9P21.3) MUTATED         1       68      113        1        55
  DEL PEAK 24(9P21.3) WILD-TYPE       1       19       38        1         8
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(9P21.3) MUTATED          65         2         53         14
  DEL PEAK 24(9P21.3) WILD-TYPE        27         1          9          7
                               vv
clus                            STAGE IV
  DEL PEAK 24(9P21.3) MUTATED          6
  DEL PEAK 24(9P21.3) WILD-TYPE        1
D54V3, multiclass
            clus
vv           DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            68                            19
  STAGE IB                           113                            38
  STAGE II                             1                             1
  STAGE IIA                           55                             8
  STAGE IIB                           65                            27
  STAGE III                            2                             1
  STAGE IIIA                          53                             9
  STAGE IIIB                          14                             7
  STAGE IV                             6                             1
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 24(9P21.3) MUTATED    88 224  52  17
  DEL PEAK 24(9P21.3) WILD-TYPE  23  66  17   6
D54V4, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  T1                          88                            23
  T2                         224                            66
  T3                          52                            17
  T4                          17                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 24(9P21.3) MUTATED   237 100  37   3
  DEL PEAK 24(9P21.3) WILD-TYPE  75  31   2   2
D54V5, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  N0                         237                            75
  N1                         100                            31
  N2                          37                             2
  N3                           3                             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"
D54V6, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED   313   6
  DEL PEAK 24(9P21.3) WILD-TYPE  91   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED    313    6
  DEL PEAK 24(9P21.3) WILD-TYPE   91    1
   clus
vv  DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  0                         313                            91
  1                           6                             1
[1] 2 2
[1] FALSE
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED    91 290
  DEL PEAK 24(9P21.3) WILD-TYPE  36  76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED     91  290
  DEL PEAK 24(9P21.3) WILD-TYPE   36   76
        clus
vv       DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  FEMALE                          91                            36
  MALE                           290                            76
[1] 2 2
[1] FALSE
D54V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(9P21.3) MUTATED                                       7
  DEL PEAK 24(9P21.3) WILD-TYPE                                     8
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(9P21.3) MUTATED                                         1
  DEL PEAK 24(9P21.3) WILD-TYPE                                       0
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 24(9P21.3) MUTATED                                        4
  DEL PEAK 24(9P21.3) WILD-TYPE                                      2
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(9P21.3) MUTATED                                         0
  DEL PEAK 24(9P21.3) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(9P21.3) MUTATED                                                           369
  DEL PEAK 24(9P21.3) WILD-TYPE                                                         101
D54V9, multiclass
                                                             clus
vv                                                            DEL PEAK 24(9P21.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         369
                                                             clus
vv                                                            DEL PEAK 24(9P21.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           101
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED     9 372
  DEL PEAK 24(9P21.3) WILD-TYPE   4 108
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED      9  372
  DEL PEAK 24(9P21.3) WILD-TYPE    4  108
     clus
vv    DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  NO                            9                             4
  YES                         372                           108
[1] 2 2
[1] FALSE
D54V11, continuous
D54V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 24(9P21.3) MUTATED   306   7   3  17
  DEL PEAK 24(9P21.3) WILD-TYPE  88   5   1   5
D54V13, multiclass
    clus
vv   DEL PEAK 24(9P21.3) MUTATED DEL PEAK 24(9P21.3) WILD-TYPE
  R0                         306                            88
  R1                           7                             5
  R2                           3                             1
  RX                          17                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(9P21.3) MUTATED       8                        25   258
  DEL PEAK 24(9P21.3) WILD-TYPE     1                         6    82
D54V14, multiclass
                           clus
vv                          DEL PEAK 24(9P21.3) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          25
  WHITE                                             258
                           clus
vv                          DEL PEAK 24(9P21.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V15, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.3) MUTATED     5 235
  DEL PEAK 24(9P21.3) WILD-TYPE   3  74
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.3) MUTATED      5  235
  DEL PEAK 24(9P21.3) WILD-TYPE    3   74
                        clus
vv                       DEL PEAK 24(9P21.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         235
                        clus
vv                       DEL PEAK 24(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            74
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 25(9P21.1) MUTATION ANALYSIS
D55V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 25(9P21.1) MUTATED   186 121
  DEL PEAK 25(9P21.1) WILD-TYPE  95  75
  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                          307                           170 
  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                          121                            75 
$`DEL PEAK 25(9P21.1) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       12.20        79.46         4.80       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       92.15         1.64         6.18         2.79       154.32        49.94 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5783 
       46.88        99.16       122.43       119.80        43.23        88.11 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
       33.93        10.82        32.19         7.33         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
        1.74        14.10        27.02        20.48        35.08        48.33 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       38.17        34.75        13.12        19.30         9.57        11.77 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 TCGA-22-5483 
       31.73        64.93        44.25         0.79        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4538 TCGA-33-4547 
       30.12        62.86        56.32        22.06        98.01        79.53 
TCGA-33-4582 TCGA-33-6737 TCGA-33-6738 TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
      103.53        19.76        27.02        36.62         6.94       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 
       44.19       118.36        27.16         2.63        61.61        31.50 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 
       28.96        32.88        31.27        65.23        67.79        16.93 
TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       30.94         4.96        27.19         4.04        26.43        20.91 
TCGA-37-3789 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 
        0.43         8.12         6.81         0.39         3.39        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
       74.07        44.75        68.58        70.03        60.79         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 
       24.33         1.94        35.64        17.06        40.21        27.02 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       33.11        18.38        27.91        24.89        21.47         5.46 
TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
       19.59         7.76        13.38        11.77         2.93        11.61 
TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 
       12.03         9.99        13.91         0.39        29.95         5.46 
TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
       30.35        28.96         0.10        18.25         2.04         0.62 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
        0.43         0.99         1.45         1.32         0.85         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.10        17.49         3.48        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35        16.77         1.81         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ 
       20.25        15.81        20.94        19.23        13.32        21.04 
TCGA-56-A5DS TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
        0.26        13.25        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 
       85.12        56.65         3.58        10.22        96.82        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2713 TCGA-60-2720 TCGA-60-2721 
       21.93        80.45        41.42        56.91         3.19        32.32 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG 
       29.85        35.90        23.57        26.83        11.77        70.62 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       66.61        58.65        25.28        89.29        78.28        16.37 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
       53.88        16.96        43.10         2.01        21.07         1.02 
TCGA-66-2755 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
        0.92         2.01         1.02         2.01         7.07        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 
       19.00         3.02        19.00         3.98        12.00         1.97 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-68-7757 
       25.97        22.98         4.04        22.98        10.06         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       13.35        16.18        14.73        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       11.18         0.49        42.28        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 
       46.78        15.75        86.76        53.95        82.92        53.92 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
       17.72        11.54        26.40        27.39         6.97         9.63 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
       65.49        35.90       132.36        22.29         5.92        42.41 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       38.86         9.67        11.97        36.53        34.95        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       32.91         1.38         1.15        29.95        18.94        25.15 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       34.52         0.76        13.22        22.45        16.77         5.29 
TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
        0.72        14.63         0.10        15.62        25.68        19.33 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       17.72        14.96        19.73        12.56        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
       14.96         0.79        12.39         3.65         9.50         2.93 
TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       14.07        22.62        10.59         2.70         3.48         4.01 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        2.30        21.04         0.16        11.70         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
       26.63        14.14        16.14        17.69        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8020 TCGA-98-8021 
       18.31        17.46        19.36        16.57         2.76        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B 
       30.67        21.34        27.16         3.88        18.15         2.01 
TCGA-98-A53J TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HG TCGA-NC-A5HI 
       20.71        16.11        11.84         0.07        51.78        45.37 
TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
        4.21        30.58        14.73        22.78        83.57        65.49 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W 
        3.65        16.80        33.07         3.72        43.89         8.58 
TCGA-XC-AA0X 
        0.20 

$`DEL PEAK 25(9P21.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-5595 
        7.46        75.75        31.99        36.07        86.96        27.19 
TCGA-21-1070 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
      119.54        70.16        60.89        34.78        15.58        31.73 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5784 TCGA-22-0940 TCGA-22-1000 TCGA-22-1017 
        9.34        31.63        41.69        21.99        14.93        48.82 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4605 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 
       24.13         0.56        32.02        63.55        14.63        54.28 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4566 
       71.34        79.20        16.64         7.63       133.74       174.08 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-A4WN TCGA-33-A5GW 
      151.27        14.07        54.44         1.55         4.70         0.30 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 
       56.38         9.07        23.24        12.00        18.15         1.12 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-39-5022 
        3.95         0.39         6.58         7.46         7.82        55.20 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 
       27.39        36.39        15.58        35.70        17.88        22.49 
TCGA-43-2581 TCGA-43-6143 TCGA-43-6773 TCGA-43-7658 TCGA-43-A475 TCGA-43-A56U 
       38.66        12.36         3.81        66.51         9.73        14.20 
TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-7221 
       10.65         0.39        28.34         8.75        27.45         0.99 
TCGA-56-8623 TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 
       22.75        17.85        18.74         0.13         2.76         0.03 
TCGA-58-8388 TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 
       13.55        34.36        35.24        29.92        21.11        12.23 
TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 
       37.94        49.48        66.54         9.01        50.33        35.34 
TCGA-60-2716 TCGA-60-2719 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
       48.49        42.64       102.67        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2744 TCGA-66-2754 
       11.34        25.41        36.16        34.59         0.99         2.01 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 
        0.99        43.99        21.01        25.05         0.99         2.01 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 
        2.01        12.03        24.95        40.01         5.03        30.02 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 
       54.08         4.01        49.05         2.73         6.64         8.02 
TCGA-77-6842 TCGA-77-7139 TCGA-77-7140 TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 
       29.56        89.98        20.78         6.51        37.81        12.59 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 
       39.09       104.09        54.41         0.33       126.18       117.57 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-8049 
       42.08        30.81        27.62        12.99         6.41        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8353 
       24.13        31.56        14.07        16.87        10.09         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4PA 
       32.71         2.01         7.76        13.94        12.59        24.36 
TCGA-85-A4QQ TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-92-8064 TCGA-98-7454 
       18.18        24.92        11.77        20.22         5.26         8.42 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 
       27.02        21.21        20.32        18.58        19.10        12.89 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ 
       13.18        13.41        64.08         4.54         1.22        13.74 
TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NK-A7XE 
        2.89        39.85        37.22        24.00        29.75         0.43 
TCGA-O2-A52S TCGA-O2-A5IB 
       12.72        11.18 

  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                       154.32                        174.08 
  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE 
                        18.94                         20.55 
[1] "0.1 - 154.3 (18.9)" "0.0 - 174.1 (20.6)"
[1] "hr=" "1.1"
D55V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(9P21.1) MUTATED         2       62       98        1        44
  DEL PEAK 25(9P21.1) WILD-TYPE       0       25       53        1        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(9P21.1) MUTATED          54         1         45          8
  DEL PEAK 25(9P21.1) WILD-TYPE        38         2         17         13
                               vv
clus                            STAGE IV
  DEL PEAK 25(9P21.1) MUTATED          3
  DEL PEAK 25(9P21.1) WILD-TYPE        4
D55V3, multiclass
            clus
vv           DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                            62                            25
  STAGE IB                            98                            53
  STAGE II                             1                             1
  STAGE IIA                           44                            19
  STAGE IIB                           54                            38
  STAGE III                            1                             2
  STAGE IIIA                          45                            17
  STAGE IIIB                           8                            13
  STAGE IV                             3                             4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 25(9P21.1) MUTATED    77 186  46  11
  DEL PEAK 25(9P21.1) WILD-TYPE  34 104  23  12
D55V4, multiclass
    clus
vv   DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  T1                          77                            34
  T2                         186                           104
  T3                          46                            23
  T4                          11                            12
[1] 4 2
[1] TRUE
[1] "dimension of 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(9P21.1) MUTATED   210  80  26   2
  DEL PEAK 25(9P21.1) WILD-TYPE 102  51  13   3
D55V5, multiclass
    clus
vv   DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  N0                         210                           102
  N1                          80                            51
  N2                          26                            13
  N3                           2                             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"
D55V6, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.1) MUTATED   260   3
  DEL PEAK 25(9P21.1) WILD-TYPE 144   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.1) MUTATED    260    3
  DEL PEAK 25(9P21.1) WILD-TYPE  144    4
   clus
vv  DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  0                         260                           144
  1                           3                             4
[1] 2 2
[1] FALSE
D55V7, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.1) MUTATED    82 238
  DEL PEAK 25(9P21.1) WILD-TYPE  45 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.1) MUTATED     82  238
  DEL PEAK 25(9P21.1) WILD-TYPE   45  128
        clus
vv       DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  FEMALE                          82                            45
  MALE                           238                           128
[1] 2 2
[1] FALSE
D55V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(9P21.1) MUTATED                                       6
  DEL PEAK 25(9P21.1) WILD-TYPE                                     9
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(9P21.1) MUTATED                                         0
  DEL PEAK 25(9P21.1) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 25(9P21.1) MUTATED                                        2
  DEL PEAK 25(9P21.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(9P21.1) MUTATED                                         0
  DEL PEAK 25(9P21.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(9P21.1) MUTATED                                                           312
  DEL PEAK 25(9P21.1) WILD-TYPE                                                         158
D55V9, multiclass
                                                             clus
vv                                                            DEL PEAK 25(9P21.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         312
                                                             clus
vv                                                            DEL PEAK 25(9P21.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           158
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.1) MUTATED     7 313
  DEL PEAK 25(9P21.1) WILD-TYPE   6 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.1) MUTATED      7  313
  DEL PEAK 25(9P21.1) WILD-TYPE    6  167
     clus
vv    DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  NO                            7                             6
  YES                         313                           167
[1] 2 2
[1] FALSE
D55V11, continuous
D55V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 25(9P21.1) MUTATED   250   7   3  17
  DEL PEAK 25(9P21.1) WILD-TYPE 144   5   1   5
D55V13, multiclass
    clus
vv   DEL PEAK 25(9P21.1) MUTATED DEL PEAK 25(9P21.1) WILD-TYPE
  R0                         250                           144
  R1                           7                             5
  R2                           3                             1
  RX                          17                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(9P21.1) MUTATED       8                        23   224
  DEL PEAK 25(9P21.1) WILD-TYPE     1                         8   116
D55V14, multiclass
                           clus
vv                          DEL PEAK 25(9P21.1) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          23
  WHITE                                             224
                           clus
vv                          DEL PEAK 25(9P21.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V15, binary
                               cls
clus                              0   1
  DEL PEAK 25(9P21.1) MUTATED     4 209
  DEL PEAK 25(9P21.1) WILD-TYPE   4 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 25(9P21.1) MUTATED      4  209
  DEL PEAK 25(9P21.1) WILD-TYPE    4  100
                        clus
vv                       DEL PEAK 25(9P21.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         209
                        clus
vv                       DEL PEAK 25(9P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           100
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 26(9Q21.11) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(9Q21.11) MUTATED   153  90
  DEL PEAK 26(9Q21.11) WILD-TYPE 128 106
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                           243                            234 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                            90                            106 
$`DEL PEAK 26(9Q21.11) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3411 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       12.20        79.46       117.57        36.07         1.64        86.96 
TCGA-18-4083 TCGA-21-1070 TCGA-21-1075 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
        6.18       119.54        70.16       119.80        43.23        31.63 
TCGA-21-5786 TCGA-21-A5DI TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
       33.93        32.19         4.31        64.21         1.74        27.02 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4601 TCGA-22-4604 
       48.82        20.48        35.08        48.33        34.75        13.12 
TCGA-22-4607 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5481 TCGA-22-5483 
       19.30        63.55        14.63         0.79        79.20        18.84 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4582 TCGA-33-4587 TCGA-33-6737 
       22.06         7.63        79.53       103.53        54.44        19.76 
TCGA-33-6738 TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASI TCGA-34-2600 TCGA-34-2604 
       27.02         0.30       110.99        44.19        61.61        31.50 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 
       32.88        31.27        65.23        67.79        16.93        30.94 
TCGA-34-5928 TCGA-34-5929 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4130 
       18.15         4.96         4.04        26.43        20.91         8.12 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5024 
        6.81         0.39         3.39        47.80        44.75        70.03 
TCGA-39-5028 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-3920 
        1.71        36.39        15.58        17.06        40.21        33.11 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
       27.91        12.36        24.89        21.47         5.46        19.59 
TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A56V TCGA-46-6026 
        7.76        13.38        11.77         2.93        12.03        13.91 
TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        5.46        30.35        28.96         0.10        18.25         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 
        0.62         0.99         0.43         1.45         1.32         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 
       17.49         3.48        26.89         1.35         1.81         1.18 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZJ 
        9.93        20.25        15.81        20.94        19.23        21.04 
TCGA-56-A5DS TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-60-2696 
        0.26        29.95        16.47        34.78        85.12         3.58 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2708 TCGA-60-2712 TCGA-60-2714 
       10.22        96.82        92.71        80.45         9.01        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 
       42.64         3.19        32.32        35.90        23.57        11.77 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MR TCGA-63-A5MS 
      102.67        70.62        66.61        58.65        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       16.37        36.16        53.88        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 
        2.01        21.07         1.02         0.99        21.01         0.99 
TCGA-66-2766 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 
        1.02         7.07        19.00         3.02        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        3.98        12.00         1.97        22.98         4.04        22.98 
TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       10.06        49.05         2.73         6.94         8.02        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       16.18        14.73        29.56        73.12        75.09        23.28 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 TCGA-77-8136 TCGA-77-8138 
       46.78         6.51        86.76        82.92        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 
      104.09        11.54        26.40        54.41        35.90         0.33 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 
      132.36        22.29         5.92        38.86        11.97        34.95 
TCGA-85-7843 TCGA-85-8048 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
        1.15        25.15         0.76        13.22        22.45        16.77 
TCGA-85-8352 TCGA-85-8479 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
        5.29         0.72         0.10        15.62        19.33        17.72 
TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 
       14.96        19.73        12.56        16.21        15.85         0.79 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4EE 
       12.39         3.65         9.50         2.93        14.07        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       10.59         2.70         2.30        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        4.01        26.63        14.14        17.69        49.87        18.31 
TCGA-96-8170 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       17.46         2.76        30.81        30.67        21.34        27.16 
TCGA-98-A539 TCGA-98-A53B TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
        3.88         2.01        12.89        13.41        11.84         0.07 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN 
        4.54        51.78        45.37         4.21        39.85        37.22 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-O2-A52Q 
       24.00        14.73        22.78        65.49         3.65         3.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       43.89         8.58        11.18 

$`DEL PEAK 26(9Q21.11) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
        7.46        75.75         4.80        11.34        23.54        92.15 
TCGA-18-3416 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 
       31.99         2.79       154.32        49.94        27.19        46.88 
TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       99.16        60.89        34.78        15.58        31.73       122.43 
TCGA-21-1081 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
        9.34        88.11        41.69        10.82        21.99         7.33 
TCGA-22-1000 TCGA-22-1012 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4605 
       14.93        14.10        24.13         0.56        38.17        32.02 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5477 TCGA-22-5479 
        9.57        11.77        31.73        64.93        44.25        54.28 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       71.34        11.74        30.12        62.86        56.32        16.64 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 
      133.74        98.01       174.08       151.27        14.07         1.55 
TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 
        4.70        36.62         6.94       118.36        27.16         2.63 
TCGA-34-2605 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-7107 
       28.96        56.38         9.07        23.24        12.00         1.12 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
       27.19         3.95         0.43         0.39         6.58         7.46 
TCGA-37-4133 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5029 
        7.82        74.07        68.58        55.20        60.79        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2578 
        1.94        27.39        35.64        35.70        17.88        22.49 
TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-43-6773 TCGA-43-7658 TCGA-43-A474 
       38.66        27.02        18.38         3.81        66.51        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
        9.73        14.20         9.99        10.65         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-7223 TCGA-56-7582 
       29.95        28.34         8.75        27.45         0.99         0.85 
TCGA-56-7730 TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8623 TCGA-56-8625 
        6.51        17.00        14.07        16.77        22.75        10.36 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 
       13.32        17.85        18.74         0.13         2.76         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       13.25        13.55        71.24        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2704 TCGA-60-2707 TCGA-60-2709 
       29.92        21.11        12.23        37.94        21.93        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2722 
       66.54        41.42        56.91        35.34        48.49        29.85 
TCGA-60-2725 TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       26.83        59.97        45.57        14.99        11.34        25.28 
TCGA-63-A5MU TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 
       25.41         0.99         2.01         0.92        43.99        25.05 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2777 TCGA-66-2783 
        2.01         2.01         2.01        23.01         2.01        24.95 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
       25.97        40.01         5.03        30.02        54.08         4.01 
TCGA-68-7756 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
        6.64        11.18        89.98        20.78         0.49        42.28 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
       70.13       106.95         0.16        15.75        53.95        37.81 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 
       12.59        53.92        27.39         6.97         9.63        65.49 
TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
      126.18       117.57        42.41        42.08        30.81        27.62 
TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 
        9.67        12.99         6.41        36.53        31.30        32.91 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
        1.38        29.95        18.94        19.04        24.13        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 
       14.07        16.87        34.52        10.09         3.09        32.71 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL 
        2.01         7.76        14.63        13.94        12.59        25.68 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A511 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED 
       24.36        18.18        14.96        24.92        11.77        20.22 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-8490 TCGA-94-A5I4 TCGA-96-7545 
        3.48         4.01         5.26         5.03        16.14        57.07 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D 
       19.36        16.57         8.42        18.15        27.02        21.21 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 
       20.32        18.58        20.71        19.10        16.11        13.18 
TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HR 
       64.08         1.22        13.74         2.89        30.58        29.75 
TCGA-NK-A5CR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52S TCGA-XC-AA0X 
       83.57        16.80         0.43        33.07        12.72         0.20 

  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                        132.36                         174.08 
  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE 
                        18.250                         20.745 
[1] "0.1 - 132.4 (18.2)" "0.0 - 174.1 (20.7)"
[1] "hr=" "1.1"
D56V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(9Q21.11) MUTATED         1       48       69        1        33
  DEL PEAK 26(9Q21.11) WILD-TYPE       1       39       82        1        30
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(9Q21.11) MUTATED          48         2         31          8
  DEL PEAK 26(9Q21.11) WILD-TYPE        44         1         31         13
                                vv
clus                             STAGE IV
  DEL PEAK 26(9Q21.11) MUTATED          4
  DEL PEAK 26(9Q21.11) WILD-TYPE        3
D56V3, multiclass
            clus
vv           DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             48                             39
  STAGE IB                             69                             82
  STAGE II                              1                              1
  STAGE IIA                            33                             30
  STAGE IIB                            48                             44
  STAGE III                             2                              1
  STAGE IIIA                           31                             31
  STAGE IIIB                            8                             13
  STAGE IV                              4                              3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 26(9Q21.11) MUTATED    61 142  37   8
  DEL PEAK 26(9Q21.11) WILD-TYPE  50 148  32  15
D56V4, multiclass
    clus
vv   DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  T1                           61                             50
  T2                          142                            148
  T3                           37                             32
  T4                            8                             15
[1] 4 2
[1] TRUE
[1] "dimension of 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(9Q21.11) MUTATED   161  65  18   2
  DEL PEAK 26(9Q21.11) WILD-TYPE 151  66  21   3
D56V5, multiclass
    clus
vv   DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  N0                          161                            151
  N1                           65                             66
  N2                           18                             21
  N3                            2                              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"
D56V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED   199   4
  DEL PEAK 26(9Q21.11) WILD-TYPE 205   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED    199    4
  DEL PEAK 26(9Q21.11) WILD-TYPE  205    3
   clus
vv  DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  0                          199                            205
  1                            4                              3
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED    71 177
  DEL PEAK 26(9Q21.11) WILD-TYPE  56 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED     71  177
  DEL PEAK 26(9Q21.11) WILD-TYPE   56  189
        clus
vv       DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  FEMALE                           71                             56
  MALE                            177                            189
[1] 2 2
[1] FALSE
D56V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(9Q21.11) MUTATED                                       4
  DEL PEAK 26(9Q21.11) WILD-TYPE                                    11
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(9Q21.11) MUTATED                                         1
  DEL PEAK 26(9Q21.11) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 26(9Q21.11) MUTATED                                        1
  DEL PEAK 26(9Q21.11) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(9Q21.11) MUTATED                                         1
  DEL PEAK 26(9Q21.11) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(9Q21.11) MUTATED                                                           241
  DEL PEAK 26(9Q21.11) WILD-TYPE                                                         229
D56V9, multiclass
                                                             clus
vv                                                            DEL PEAK 26(9Q21.11) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          241
                                                             clus
vv                                                            DEL PEAK 26(9Q21.11) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            229
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED     4 244
  DEL PEAK 26(9Q21.11) WILD-TYPE   9 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED      4  244
  DEL PEAK 26(9Q21.11) WILD-TYPE    9  236
     clus
vv    DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  NO                             4                              9
  YES                          244                            236
[1] 2 2
[1] FALSE
D56V11, continuous
D56V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(9Q21.11) MUTATED   194   2   2   9
  DEL PEAK 26(9Q21.11) WILD-TYPE 200  10   2  13
D56V13, multiclass
    clus
vv   DEL PEAK 26(9Q21.11) MUTATED DEL PEAK 26(9Q21.11) WILD-TYPE
  R0                          194                            200
  R1                            2                             10
  R2                            2                              2
  RX                            9                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(9Q21.11) MUTATED       3                        16   173
  DEL PEAK 26(9Q21.11) WILD-TYPE     6                        15   167
D56V14, multiclass
                           clus
vv                          DEL PEAK 26(9Q21.11) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              173
                           clus
vv                          DEL PEAK 26(9Q21.11) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                167
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V15, binary
                                cls
clus                               0   1
  DEL PEAK 26(9Q21.11) MUTATED     1 157
  DEL PEAK 26(9Q21.11) WILD-TYPE   7 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(9Q21.11) MUTATED      1  157
  DEL PEAK 26(9Q21.11) WILD-TYPE    7  152
                        clus
vv                       DEL PEAK 26(9Q21.11) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          157
                        clus
vv                       DEL PEAK 26(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            152
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 27(10P15.2) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(10P15.2) MUTATED   130  80
  DEL PEAK 27(10P15.2) WILD-TYPE 151 116
  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                           210                            267 
  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                            80                            116 
$`DEL PEAK 27(10P15.2) MUTATED`
TCGA-18-3406 TCGA-18-3411 TCGA-18-3421 TCGA-18-4083 TCGA-18-5595 TCGA-21-1072 
       12.20       117.57        86.96         6.18        27.19        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 
       70.16        60.89        34.78        31.73       122.43       119.80 
TCGA-21-5782 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 TCGA-22-1011 
       31.63        33.93        32.19        21.99        14.93         1.74 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
       27.02        20.48        35.08        24.13         0.56        38.17 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
        9.57        11.77        31.73        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-33-4533 TCGA-33-4582 
       54.28        11.74        18.84        56.32       133.74       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-34-2596 
      151.27        14.07         0.30        36.62       110.99         2.63 
TCGA-34-2605 TCGA-34-5236 TCGA-34-5240 TCGA-34-5927 TCGA-34-8454 TCGA-34-8456 
       28.96         9.07        12.00        30.94        27.19        26.43 
TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 TCGA-37-4135 TCGA-39-5011 TCGA-39-5019 
       20.91         0.43         0.39         6.81        47.80        44.75 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       68.58        60.79        24.33         1.94        27.39        36.39 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-6143 
       35.64        35.70        17.88        40.21        22.49        12.36 
TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-8118 TCGA-43-A56U TCGA-43-A56V 
       24.89        21.47        19.59         2.93        14.20        12.03 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-56-5898 TCGA-56-7223 
        0.39        29.95        28.34        30.35        18.25         0.99 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-8307 TCGA-56-8503 TCGA-56-8626 
        1.32         0.85         6.51        26.89         1.35         9.93 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8391 
       15.81        20.94        17.85        18.74         2.76        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 TCGA-60-2703 
       16.47        34.78        34.36        35.24        21.11        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2719 
       37.94        92.71        80.45        49.48        66.54        42.64 
TCGA-60-2722 TCGA-60-2723 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML 
       29.85        35.90       102.67        66.61        59.97        45.57 
TCGA-63-A5MM TCGA-63-A5MP TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       14.99        25.28         2.01         1.02         2.01         0.92 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2770 TCGA-66-2771 
       43.99        21.01        25.05         1.02        23.01        19.00 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
        2.01        12.03        25.97        40.01        22.98         4.04 
TCGA-66-2791 TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        5.03        10.06        49.05         2.73         6.64         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 
        8.02        13.35        14.73        29.56        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7465 TCGA-77-8009 
       89.98         0.49        42.28         0.16        15.75        53.95 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       82.92        53.92        39.09        17.72       104.09        11.54 
TCGA-77-8144 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 
       27.39        65.49         0.33       117.57        22.29        42.41 
TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-7844 
       30.81        27.62         6.41        36.53        32.91        29.95 
TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 TCGA-85-8287 
       18.94        24.13        31.56        14.07        10.09         0.76 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 TCGA-85-A4CN TCGA-85-A4JC 
       16.77         3.09         0.72        14.63        19.33        14.96 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE 
       18.18        19.73        16.21         3.65        11.77        22.62 
TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-A5I6 
        4.01         5.26        21.04         0.16         4.01        17.69 
TCGA-96-8170 TCGA-96-A4JK TCGA-98-8020 TCGA-98-8021 TCGA-98-8023 TCGA-98-A53A 
       17.46        19.36         2.76        30.81        21.34        18.15 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
       20.71        19.10        12.89        16.11        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP 
       11.84         0.07         2.89        39.85        30.58        24.00 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       29.75        65.49        16.80        33.07         3.72        12.72 

$`DEL PEAK 27(10P15.2) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 
        7.46        75.75        79.46         4.80        11.34        23.54 
TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 
       92.15        31.99        36.07         1.64         2.79       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1078 TCGA-21-1081 TCGA-21-1083 
       49.94       119.54        46.88        15.58         9.34        43.23 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
       88.11        41.69        10.82         7.33         4.31        64.21 
TCGA-22-1012 TCGA-22-1017 TCGA-22-4594 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       14.10        48.82        48.33        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-5472 TCGA-22-5473 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 
       19.30        64.93        63.55        71.34        79.20        30.12 
TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 
       62.86        16.64        22.06         7.63        98.01        79.53 
TCGA-33-4566 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
      174.08        54.44         1.55        19.76        27.02         4.70 
TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 
        6.94        44.19       118.36        27.16        61.61        31.50 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
       32.88        31.27        65.23        67.79        56.38        23.24 
TCGA-34-5241 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8455 TCGA-37-3783 
       16.93        18.15         4.96         1.12         4.04         3.95 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 
        6.58         8.12         7.46         7.82         0.39         3.39 
TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5035 TCGA-39-5040 
       74.07        55.20        70.03         1.71        15.58        17.06 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6771 
       38.66        27.02        33.11        18.38        27.91         5.46 
TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 
        3.81         7.76        66.51        13.38        11.77        11.61 
TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-52-7809 
        9.73         9.99        10.65        13.91         0.39         5.46 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 
        8.75        27.45        28.96         0.10         2.04         0.62 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 
        0.99         0.43         1.45         0.10        17.49         3.48 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       17.00        14.07        16.77         1.81        22.75         1.18 
TCGA-56-8625 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR 
       10.36        20.25        19.23        13.32        21.04         0.13 
TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J 
        0.26         0.03        13.25        13.55        29.95        85.12 
TCGA-58-A46L TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2707 
       56.65        29.92         3.58        12.23        10.22        21.93 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       41.42         9.01        56.91        50.33        35.34        48.49 
TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG 
        3.19        32.32        23.57        26.83        11.77        70.62 
TCGA-63-A5MI TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       58.65        11.34        89.29        78.28        16.37        25.41 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
       36.16        53.88        34.59        16.96        43.10        21.07 
TCGA-66-2744 TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 
        0.99         0.99         0.99         2.01         2.01         2.01 
TCGA-66-2769 TCGA-66-2773 TCGA-66-2778 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        7.07         3.02        19.00         3.98        12.00        24.95 
TCGA-66-2785 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-A59I 
        1.97        22.98        30.02        54.08         4.01        16.18 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7140 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 
       73.12        75.09        20.78        70.13       106.95        46.78 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 TCGA-77-8143 TCGA-77-8145 
        6.51        86.76        37.81        12.59        26.40         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 
        9.63        54.41        35.90       126.18       132.36         5.92 
TCGA-77-A5GA TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 
       42.08        38.86         9.67        11.97        12.99        34.95 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8072 
       31.30         1.38         1.15        25.15        19.04        16.87 
TCGA-85-8276 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 
       34.52        13.22        22.45         5.29        32.71         2.01 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
        7.76        13.94        12.59         0.10        15.62        25.68 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       17.72        24.36        12.56        15.85        14.96         0.79 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED 
       12.39        24.92         9.50         2.93        14.07        20.22 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8065 TCGA-94-7943 TCGA-94-8490 
       10.59         2.70         3.48         2.30        11.70         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
       26.63        14.14        16.14        49.87        57.07        18.31 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53B 
       16.57         8.42        30.67        27.16         3.88         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-NC-A5HE TCGA-NC-A5HF 
       27.02        21.21        20.32        18.58        64.08         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN 
       51.78         1.22        45.37        13.74         4.21        37.22 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52V 
       14.73        22.78        83.57         3.65         0.43        43.89 
TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        8.58        11.18         0.20 

  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                        151.27                         174.08 
  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE 
                        21.025                         17.000 
[1] "0.1 - 151.3 (21.0)" "0.0 - 174.1 (17.0)"
[1] "hr=" "1.2"
D57V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(10P15.2) MUTATED         1       36       73        0        27
  DEL PEAK 27(10P15.2) WILD-TYPE       1       51       78        2        36
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(10P15.2) MUTATED          41         2         28          7
  DEL PEAK 27(10P15.2) WILD-TYPE        51         1         34         14
                                vv
clus                             STAGE IV
  DEL PEAK 27(10P15.2) MUTATED          1
  DEL PEAK 27(10P15.2) WILD-TYPE        6
D57V3, multiclass
            clus
vv           DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             36                             51
  STAGE IB                             73                             78
  STAGE II                              0                              2
  STAGE IIA                            27                             36
  STAGE IIB                            41                             51
  STAGE III                             2                              1
  STAGE IIIA                           28                             34
  STAGE IIIB                            7                             14
  STAGE IV                              1                              6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 27(10P15.2) MUTATED    49 132  27   8
  DEL PEAK 27(10P15.2) WILD-TYPE  62 158  42  15
D57V4, multiclass
    clus
vv   DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  T1                           49                             62
  T2                          132                            158
  T3                           27                             42
  T4                            8                             15
[1] 4 2
[1] TRUE
[1] "dimension of 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(10P15.2) MUTATED   138  57  18   2
  DEL PEAK 27(10P15.2) WILD-TYPE 174  74  21   3
D57V5, multiclass
    clus
vv   DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  N0                          138                            174
  N1                           57                             74
  N2                           18                             21
  N3                            2                              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"
D57V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.2) MUTATED   180   1
  DEL PEAK 27(10P15.2) WILD-TYPE 224   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.2) MUTATED    180    1
  DEL PEAK 27(10P15.2) WILD-TYPE  224    6
   clus
vv  DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  0                          180                            224
  1                            1                              6
[1] 2 2
[1] FALSE
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.2) MUTATED    54 162
  DEL PEAK 27(10P15.2) WILD-TYPE  73 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.2) MUTATED     54  162
  DEL PEAK 27(10P15.2) WILD-TYPE   73  204
        clus
vv       DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  FEMALE                           54                             73
  MALE                            162                            204
[1] 2 2
[1] FALSE
D57V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(10P15.2) MUTATED                                       7
  DEL PEAK 27(10P15.2) WILD-TYPE                                     8
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(10P15.2) MUTATED                                         0
  DEL PEAK 27(10P15.2) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 27(10P15.2) MUTATED                                        2
  DEL PEAK 27(10P15.2) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(10P15.2) MUTATED                                         0
  DEL PEAK 27(10P15.2) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(10P15.2) MUTATED                                                           207
  DEL PEAK 27(10P15.2) WILD-TYPE                                                         263
D57V9, multiclass
                                                             clus
vv                                                            DEL PEAK 27(10P15.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          207
                                                             clus
vv                                                            DEL PEAK 27(10P15.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            263
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.2) MUTATED     6 210
  DEL PEAK 27(10P15.2) WILD-TYPE   7 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.2) MUTATED      6  210
  DEL PEAK 27(10P15.2) WILD-TYPE    7  270
     clus
vv    DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  NO                             6                              7
  YES                          210                            270
[1] 2 2
[1] FALSE
D57V11, continuous
D57V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(10P15.2) MUTATED   173   6   1  10
  DEL PEAK 27(10P15.2) WILD-TYPE 221   6   3  12
D57V13, multiclass
    clus
vv   DEL PEAK 27(10P15.2) MUTATED DEL PEAK 27(10P15.2) WILD-TYPE
  R0                          173                            221
  R1                            6                              6
  R2                            1                              3
  RX                           10                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(10P15.2) MUTATED       2                        14   153
  DEL PEAK 27(10P15.2) WILD-TYPE     7                        17   187
D57V14, multiclass
                           clus
vv                          DEL PEAK 27(10P15.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              153
                           clus
vv                          DEL PEAK 27(10P15.2) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             17
  WHITE                                                187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V15, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.2) MUTATED     3 133
  DEL PEAK 27(10P15.2) WILD-TYPE   5 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.2) MUTATED      3  133
  DEL PEAK 27(10P15.2) WILD-TYPE    5  176
                        clus
vv                       DEL PEAK 27(10P15.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          133
                        clus
vv                       DEL PEAK 27(10P15.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            176
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 28(10Q23.31) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(10Q23.31) MUTATED   156 102
  DEL PEAK 28(10Q23.31) WILD-TYPE 125  94
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            258                             219 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            102                              94 
$`DEL PEAK 28(10Q23.31) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 
       12.20         7.46         4.80       117.57        11.34        92.15 
TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        6.18       154.32        49.94        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1081 TCGA-21-1082 TCGA-21-5783 TCGA-21-A5DI 
       60.89        34.78         9.34       119.80        88.11        32.19 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 
       21.99         7.33        14.93        64.21         1.74        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       48.33        24.13        38.17         9.57        11.77        63.55 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       14.63         0.79        54.28        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4533 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 
       62.86        56.32       133.74        98.01       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 TCGA-33-A5GW TCGA-33-AAS8 
       14.07        54.44        19.76        27.02         0.30        36.62 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2605 
        6.94       110.99       118.36        27.16         2.63        28.96 
TCGA-34-5236 TCGA-34-5927 TCGA-34-5929 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3792 
        9.07        30.94         4.96        26.43        20.91         0.39 
TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        6.81         3.39        47.80        74.07        44.75        68.58 
TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 
       60.79        24.33         1.94        27.39        35.64        35.70 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
       17.06        40.21        22.49        27.02        33.11        18.38 
TCGA-43-6770 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
       21.47        66.51        11.61        14.20        12.03         9.99 
TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       10.65         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 
       30.35        28.96         0.10        18.25         0.99         0.43 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 TCGA-56-8307 
        0.99         1.32         0.85         6.51         3.48        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8622 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 
       17.00        14.07         1.81        10.36        20.25        15.81 
TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 
       13.32        17.85        18.74         2.76         0.03        13.55 
TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M 
       71.24        16.47        34.78        85.12        34.36        35.24 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
       21.11        10.22        37.94        92.71        80.45        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2715 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       66.54        56.91        35.34        42.64         3.19        29.85 
TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ 
       26.83       102.67        70.62        66.61        58.65        59.97 
TCGA-63-A5ML TCGA-66-2727 TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 
       45.57        16.96         2.01         1.02         2.01         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2770 TCGA-66-2771 
       43.99        21.01        25.05         0.99        23.01        19.00 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
        3.02        19.00        12.00        24.95         1.97        40.01 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 
        4.04         5.03        30.02        10.06        49.05         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 
        6.64         6.94         8.02        13.35        14.73        29.56 
TCGA-77-6843 TCGA-77-7139 TCGA-77-7140 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 
       73.12        89.98        20.78       106.95        46.78        15.75 
TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       53.95        82.92        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       11.54        26.40        27.39         9.63        54.41        65.49 
TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6560 
        0.33       117.57         5.92        30.81        27.62        11.97 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7844 
       12.99         6.41        36.53        31.30        32.91        29.95 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8277 TCGA-85-8351 
       18.94        19.04        24.13        31.56        10.09        16.77 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 TCGA-85-A4CL 
        3.09        32.71         0.72        14.63         0.10        25.68 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z 
       19.33        17.72        14.96        18.18        12.56        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-92-7341 TCGA-92-8064 
       15.85        14.96        12.39         3.65         3.48         5.26 
TCGA-94-7033 TCGA-94-7943 TCGA-94-8035 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 
       21.04        11.70         4.01        16.14        17.69        57.07 
TCGA-96-8170 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
       17.46        19.36        30.81        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
       18.15        18.58        20.71        19.10        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HH TCGA-NC-A5HI 
       13.18        13.41        11.84         0.07         1.22        45.37 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
       39.85        37.22        30.58        29.75        22.78        83.57 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       16.80         0.43        43.89         8.58        11.18         0.20 

$`DEL PEAK 28(10Q23.31) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
       75.75        79.46        23.54        31.99        36.07         1.64 
TCGA-18-3421 TCGA-18-4086 TCGA-18-5595 TCGA-21-1070 TCGA-21-1078 TCGA-21-1079 
       86.96         2.79        27.19       119.54        15.58        31.73 
TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
      122.43        43.23        31.63        41.69        33.93        10.82 
TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4596 
        4.31        14.10        27.02        48.82        20.48         0.56 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5471 TCGA-22-5472 
       34.75        13.12        32.02        19.30        31.73        64.93 
TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
       44.25        71.34        79.20        16.64        22.06         7.63 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4589 TCGA-33-A4WN TCGA-33-AASI TCGA-34-2600 
       79.53       174.08         1.55         4.70        44.19        61.61 
TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       31.50        32.88        31.27        65.23        67.79        56.38 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 
       23.24        12.00        16.93        18.15         1.12        27.19 
TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        4.04         3.95         0.43         6.58         8.12         7.46 
TCGA-37-4133 TCGA-37-4141 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5034 
        7.82         0.39        55.20        70.03         1.71        36.39 
TCGA-39-5035 TCGA-39-5039 TCGA-43-2581 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       15.58        17.88        38.66        27.91        12.36        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-8116 
        5.46         3.81        19.59         7.76        13.38        11.77 
TCGA-43-8118 TCGA-43-A475 TCGA-46-6026 TCGA-52-7811 TCGA-52-7812 TCGA-56-6545 
        2.93         9.73        13.91         8.75        27.45         2.04 
TCGA-56-6546 TCGA-56-7579 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 
        0.62         1.45         0.10        17.49         1.35        16.77 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZJ 
       22.75         1.18         9.93        20.94        19.23        21.04 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8387 TCGA-58-8390 TCGA-58-A46L TCGA-58-A46N 
        0.13         0.26        13.25        29.95        56.65        29.92 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2707 TCGA-60-2711 TCGA-60-2712 
        3.58        12.23        96.82        21.93        41.42         9.01 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 
       50.33        48.49        32.32        35.90        23.57        11.77 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       14.99        11.34        25.28        89.29        78.28        16.37 
TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2742 
       25.41        36.16        53.88        34.59        43.10        21.07 
TCGA-66-2744 TCGA-66-2755 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
        0.99         0.92         2.01         1.02         2.01         2.01 
TCGA-66-2769 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2786 TCGA-66-2788 
        7.07         2.01        12.03         3.98        25.97        22.98 
TCGA-66-2790 TCGA-66-2794 TCGA-66-2795 TCGA-68-A59I TCGA-77-6844 TCGA-77-6845 
       22.98        54.08         4.01        16.18        75.09        23.28 
TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-8007 
       11.18         0.49        42.28        70.13         0.16         6.51 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 TCGA-77-8145 TCGA-77-8154 TCGA-77-A5FZ 
       86.76        37.81        12.59         6.97        35.90       126.18 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GH TCGA-85-6175 
      132.36        22.29        42.41        42.08        38.86         9.67 
TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 
       34.95         1.38         1.15        25.15        14.07        16.87 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8355 
       34.52         0.76        13.22        22.45         5.29         2.01 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QR 
        7.76        13.94        12.59        15.62        24.36        19.73 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
        0.79        24.92         9.50         2.93        11.77        14.07 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 
       20.22        22.62        10.59         2.70         4.01         2.30 
TCGA-94-7557 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        0.16         5.03        26.63        14.14        49.87        18.31 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 TCGA-98-A53B TCGA-98-A53C 
       16.57         8.42         2.76        30.67         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HJ 
       21.21        20.32        64.08         4.54        51.78        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CT TCGA-NK-A5CX 
        4.21         2.89        24.00        14.73        65.49         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       33.07         3.72        12.72 

  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                         154.32                          174.08 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                          19.56                           17.88 
[1] "0.0 - 154.3 (19.6)" "0.1 - 174.1 (17.9)"
[1] "hr=" "1.2"
D58V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(10Q23.31) MUTATED         1       48       84        1        34
  DEL PEAK 28(10Q23.31) WILD-TYPE       1       39       67        1        29
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(10Q23.31) MUTATED          46         1         35         11
  DEL PEAK 28(10Q23.31) WILD-TYPE        46         2         27         10
                                 vv
clus                              STAGE IV
  DEL PEAK 28(10Q23.31) MUTATED          1
  DEL PEAK 28(10Q23.31) WILD-TYPE        6
D58V3, multiclass
            clus
vv           DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  STAGE I                                1                               1
  STAGE IA                              48                              39
  STAGE IB                              84                              67
  STAGE II                               1                               1
  STAGE IIA                             34                              29
  STAGE IIB                             46                              46
  STAGE III                              1                               2
  STAGE IIIA                            35                              27
  STAGE IIIB                            11                              10
  STAGE IV                               1                               6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 28(10Q23.31) MUTATED    63 156  37   8
  DEL PEAK 28(10Q23.31) WILD-TYPE  48 134  32  15
D58V4, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  T1                            63                              48
  T2                           156                             134
  T3                            37                              32
  T4                             8                              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2  N3
  DEL PEAK 28(10Q23.31) MUTATED   166  70  20   4
  DEL PEAK 28(10Q23.31) WILD-TYPE 146  61  19   1
D58V5, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  N0                           166                             146
  N1                            70                              61
  N2                            20                              19
  N3                             4                               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"
D58V6, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED   217   1
  DEL PEAK 28(10Q23.31) WILD-TYPE 187   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED    217    1
  DEL PEAK 28(10Q23.31) WILD-TYPE  187    6
   clus
vv  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  0                           217                             187
  1                             1                               6
[1] 2 2
[1] FALSE
D58V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED    59 205
  DEL PEAK 28(10Q23.31) WILD-TYPE  68 161
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED     59  205
  DEL PEAK 28(10Q23.31) WILD-TYPE   68  161
        clus
vv       DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  FEMALE                            59                              68
  MALE                             205                             161
[1] 2 2
[1] FALSE
D58V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(10Q23.31) MUTATED                                       9
  DEL PEAK 28(10Q23.31) WILD-TYPE                                     6
                                 vv
clus                              LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(10Q23.31) MUTATED                                         0
  DEL PEAK 28(10Q23.31) WILD-TYPE                                       1
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 28(10Q23.31) MUTATED                                        2
  DEL PEAK 28(10Q23.31) WILD-TYPE                                      4
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 28(10Q23.31) MUTATED                                         1
  DEL PEAK 28(10Q23.31) WILD-TYPE                                       0
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(10Q23.31) MUTATED                                                           252
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                         218
D58V9, multiclass
                                                             clus
vv                                                            DEL PEAK 28(10Q23.31) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           252
                                                             clus
vv                                                            DEL PEAK 28(10Q23.31) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             218
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED     6 258
  DEL PEAK 28(10Q23.31) WILD-TYPE   7 222
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED      6  258
  DEL PEAK 28(10Q23.31) WILD-TYPE    7  222
     clus
vv    DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  NO                              6                               7
  YES                           258                             222
[1] 2 2
[1] FALSE
D58V11, continuous
D58V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(10Q23.31) MUTATED   215   5   2  11
  DEL PEAK 28(10Q23.31) WILD-TYPE 179   7   2  11
D58V13, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  R0                           215                             179
  R1                             5                               7
  R2                             2                               2
  RX                            11                              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(10Q23.31) MUTATED       5                        20   180
  DEL PEAK 28(10Q23.31) WILD-TYPE     4                        11   160
D58V14, multiclass
                           clus
vv                          DEL PEAK 28(10Q23.31) MUTATED
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               180
                           clus
vv                          DEL PEAK 28(10Q23.31) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                              11
  WHITE                                                 160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V15, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED     4 165
  DEL PEAK 28(10Q23.31) WILD-TYPE   4 144
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED      4  165
  DEL PEAK 28(10Q23.31) WILD-TYPE    4  144
                        clus
vv                       DEL PEAK 28(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           165
                        clus
vv                       DEL PEAK 28(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             144
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 29(11P15.5) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(11P15.5) MUTATED   143  92
  DEL PEAK 29(11P15.5) WILD-TYPE 138 104
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           235                            242 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                            92                            104 
$`DEL PEAK 29(11P15.5) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 
       12.20        75.75        79.46         4.80        11.34        23.54 
TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-5592 TCGA-21-1070 
       31.99        36.07         1.64        86.96        49.94       119.54 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
       46.88        60.89        34.78       122.43       119.80        43.23 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1017 TCGA-22-4593 
       31.63        33.93        10.82        32.19        48.82        35.08 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4607 TCGA-22-5471 TCGA-22-5473 
       24.13         0.56        34.75        19.30        31.73        63.55 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
       44.25         0.79        54.28        79.20        11.74        18.84 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
       22.06         7.63       133.74        98.01        79.53       103.53 
TCGA-33-4587 TCGA-33-6737 TCGA-33-6738 TCGA-33-AASB TCGA-33-AASI TCGA-34-2600 
       54.44        19.76        27.02         6.94        44.19        61.61 
TCGA-34-2605 TCGA-34-5231 TCGA-34-5232 TCGA-34-5236 TCGA-34-5241 TCGA-34-5928 
       28.96        65.23        67.79         9.07        16.93        18.15 
TCGA-34-5929 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4132 
        4.96        27.19         3.95         0.43         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5022 
        7.82         6.81         0.39        47.80        44.75        55.20 
TCGA-39-5027 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-43-2578 
       60.79        27.39        36.39        15.58        35.70        22.49 
TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 
       38.66        33.11        18.38        27.91        12.36        19.59 
TCGA-43-7657 TCGA-43-8115 TCGA-43-A474 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 
        7.76        13.38        11.61        12.03         9.99        10.65 
TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-6545 TCGA-56-7222 
       13.91         5.46        30.35        28.96         2.04         0.43 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 TCGA-56-8503 
        1.45         1.32        17.49        26.89        17.00         1.35 
TCGA-56-8624 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A4ZK 
        1.18        20.25        15.81        20.94        21.04        18.74 
TCGA-56-A5DR TCGA-56-A62T TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-60-2695 
        0.13         2.76        13.25        29.95        71.24        21.11 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 TCGA-60-2712 TCGA-60-2714 TCGA-60-2720 
       10.22        96.82        80.45         9.01        50.33         3.19 
TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH 
       32.32        35.90        23.57        11.77       102.67        66.61 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2742 
       59.97        45.57        16.37        53.88        34.59        21.07 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 
       21.01        25.05         0.99         1.02         2.01         7.07 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 
       19.00         3.02        12.03         3.98        12.00         1.97 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 
       22.98         4.04         5.03        30.02        10.06         4.01 
TCGA-66-2800 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
       49.05         6.94         8.02        13.35        16.18        14.73 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7337 TCGA-77-7338 
       75.09        23.28        89.98         0.49       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 
       46.78        15.75         6.51        86.76        53.95        82.92 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 
       53.92        17.72        11.54        26.40         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
       65.49        35.90         0.33        22.29         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 
       42.08        27.62        12.99        36.53        34.95        32.91 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 TCGA-85-8276 TCGA-85-8288 TCGA-85-8351 
        1.15        18.94        25.15        34.52        13.22        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 TCGA-85-8481 TCGA-85-A4CL TCGA-85-A4CN 
        5.29         3.09         0.72         7.76        25.68        19.33 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-7769 TCGA-90-7964 
       14.96        18.18        19.73         3.65        11.77        14.07 
TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 TCGA-94-8490 
       10.59         4.01         2.30        21.04         4.01         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-98-8020 TCGA-98-8023 
       26.63        14.14        49.87        18.31         2.76        21.34 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
       18.15         2.01        20.71        13.41        11.84         0.07 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL 
       64.08         4.54        51.78        45.37        13.74         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
       37.22        30.58        14.73        29.75        22.78        83.57 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W 
       65.49        16.80        33.07         3.72        43.89         8.58 
TCGA-XC-AA0X 
        0.20 

$`DEL PEAK 29(11P15.5) WILD-TYPE`
TCGA-18-3407 TCGA-18-3411 TCGA-18-3415 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 
        7.46       117.57        92.15         6.18         2.79       154.32 
TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 
       27.19        99.16        70.16        15.58        31.73         9.34 
TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       88.11        41.69        21.99         7.33        14.93         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 
       64.21         1.74        14.10        27.02        20.48        48.33 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 
       38.17        13.12        32.02         9.57        11.77        64.93 
TCGA-22-5474 TCGA-22-5480 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       14.63        71.34        30.12        62.86        56.32        16.64 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-A4WN TCGA-33-A5GW 
      174.08       151.27        14.07         1.55         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2604 
       36.62       110.99       118.36        27.16         2.63        31.50 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 
       32.88        31.27        56.38        23.24        12.00        30.94 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4129 
        1.12         4.04        26.43        20.91         0.39         6.58 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5021 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
        3.39        74.07        68.58        70.03         1.71        24.33 
TCGA-39-5030 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 
        1.94        35.64        17.88        17.06        40.21        27.02 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7658 TCGA-43-8116 
       24.89        21.47         5.46         3.81        66.51        11.77 
TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        2.93         9.73        14.20         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 
       28.34         8.75        27.45         0.10        18.25         0.62 
TCGA-56-7221 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 
        0.99         0.99         0.85         6.51         0.10         3.48 
TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 
       14.07        16.77         1.81        22.75        10.36         9.93 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8386 TCGA-58-8388 
       19.23        13.32        17.85         0.26         0.03        13.55 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       16.47        34.78        85.12        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       29.92         3.58        12.23        37.94        92.71        21.93 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 
       49.48        66.54        41.42        56.91        35.34        48.49 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM 
       42.64        29.85        26.83        70.62        58.65        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MU TCGA-63-A5MV 
       11.34        25.28        89.29        78.28        25.41        36.16 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       16.96        43.10         2.01         0.99         1.02         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2765 TCGA-66-2767 TCGA-66-2770 
        0.92         0.99        43.99         2.01         2.01        23.01 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 
        2.01        19.00        24.95        25.97        40.01        22.98 
TCGA-66-2794 TCGA-68-7755 TCGA-68-7756 TCGA-77-6842 TCGA-77-6843 TCGA-77-7138 
       54.08         2.73         6.64        29.56        73.12        11.18 
TCGA-77-7140 TCGA-77-7142 TCGA-77-7335 TCGA-77-8128 TCGA-77-8131 TCGA-77-8136 
       20.78        42.28        70.13        37.81        12.59        39.09 
TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
      104.09        27.39         6.97       126.18       132.36       117.57 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7698 
       30.81        38.86         9.67        11.97         6.41        31.30 
TCGA-85-7710 TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
        1.38        29.95        19.04        24.13        31.56        14.07 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8354 TCGA-85-8355 
       16.87        10.09         0.76        22.45        32.71         2.01 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB 
       14.63        13.94        12.59         0.10        15.62        17.72 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       24.36        12.56        16.21        15.85        14.96         0.79 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE 
       12.39        24.92         9.50         2.93        20.22        22.62 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
        2.70         3.48         5.26         0.16        11.70        16.14 
TCGA-94-A5I6 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
       17.69        57.07        17.46        19.36        16.57         8.42 
TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53C TCGA-98-A53D 
       30.81        30.67        27.16         3.88        27.02        21.21 
TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       20.32        18.58        19.10        12.89        16.11        13.18 
TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HP TCGA-NK-A5CX TCGA-NK-A7XE 
        1.22         4.21        39.85        24.00         3.65         0.43 
TCGA-O2-A52S TCGA-O2-A5IB 
       12.72        11.18 

  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                        133.74                         174.08 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                        19.730                         18.415 
[1] "0.1 - 133.7 (19.7)" "0.0 - 174.1 (18.4)"
[1] "hr=" "1.1"
D59V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(11P15.5) MUTATED         2       34       72        1        31
  DEL PEAK 29(11P15.5) WILD-TYPE       0       53       79        1        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(11P15.5) MUTATED          49         1         36         10
  DEL PEAK 29(11P15.5) WILD-TYPE        43         2         26         11
                                vv
clus                             STAGE IV
  DEL PEAK 29(11P15.5) MUTATED          4
  DEL PEAK 29(11P15.5) WILD-TYPE        3
D59V3, multiclass
            clus
vv           DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             34                             53
  STAGE IB                             72                             79
  STAGE II                              1                              1
  STAGE IIA                            31                             32
  STAGE IIB                            49                             43
  STAGE III                             1                              2
  STAGE IIIA                           36                             26
  STAGE IIIB                           10                             11
  STAGE IV                              4                              3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 29(11P15.5) MUTATED    47 141  43  11
  DEL PEAK 29(11P15.5) WILD-TYPE  64 149  26  12
D59V4, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  T1                           47                             64
  T2                          141                            149
  T3                           43                             26
  T4                           11                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 29(11P15.5) MUTATED   152  70  17   2
  DEL PEAK 29(11P15.5) WILD-TYPE 160  61  22   3
D59V5, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  N0                          152                            160
  N1                           70                             61
  N2                           17                             22
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED   201   4
  DEL PEAK 29(11P15.5) WILD-TYPE 203   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED    201    4
  DEL PEAK 29(11P15.5) WILD-TYPE  203    3
   clus
vv  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  0                          201                            203
  1                            4                              3
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED    56 186
  DEL PEAK 29(11P15.5) WILD-TYPE  71 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     56  186
  DEL PEAK 29(11P15.5) WILD-TYPE   71  180
        clus
vv       DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  FEMALE                           56                             71
  MALE                            186                            180
[1] 2 2
[1] FALSE
D59V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(11P15.5) MUTATED                                       7
  DEL PEAK 29(11P15.5) WILD-TYPE                                     8
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(11P15.5) MUTATED                                         0
  DEL PEAK 29(11P15.5) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 29(11P15.5) MUTATED                                        3
  DEL PEAK 29(11P15.5) WILD-TYPE                                      3
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 29(11P15.5) MUTATED                                         1
  DEL PEAK 29(11P15.5) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(11P15.5) MUTATED                                                           231
  DEL PEAK 29(11P15.5) WILD-TYPE                                                         239
D59V9, multiclass
                                                             clus
vv                                                            DEL PEAK 29(11P15.5) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          231
                                                             clus
vv                                                            DEL PEAK 29(11P15.5) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            239
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED     8 234
  DEL PEAK 29(11P15.5) WILD-TYPE   5 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED      8  234
  DEL PEAK 29(11P15.5) WILD-TYPE    5  246
     clus
vv    DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  NO                             8                              5
  YES                          234                            246
[1] 2 2
[1] FALSE
D59V11, continuous
D59V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(11P15.5) MUTATED   192   7   2   9
  DEL PEAK 29(11P15.5) WILD-TYPE 202   5   2  13
D59V13, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  R0                          192                            202
  R1                            7                              5
  R2                            2                              2
  RX                            9                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(11P15.5) MUTATED       2                        18   164
  DEL PEAK 29(11P15.5) WILD-TYPE     7                        13   176
D59V14, multiclass
                           clus
vv                          DEL PEAK 29(11P15.5) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           18
  WHITE                                              164
                           clus
vv                          DEL PEAK 29(11P15.5) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V15, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED     2 146
  DEL PEAK 29(11P15.5) WILD-TYPE   6 163
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED      2  146
  DEL PEAK 29(11P15.5) WILD-TYPE    6  163
                        clus
vv                       DEL PEAK 29(11P15.5) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          146
                        clus
vv                       DEL PEAK 29(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            163
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 30(11Q22.1) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(11Q22.1) MUTATED    93  65
  DEL PEAK 30(11Q22.1) WILD-TYPE 188 131
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                           158                            319 
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                            65                            131 
$`DEL PEAK 30(11Q22.1) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3412 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 
       12.20        79.46        11.34        31.99        36.07        86.96 
TCGA-18-5595 TCGA-21-1076 TCGA-21-1080 TCGA-21-5783 TCGA-21-5787 TCGA-22-0940 
       27.19        60.89       122.43        88.11        10.82        21.99 
TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4601 TCGA-22-4613 
        4.31         1.74        14.10        35.08        34.75        11.77 
TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5481 TCGA-33-4589 TCGA-33-AASB 
       63.55        44.25         0.79        79.20         1.55         6.94 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-5232 TCGA-34-5239 
       27.16         2.63        61.61        28.96        67.79        23.24 
TCGA-34-5928 TCGA-34-8454 TCGA-37-4130 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
       18.15        27.19         8.12        74.07        44.75        68.58 
TCGA-39-5022 TCGA-39-5027 TCGA-39-5031 TCGA-39-5037 TCGA-43-2581 TCGA-43-3920 
       55.20        60.79        27.39        35.70        38.66        33.11 
TCGA-43-6771 TCGA-43-7657 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
        5.46         7.76        11.77         2.93        11.61        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-52-7809 TCGA-56-7221 
        9.99        10.65        13.91         0.39         5.46         0.99 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-56-8503 
        0.43         0.99         1.32         0.85        17.49         1.35 
TCGA-56-8504 TCGA-56-8624 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
       16.77         1.18        15.81        19.23        13.32        17.85 
TCGA-56-A4ZK TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-60-2695 
       18.74         0.03        13.25        29.95        71.24        21.11 
TCGA-60-2698 TCGA-60-2708 TCGA-60-2712 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
       10.22        80.45         9.01        29.85        35.90        26.83 
TCGA-60-2726 TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MS TCGA-63-A5MU 
       11.77        66.61        59.97        45.57        78.28        25.41 
TCGA-66-2727 TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2781 
       16.96        21.01         1.02         2.01         2.01         3.98 
TCGA-66-2790 TCGA-66-2794 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-7139 
       22.98        54.08         8.02        13.35        14.73        89.98 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        0.16        15.75        86.76        53.95        37.81        82.92 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 
       53.92        39.09        17.72        26.40         9.63        54.41 
TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 
       65.49       117.57        22.29         6.41        36.53        32.91 
TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8352 
       25.15        14.07        16.87        34.52        10.09         5.29 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8664 TCGA-85-A4JC TCGA-85-A4QQ 
       32.71         2.01         0.72         0.10        14.96        18.18 
TCGA-85-A50M TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-A4EE 
       12.56        14.96         3.65         9.50         2.93        22.62 
TCGA-90-A59Q TCGA-92-7341 TCGA-92-8064 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7545 
       10.59         3.48         5.26        26.63        17.69        57.07 
TCGA-96-8169 TCGA-96-A4JL TCGA-98-8020 TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J 
       18.31        16.57         2.76        27.16        18.58        20.71 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HO 
       11.84        64.08        51.78        13.74         2.89        30.58 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V 
       83.57        65.49        16.80        33.07        12.72        43.89 
TCGA-O2-A52W TCGA-O2-A5IB 
        8.58        11.18 

$`DEL PEAK 30(11Q22.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
        7.46        75.75         4.80       117.57        23.54        92.15 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
        1.64         6.18         2.79       154.32        49.94       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       46.88        99.16        70.16        34.78        15.58        31.73 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
        9.34       119.80        43.23        31.63        41.69        33.93 
TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 
       32.19         7.33        14.93        64.21        27.02        48.82 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
       20.48        48.33        24.13         0.56        38.17        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 
       32.02        19.30         9.57        31.73        64.93        14.63 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
       54.28        71.34        11.74        18.84        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
       56.32        16.64        22.06         7.63       133.74        98.01 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       79.53       174.08       103.53       151.27        14.07        54.44 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD 
       19.76        27.02         4.70         0.30        36.62       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
       44.19       118.36        31.50        32.88        31.27        65.23 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 
       56.38         9.07        12.00        16.93        30.94         4.96 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
        1.12         4.04        26.43        20.91         3.95         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        0.39         6.58         7.46         7.82         6.81         0.39 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
        3.39        47.80        70.03         1.71        24.33         1.94 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
       36.39        15.58        35.64        17.88        17.06        40.21 
TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       22.49        27.02        18.38        27.91        12.36        24.89 
TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-A475 
       21.47         3.81        19.59        66.51        13.38         9.73 
TCGA-43-A56U TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 
       14.20         0.39        29.95        28.34        30.35         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
       27.45        28.96         0.10        18.25         2.04         0.62 
TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 
        1.45         6.51         0.10         3.48        26.89        17.00 
TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
       14.07         1.81        22.75        10.36         9.93        20.25 
TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8388 
       20.94        21.04         0.13         0.26         2.76        13.55 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       16.47        34.78        85.12        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
       29.92         3.58        12.23        96.82        37.94        92.71 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
       21.93        49.48        66.54        41.42        56.91        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
       35.34        48.49        42.64         3.19        32.32        23.57 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
      102.67        70.62        58.65        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 
       89.29        16.37        36.16        53.88        34.59        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
        2.01        21.07         0.99         1.02         2.01         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2769 
        0.99        43.99        25.05         0.99         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
       23.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
       12.00        24.95         1.97        25.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 
        4.04         5.03        30.02        10.06         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 
        2.73         6.64         6.94        16.18        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
       75.09        23.28        11.18        20.78         0.49        42.28 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8131 TCGA-77-8139 
       70.13       106.95        46.78         6.51        12.59       104.09 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       11.54        27.39         6.97        35.90         0.33       126.18 
TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
      132.36         5.92        42.41        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 
       38.86         9.67        11.97        12.99        34.95        31.30 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 
        1.38         1.15        29.95        18.94        19.04        24.13 
TCGA-85-8070 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
       31.56         0.76        13.22        22.45        16.77         3.09 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL 
        7.76        14.63        13.94        12.59        15.62        25.68 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 
       19.33        17.72        24.36        19.73        16.21        15.85 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
        0.79        12.39        24.92        11.77        14.07        20.22 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
        2.70         4.01         2.30        21.04         0.16        11.70 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7544 TCGA-96-8170 
        4.01         5.03        14.14        16.14        49.87        17.46 
TCGA-96-A4JK TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 
       19.36         8.42        30.81        30.67        21.34         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH 
       18.15         2.01        27.02        21.21        20.32        19.10 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HF 
       12.89        16.11        13.18        13.41         0.07         4.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP 
        1.22        45.37         4.21        39.85        37.22        24.00 
TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52Q 
       14.73        29.75        22.78         3.65         0.43         3.72 
TCGA-XC-AA0X 
        0.20 

  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                        122.43                         174.08 
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                         18.00                          19.73 
[1] "0.0 - 122.4 (18.0)" "0.1 - 174.1 (19.7)"
[1] "hr=" "1"  
D60V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(11Q22.1) MUTATED         2       23       46        1        25
  DEL PEAK 30(11Q22.1) WILD-TYPE       0       64      105        1        38
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(11Q22.1) MUTATED          30         2         21          4
  DEL PEAK 30(11Q22.1) WILD-TYPE        62         1         41         17
                                vv
clus                             STAGE IV
  DEL PEAK 30(11Q22.1) MUTATED          2
  DEL PEAK 30(11Q22.1) WILD-TYPE        5
D60V3, multiclass
            clus
vv           DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             23                             64
  STAGE IB                             46                            105
  STAGE II                              1                              1
  STAGE IIA                            25                             38
  STAGE IIB                            30                             62
  STAGE III                             2                              1
  STAGE IIIA                           21                             41
  STAGE IIIB                            4                             17
  STAGE IV                              2                              5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 30(11Q22.1) MUTATED    31 103  19   6
  DEL PEAK 30(11Q22.1) WILD-TYPE  80 187  50  17
D60V4, multiclass
    clus
vv   DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  T1                           31                             80
  T2                          103                            187
  T3                           19                             50
  T4                            6                             17
[1] 4 2
[1] TRUE
[1] "dimension of 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(11Q22.1) MUTATED    91  55  11   1
  DEL PEAK 30(11Q22.1) WILD-TYPE 221  76  28   4
D60V5, multiclass
    clus
vv   DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  N0                           91                            221
  N1                           55                             76
  N2                           11                             28
  N3                            1                              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"
D60V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q22.1) MUTATED   128   2
  DEL PEAK 30(11Q22.1) WILD-TYPE 276   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q22.1) MUTATED    128    2
  DEL PEAK 30(11Q22.1) WILD-TYPE  276    5
   clus
vv  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  0                          128                            276
  1                            2                              5
[1] 2 2
[1] FALSE
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q22.1) MUTATED    36 123
  DEL PEAK 30(11Q22.1) WILD-TYPE  91 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q22.1) MUTATED     36  123
  DEL PEAK 30(11Q22.1) WILD-TYPE   91  243
        clus
vv       DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  FEMALE                           36                             91
  MALE                            123                            243
[1] 2 2
[1] FALSE
D60V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 30(11Q22.1) MUTATED                                       6
  DEL PEAK 30(11Q22.1) WILD-TYPE                                     9
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 30(11Q22.1) MUTATED                                         0
  DEL PEAK 30(11Q22.1) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 30(11Q22.1) MUTATED                                        1
  DEL PEAK 30(11Q22.1) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 30(11Q22.1) MUTATED                                         0
  DEL PEAK 30(11Q22.1) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(11Q22.1) MUTATED                                                           152
  DEL PEAK 30(11Q22.1) WILD-TYPE                                                         318
D60V9, multiclass
                                                             clus
vv                                                            DEL PEAK 30(11Q22.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          152
                                                             clus
vv                                                            DEL PEAK 30(11Q22.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            318
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q22.1) MUTATED     4 155
  DEL PEAK 30(11Q22.1) WILD-TYPE   9 325
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q22.1) MUTATED      4  155
  DEL PEAK 30(11Q22.1) WILD-TYPE    9  325
     clus
vv    DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  NO                             4                              9
  YES                          155                            325
[1] 2 2
[1] FALSE
D60V11, continuous
D60V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(11Q22.1) MUTATED   125   2   1   5
  DEL PEAK 30(11Q22.1) WILD-TYPE 269  10   3  17
D60V13, multiclass
    clus
vv   DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  R0                          125                            269
  R1                            2                             10
  R2                            1                              3
  RX                            5                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(11Q22.1) MUTATED       2                        11   111
  DEL PEAK 30(11Q22.1) WILD-TYPE     7                        20   229
D60V14, multiclass
                           clus
vv                          DEL PEAK 30(11Q22.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              111
                           clus
vv                          DEL PEAK 30(11Q22.1) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             20
  WHITE                                                229
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q22.1) MUTATED     2 104
  DEL PEAK 30(11Q22.1) WILD-TYPE   6 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q22.1) MUTATED      2  104
  DEL PEAK 30(11Q22.1) WILD-TYPE    6  205
                        clus
vv                       DEL PEAK 30(11Q22.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          104
                        clus
vv                       DEL PEAK 30(11Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            205
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 31(11Q25) MUTATION ANALYSIS
D61V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 31(11Q25) MUTATED   105  75
  DEL PEAK 31(11Q25) WILD-TYPE 176 121
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                         180                          297 
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                          75                          121 
$`DEL PEAK 31(11Q25) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 
       12.20        75.75        79.46        11.34        23.54        31.99 
TCGA-18-3417 TCGA-18-3421 TCGA-18-5595 TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 
       36.07        86.96        27.19        60.89       122.43       119.80 
TCGA-21-5783 TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 TCGA-22-1011 TCGA-22-1016 
       88.11        10.82        21.99         4.31         1.74        27.02 
TCGA-22-4593 TCGA-22-4601 TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
       35.08        34.75        11.77        63.55        44.25         0.79 
TCGA-22-5481 TCGA-22-5489 TCGA-33-4532 TCGA-33-4533 TCGA-33-4587 TCGA-33-4589 
       79.20        62.86         7.63       133.74        54.44         1.55 
TCGA-33-6737 TCGA-33-AASB TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 
       19.76         6.94        27.16         2.63        61.61        28.96 
TCGA-34-5232 TCGA-34-5236 TCGA-34-5239 TCGA-34-5928 TCGA-34-A5IX TCGA-37-3789 
       67.79         9.07        23.24        18.15        20.91         0.43 
TCGA-37-4135 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 
        6.81        74.07        44.75        68.58        55.20        60.79 
TCGA-39-5031 TCGA-39-5037 TCGA-43-2581 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 
       27.39        35.70        38.66        33.11        24.89        21.47 
TCGA-43-6771 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-A474 TCGA-43-A56V 
        5.46         7.76        66.51        11.77        11.61        12.03 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-52-7809 TCGA-56-7221 
        9.99        10.65        13.91         0.39         5.46         0.99 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-56-8308 
        0.43         0.99         1.32         0.85        17.49        17.00 
TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
       16.77         1.18        10.36        15.81        19.23        13.32 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8390 TCGA-58-A46J TCGA-60-2695 TCGA-60-2698 
       17.85        18.74        29.95        85.12        21.11        10.22 
TCGA-60-2708 TCGA-60-2712 TCGA-60-2715 TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 
       80.45         9.01        35.34        29.85        26.83        11.77 
TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MS TCGA-63-A5MU 
      102.67        66.61        59.97        45.57        78.28        25.41 
TCGA-66-2727 TCGA-66-2753 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
       16.96         1.02         0.99        43.99        21.01        25.05 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2773 TCGA-66-2790 TCGA-66-2792 
        2.01         2.01         2.01         3.02        22.98        30.02 
TCGA-66-2794 TCGA-66-2800 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59J TCGA-77-7139 
       54.08        49.05         8.02        13.35        14.73        89.98 
TCGA-77-7140 TCGA-77-7142 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
       20.78        42.28         0.16        15.75        86.76        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       37.81        82.92        12.59        53.92        39.09        17.72 
TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-85-6798 
       26.40         9.63        54.41        65.49       117.57         6.41 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 
       36.53        31.30        32.91        25.15        14.07        16.87 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 
       34.52        10.09         0.76         5.29        32.71         2.01 
TCGA-85-8481 TCGA-85-8664 TCGA-85-A4JC TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
        7.76         0.10        14.96        12.56        16.21        14.96 
TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 
        3.65         9.50         2.93        22.62        10.59         3.48 
TCGA-92-8063 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7545 TCGA-98-8020 TCGA-98-8023 
        4.01        26.63        17.69        57.07         2.76        21.34 
TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       27.16        18.58        20.71        11.84         0.07        64.08 
TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NK-A5CR TCGA-NK-A5CT 
       51.78        13.74         4.21        30.58        83.57        65.49 
TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       16.80        33.07        12.72        43.89         8.58        11.18 

$`DEL PEAK 31(11Q25) WILD-TYPE`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3411 TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 
        7.46         4.80       117.57        92.15         1.64         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        2.79       154.32        49.94       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1083 
       70.16        34.78        15.58        31.73         9.34        43.23 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 
       31.63        41.69        33.93        32.19         7.33        14.93 
TCGA-22-1005 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
       64.21        14.10        48.82        20.48        48.33        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
        0.56        38.17        13.12        32.02        19.30         9.57 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 
       31.73        64.93        14.63        54.28        71.34        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4538 
       18.84        30.12        56.32        16.64        22.06        98.01 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 
       79.53       174.08       103.53       151.27        14.07        27.02 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
        4.70         0.30        36.62       110.99        44.19       118.36 
TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 TCGA-34-5240 
       31.50        32.88        31.27        65.23        56.38        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       16.93        30.94         4.96         1.12        27.19         4.04 
TCGA-34-8456 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       26.43         3.95         0.39         6.58         8.12         7.46 
TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5024 TCGA-39-5028 
        7.82         0.39         3.39        47.80        70.03         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 
       24.33         1.94        36.39        15.58        35.64        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 
       17.06        40.21        22.49        27.02        18.38        27.91 
TCGA-43-6143 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8118 TCGA-43-A475 
       12.36         3.81        19.59        13.38         2.93         9.73 
TCGA-43-A56U TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 
       14.20         0.39        29.95        28.34        30.35         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
       27.45        28.96         0.10        18.25         2.04         0.62 
TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
        1.45         6.51         0.10         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D 
        1.35         1.81        22.75         9.93        20.25        20.94 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       21.04         0.13         0.26         2.76         0.03        13.25 
TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L 
       13.55        71.24        16.47        34.78        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 
       35.24        29.92         3.58        12.23        96.82        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 
       92.71        21.93        49.48        66.54        41.42        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 
       50.33        48.49        42.64         3.19        32.32        35.90 
TCGA-60-2724 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       23.57        70.62        58.65        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 
       89.29        16.37        36.16        53.88        34.59        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2763 
        2.01        21.07         0.99         2.01         0.92         0.99 
TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 
        1.02         7.07        23.01        19.00         2.01        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       12.03         3.98        12.00        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 
       40.01        22.98         4.04         5.03        10.06         4.01 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 
        2.73         6.64         6.94        16.18        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 
       75.09        23.28        11.18         0.49        70.13       106.95 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 
       46.78         6.51       104.09        11.54        27.39         6.97 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
       35.90         0.33       126.18       132.36        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       42.41        42.08        30.81        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
       11.97        12.99        34.95         1.38         1.15        29.95 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8288 TCGA-85-8350 
       18.94        19.04        24.13        31.56        13.22        22.45 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
       16.77         3.09         0.72        14.63        13.94        12.59 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ 
       15.62        25.68        19.33        17.72        24.36        18.18 
TCGA-85-A4QR TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 
       19.73        15.85         0.79        12.39        24.92        11.77 
TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
       14.07        20.22         2.70         5.26         2.30        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 
        0.16        11.70         4.01         5.03        14.14        16.14 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
       49.87        18.31        17.46        19.36        16.57         8.42 
TCGA-98-8021 TCGA-98-8022 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.81        30.67         3.88        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       21.21        20.32        19.10        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HM 
       13.41         4.54         1.22        45.37         2.89        39.85 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CX 
       37.22        24.00        14.73        29.75        22.78         3.65 
TCGA-NK-A7XE TCGA-O2-A52Q TCGA-XC-AA0X 
        0.43         3.72         0.20 

  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                        0.07                         0.03 
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                      133.74                       174.08 
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                      20.745                       19.000 
[1] "0.1 - 133.7 (20.7)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1"  
D61V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(11Q25) MUTATED         2       26       54        1        23
  DEL PEAK 31(11Q25) WILD-TYPE       0       61       97        1        40
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(11Q25) MUTATED          39         2         23          7
  DEL PEAK 31(11Q25) WILD-TYPE        53         1         39         14
                              vv
clus                           STAGE IV
  DEL PEAK 31(11Q25) MUTATED          2
  DEL PEAK 31(11Q25) WILD-TYPE        5
D61V3, multiclass
            clus
vv           DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  STAGE I                             2                            0
  STAGE IA                           26                           61
  STAGE IB                           54                           97
  STAGE II                            1                            1
  STAGE IIA                          23                           40
  STAGE IIB                          39                           53
  STAGE III                           2                            1
  STAGE IIIA                         23                           39
  STAGE IIIB                          7                           14
  STAGE IV                            2                            5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  DEL PEAK 31(11Q25) MUTATED    33 115  25   9
  DEL PEAK 31(11Q25) WILD-TYPE  78 175  44  14
D61V4, multiclass
    clus
vv   DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  T1                         33                           78
  T2                        115                          175
  T3                         25                           44
  T4                          9                           14
[1] 4 2
[1] TRUE
[1] "dimension of 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(11Q25) MUTATED   108  61  11   1
  DEL PEAK 31(11Q25) WILD-TYPE 204  70  28   4
D61V5, multiclass
    clus
vv   DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  N0                        108                          204
  N1                         61                           70
  N2                         11                           28
  N3                          1                            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"
D61V6, binary
                              cls
clus                             0   1
  DEL PEAK 31(11Q25) MUTATED   145   2
  DEL PEAK 31(11Q25) WILD-TYPE 259   5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(11Q25) MUTATED    145    2
  DEL PEAK 31(11Q25) WILD-TYPE  259    5
   clus
vv  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  0                        145                          259
  1                          2                            5
[1] 2 2
[1] FALSE
D61V7, binary
                              cls
clus                             0   1
  DEL PEAK 31(11Q25) MUTATED    39 143
  DEL PEAK 31(11Q25) WILD-TYPE  88 223
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(11Q25) MUTATED     39  143
  DEL PEAK 31(11Q25) WILD-TYPE   88  223
        clus
vv       DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  FEMALE                         39                           88
  MALE                          143                          223
[1] 2 2
[1] FALSE
D61V8, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(11Q25) MUTATED                                       6
  DEL PEAK 31(11Q25) WILD-TYPE                                     9
                              vv
clus                           LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(11Q25) MUTATED                                         0
  DEL PEAK 31(11Q25) WILD-TYPE                                       1
                              vv
clus                           LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 31(11Q25) MUTATED                                        1
  DEL PEAK 31(11Q25) WILD-TYPE                                      5
                              vv
clus                           LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(11Q25) MUTATED                                         1
  DEL PEAK 31(11Q25) WILD-TYPE                                       0
                              vv
clus                           LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(11Q25) MUTATED                                                           174
  DEL PEAK 31(11Q25) WILD-TYPE                                                         296
D61V9, multiclass
                                                             clus
vv                                                            DEL PEAK 31(11Q25) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        174
                                                             clus
vv                                                            DEL PEAK 31(11Q25) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          296
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, binary
                              cls
clus                             0   1
  DEL PEAK 31(11Q25) MUTATED     5 177
  DEL PEAK 31(11Q25) WILD-TYPE   8 303
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(11Q25) MUTATED      5  177
  DEL PEAK 31(11Q25) WILD-TYPE    8  303
     clus
vv    DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  NO                           5                            8
  YES                        177                          303
[1] 2 2
[1] FALSE
D61V11, continuous
D61V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 31(11Q25) MUTATED   140   3   1  10
  DEL PEAK 31(11Q25) WILD-TYPE 254   9   3  12
D61V13, multiclass
    clus
vv   DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  R0                        140                          254
  R1                          3                            9
  R2                          1                            3
  RX                         10                           12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(11Q25) MUTATED       3                        13   125
  DEL PEAK 31(11Q25) WILD-TYPE     6                        18   215
D61V14, multiclass
                           clus
vv                          DEL PEAK 31(11Q25) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                         13
  WHITE                                            125
                           clus
vv                          DEL PEAK 31(11Q25) WILD-TYPE
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           18
  WHITE                                              215
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V15, binary
                              cls
clus                             0   1
  DEL PEAK 31(11Q25) MUTATED     2 115
  DEL PEAK 31(11Q25) WILD-TYPE   6 194
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(11Q25) MUTATED      2  115
  DEL PEAK 31(11Q25) WILD-TYPE    6  194
                        clus
vv                       DEL PEAK 31(11Q25) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                        115
                        clus
vv                       DEL PEAK 31(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          194
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 32(12Q24.31) MUTATION ANALYSIS
D62V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(12Q24.31) MUTATED    55  27
  DEL PEAK 32(12Q24.31) WILD-TYPE 226 169
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                             82                             395 
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                             27                             169 
$`DEL PEAK 32(12Q24.31) MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3415 TCGA-18-4083 TCGA-18-4086 
        7.46        75.75        79.46        92.15         6.18         2.79 
TCGA-21-1072 TCGA-21-1082 TCGA-22-4595 TCGA-22-5473 TCGA-22-5478 TCGA-22-5479 
       99.16       119.80        24.13        63.55         0.79        54.28 
TCGA-22-5485 TCGA-33-4533 TCGA-33-A5GW TCGA-33-AASL TCGA-34-5232 TCGA-34-A5IX 
       30.12       133.74         0.30        27.16        67.79        20.91 
TCGA-37-4129 TCGA-37-4141 TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
        6.58         0.39        38.66        18.38        27.91        12.36 
TCGA-43-A56V TCGA-46-6026 TCGA-52-7809 TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 
       12.03        13.91         5.46        18.25         0.43         0.99 
TCGA-56-7822 TCGA-56-8624 TCGA-56-A49D TCGA-60-2698 TCGA-60-2703 TCGA-60-2722 
       17.49         1.18        20.94        10.22        96.82        29.85 
TCGA-60-2723 TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5ML TCGA-66-2763 TCGA-66-2766 
       35.90        26.83       102.67        45.57         0.99         1.02 
TCGA-66-2773 TCGA-66-2781 TCGA-68-7757 TCGA-68-8250 TCGA-77-7138 TCGA-77-8007 
        3.02         3.98         6.94         8.02        11.18         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 
       86.76        53.95        82.92        12.59        17.72       104.09 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GH 
       27.39         9.63        65.49        42.08        30.81        38.86 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7710 TCGA-85-8350 TCGA-85-8353 TCGA-85-8354 
       11.97        36.53         1.38        22.45         3.09        32.71 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A513 TCGA-90-A4ED TCGA-94-7033 TCGA-94-A4VJ 
       12.56        16.21         0.79        20.22        21.04        14.14 
TCGA-94-A5I6 TCGA-98-8021 TCGA-98-A538 TCGA-98-A53J TCGA-LA-A446 TCGA-MF-A522 
       17.69        30.81        27.16        20.71        13.18        11.84 
TCGA-NC-A5HP TCGA-NK-A5CR TCGA-O2-A52V TCGA-O2-A52W 
       24.00        83.57        43.89         8.58 

$`DEL PEAK 32(12Q24.31) WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 
       12.20         4.80       117.57        11.34        23.54        31.99 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
       36.07         1.64        86.96       154.32        49.94        27.19 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
      119.54        46.88        70.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       31.73       122.43         9.34        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-0944 
       41.69        33.93        10.82        32.19        21.99         7.33 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       14.93         4.31        64.21         1.74        14.10        27.02 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
       48.82        20.48        35.08        48.33         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       34.75        13.12        32.02        19.30         9.57        11.77 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 
       31.73        64.93        14.63        44.25        71.34        79.20 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       11.74        18.84        62.86        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
        7.63        98.01        79.53       174.08       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN 
       14.07        54.44         1.55        19.76        27.02         4.70 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 
       36.62         6.94       110.99        44.19       118.36         2.63 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 
       61.61        31.50        28.96        32.88        31.27        65.23 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       56.38         9.07        23.24        12.00        16.93        30.94 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       18.15         4.96         1.12        27.19         4.04        26.43 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        3.95         0.43         0.39         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        6.81         3.39        47.80        74.07        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        70.03        60.79         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
       27.39        36.39        15.58        35.64        35.70        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-6647 
       17.06        40.21        22.49        27.02        33.11        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
       21.47         5.46         3.81        19.59         7.76        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
       13.38        11.77         2.93        11.61         9.73        14.20 
TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        9.99        10.65         0.39         0.39        29.95        28.34 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
       30.35         8.75        27.45        28.96         0.10         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
        0.62         0.99         1.45         1.32         0.85         6.51 
TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 
        0.10         3.48        26.89        17.00        14.07         1.35 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
       16.77         1.81        22.75        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       15.81        19.23        13.32        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        0.13         0.26         2.76         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       29.95        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 
       56.65        35.24        29.92        21.11         3.58        12.23 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       41.42         9.01        56.91        50.33        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MG 
       42.64         3.19        32.32        23.57        11.77        70.62 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       66.61        58.65        59.97        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       89.29        78.28        16.37        25.41        36.16        53.88 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       34.59        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        1.02         2.01         0.92         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
       25.05         2.01         2.01         2.01         7.07        23.01 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
       19.00         2.01        19.00        12.03        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
        1.97        25.97        40.01        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        5.03        30.02        10.06        54.08         4.01        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
        2.73         6.64        13.35        16.18        14.73        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 
       73.12        75.09        23.28        89.98        20.78         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       42.28        70.13       106.95         0.16        46.78        15.75 
TCGA-77-8128 TCGA-77-8133 TCGA-77-8136 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 
       37.81        53.92        39.09        11.54        26.40         6.97 
TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       54.41        35.90         0.33       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 
       22.29         5.92        42.41        27.62         9.67        12.99 
TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 
        6.41        34.95        31.30        32.91         1.15        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       18.94        25.15        19.04        24.13        31.56        14.07 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
       16.87        34.52        10.09         0.76        13.22        16.77 
TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
        5.29         2.01         0.72         7.76        14.63        13.94 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
       12.59         0.10        15.62        25.68        19.33        17.72 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 
       14.96        24.36        18.18        19.73        15.85        14.96 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
       12.39         3.65        24.92         9.50         2.93        11.77 
TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       14.07        22.62        10.59         2.70         3.48         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        5.26         2.30         0.16        11.70         4.01         5.03 
TCGA-94-8491 TCGA-94-A5I4 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
       26.63        16.14        49.87        57.07        18.31        17.46 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 TCGA-98-8023 
       19.36        16.57         8.42         2.76        30.67        21.34 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
        3.88        18.15         2.01        27.02        21.21        20.32 
TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HD 
       18.58        19.10        12.89        16.11        13.41         0.07 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
       64.08         4.54        51.78         1.22        45.37        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HQ 
        4.21         2.89        39.85        37.22        30.58        14.73 
TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE 
       29.75        22.78        65.49         3.65        16.80         0.43 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07         3.72        12.72        11.18         0.20 

  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                           0.30                            0.03 
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                         133.74                          174.08 
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                         20.465                          19.040 
[1] "0.3 - 133.7 (20.5)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1.4"
D62V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(12Q24.31) MUTATED         1       13       35        1         7
  DEL PEAK 32(12Q24.31) WILD-TYPE       1       74      116        1        56
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(12Q24.31) MUTATED          15         0          8          0
  DEL PEAK 32(12Q24.31) WILD-TYPE        77         3         54         21
                                 vv
clus                              STAGE IV
  DEL PEAK 32(12Q24.31) MUTATED          1
  DEL PEAK 32(12Q24.31) WILD-TYPE        6
D62V3, multiclass
            clus
vv           DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  STAGE I                                1                               1
  STAGE IA                              13                              74
  STAGE IB                              35                             116
  STAGE II                               1                               1
  STAGE IIA                              7                              56
  STAGE IIB                             15                              77
  STAGE III                              0                               3
  STAGE IIIA                             8                              54
  STAGE IIIB                             0                              21
  STAGE IV                               1                               6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 32(12Q24.31) MUTATED    19  52  12   0
  DEL PEAK 32(12Q24.31) WILD-TYPE  92 238  57  23
D62V4, multiclass
    clus
vv   DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  T1                            19                              92
  T2                            52                             238
  T3                            12                              57
  T4                             0                              23
[1] 4 2
[1] TRUE
[1] "dimension of 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(12Q24.31) MUTATED    58  18   4   0
  DEL PEAK 32(12Q24.31) WILD-TYPE 254 113  35   5
D62V5, multiclass
    clus
vv   DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  N0                            58                             254
  N1                            18                             113
  N2                             4                              35
  N3                             0                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                                 cls
clus                                0   1
  DEL PEAK 32(12Q24.31) MUTATED    66   1
  DEL PEAK 32(12Q24.31) WILD-TYPE 338   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.31) MUTATED     66    1
  DEL PEAK 32(12Q24.31) WILD-TYPE  338    6
   clus
vv  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  0                            66                             338
  1                             1                               6
[1] 2 2
[1] FALSE
D62V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(12Q24.31) MUTATED    16  67
  DEL PEAK 32(12Q24.31) WILD-TYPE 111 299
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.31) MUTATED     16   67
  DEL PEAK 32(12Q24.31) WILD-TYPE  111  299
        clus
vv       DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  FEMALE                            16                             111
  MALE                              67                             299
[1] 2 2
[1] FALSE
D62V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(12Q24.31) MUTATED                                       3
  DEL PEAK 32(12Q24.31) WILD-TYPE                                    12
                                 vv
clus                              LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(12Q24.31) MUTATED                                         0
  DEL PEAK 32(12Q24.31) WILD-TYPE                                       1
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 32(12Q24.31) MUTATED                                        0
  DEL PEAK 32(12Q24.31) WILD-TYPE                                      6
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 32(12Q24.31) MUTATED                                         0
  DEL PEAK 32(12Q24.31) WILD-TYPE                                       1
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(12Q24.31) MUTATED                                                            80
  DEL PEAK 32(12Q24.31) WILD-TYPE                                                         390
D62V9, multiclass
                                                             clus
vv                                                            DEL PEAK 32(12Q24.31) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            80
                                                             clus
vv                                                            DEL PEAK 32(12Q24.31) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             390
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, binary
                                 cls
clus                                0   1
  DEL PEAK 32(12Q24.31) MUTATED     2  81
  DEL PEAK 32(12Q24.31) WILD-TYPE  11 399
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.31) MUTATED      2   81
  DEL PEAK 32(12Q24.31) WILD-TYPE   11  399
     clus
vv    DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  NO                              2                              11
  YES                            81                             399
[1] 2 2
[1] FALSE
D62V11, continuous
D62V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(12Q24.31) MUTATED    64   0   1   3
  DEL PEAK 32(12Q24.31) WILD-TYPE 330  12   3  19
D62V13, multiclass
    clus
vv   DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  R0                            64                             330
  R1                             0                              12
  R2                             1                               3
  RX                             3                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(12Q24.31) MUTATED       3                         8    46
  DEL PEAK 32(12Q24.31) WILD-TYPE     6                        23   294
D62V14, multiclass
                           clus
vv                          DEL PEAK 32(12Q24.31) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                46
                           clus
vv                          DEL PEAK 32(12Q24.31) WILD-TYPE
  ASIAN                                                   6
  BLACK OR AFRICAN AMERICAN                              23
  WHITE                                                 294
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V15, binary
                                 cls
clus                                0   1
  DEL PEAK 32(12Q24.31) MUTATED     0  51
  DEL PEAK 32(12Q24.31) WILD-TYPE   8 258
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.31) MUTATED      0   51
  DEL PEAK 32(12Q24.31) WILD-TYPE    8  258
                        clus
vv                       DEL PEAK 32(12Q24.31) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            51
                        clus
vv                       DEL PEAK 32(12Q24.31) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             258
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 33(13Q12.11) MUTATION ANALYSIS
D63V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 33(13Q12.11) MUTATED   190 127
  DEL PEAK 33(13Q12.11) WILD-TYPE  91  69
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            317                             160 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            127                              69 
$`DEL PEAK 33(13Q12.11) MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
       79.46         4.80       117.57        11.34        92.15        31.99 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
        1.64         6.18       154.32       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 TCGA-21-5783 TCGA-21-5786 
       70.16        60.89       122.43       119.80        88.11        33.93 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1011 
       10.82        32.19        21.99        14.93         4.31         1.74 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       27.02        20.48        35.08        48.33        24.13         0.56 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 
       34.75        13.12        32.02        19.30        11.77        31.73 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
       64.93        63.55        44.25         0.79        71.34        79.20 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       11.74        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        7.63        98.01       151.27        14.07        54.44         1.55 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       19.76        27.02         4.70         0.30        36.62         6.94 
TCGA-33-AASI TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 
       44.19         2.63        31.50        28.96        32.88        65.23 
TCGA-34-5232 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-37-3792 
       67.79        18.15         4.96        27.19         4.04         0.39 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5016 
        8.12         7.46         7.82         6.81         3.39        74.07 
TCGA-39-5022 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 
       55.20         1.71        24.33         1.94        27.39        35.64 
TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
       40.21        22.49        38.66        27.02        33.11        18.38 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
       12.36        24.89        21.47        66.51        13.38        11.77 
TCGA-43-A474 TCGA-43-A56U TCGA-46-6025 TCGA-51-4079 TCGA-52-7622 TCGA-52-7809 
       11.61        14.20        10.65         0.39        28.34         5.46 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 
        8.75        28.96        18.25         2.04         0.62         0.43 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 
        1.45         0.85         6.51        17.49         3.48        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
       17.00        14.07         1.18        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 
       15.81        20.94        17.85        18.74         2.76         0.03 
TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M TCGA-60-2696 
       13.55        71.24        34.78        34.36        35.24         3.58 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 
       96.82        37.94        92.71        21.93        80.45        66.54 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
       41.42         9.01        50.33        42.64         3.19        32.32 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB 
       29.85        35.90        23.57        26.83        11.77       102.67 
TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN 
       70.62        66.61        58.65        59.97        45.57        11.34 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MW TCGA-63-A5MY 
       89.29        78.28        16.37        25.41        53.88        34.59 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
       16.96        43.10         1.02         2.01         0.92         0.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       21.01        25.05         1.02         2.01         2.01         7.07 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
       19.00         3.02         2.01        19.00        12.03        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 
       24.95         1.97        25.97        40.01        22.98        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
        5.03        30.02         4.01        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 
        6.94         8.02        13.35        16.18        29.56        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 
       23.28        11.18        89.98         0.49        42.28       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 
        0.16        46.78        15.75         6.51        53.95        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       82.92        12.59        53.92        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       26.40        27.39         9.63        54.41        65.49        35.90 
TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        0.33       132.36       117.57        22.29         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 
       42.08        27.62         9.67        11.97        12.99        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
       31.30        32.91         1.15        29.95        18.94        19.04 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
       31.56        16.87        10.09         0.76        13.22        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 
        5.29         3.09        32.71         0.72        14.63         0.10 
TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       15.62        19.33        18.18        19.73        12.56        16.21 
TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
       15.85        12.39         3.65         9.50         2.93        11.77 
TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       14.07        22.62        10.59         2.70         3.48         4.01 
TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        5.26        21.04         0.16         4.01         5.03        26.63 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-98-7454 
       16.14        17.69        49.87        57.07        18.31         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        2.76        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       18.15         2.01        18.58        20.71        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG 
       16.11        13.41         0.07        64.08         4.54        51.78 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO 
       45.37        13.74         4.21         2.89        39.85        30.58 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX 
       24.00        14.73        22.78        83.57        65.49         3.65 
TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       16.80         3.72        12.72        43.89         0.20 

$`DEL PEAK 33(13Q12.11) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
       12.20         7.46        75.75        23.54        36.07        86.96 
TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
        2.79        49.94        27.19        34.78        15.58        31.73 
TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-22-0944 TCGA-22-1005 
        9.34        43.23        31.63        41.69         7.33        64.21 
TCGA-22-1012 TCGA-22-1017 TCGA-22-4599 TCGA-22-4609 TCGA-22-5474 TCGA-22-5479 
       14.10        48.82        38.17         9.57        14.63        54.28 
TCGA-22-5483 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-AASD 
       18.84       133.74        79.53       174.08       103.53       110.99 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2609 TCGA-34-5234 TCGA-34-5236 
      118.36        27.16        61.61        31.27        56.38         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-7107 TCGA-34-8456 
       23.24        12.00        16.93        30.94         1.12        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4141 TCGA-39-5011 
       20.91         3.95         0.43         6.58         0.39        47.80 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 
       44.75        68.58        70.03        60.79        36.39        15.58 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-5670 TCGA-43-6771 TCGA-43-6773 
       35.70        17.88        17.06        27.91         5.46         3.81 
TCGA-43-7656 TCGA-43-7657 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56V TCGA-46-3768 
       19.59         7.76         2.93         9.73        12.03         9.99 
TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 
       13.91         0.39        29.95        30.35        27.45         0.10 
TCGA-56-7221 TCGA-56-7223 TCGA-56-7580 TCGA-56-7731 TCGA-56-8503 TCGA-56-8504 
        0.99         0.99         1.32         0.10         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR 
        1.81        22.75        19.23        13.32        21.04         0.13 
TCGA-56-A5DS TCGA-58-8387 TCGA-58-8390 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L 
        0.26        13.25        29.95        16.47        85.12        56.65 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2709 TCGA-60-2713 
       29.92        21.11        12.23        10.22        49.48        56.91 
TCGA-60-2715 TCGA-60-2716 TCGA-63-A5MM TCGA-63-A5MP TCGA-63-A5MV TCGA-66-2737 
       35.34        48.49        14.99        25.28        36.16         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2757 TCGA-66-2763 TCGA-66-2765 TCGA-66-2770 
       21.07         0.99        43.99         0.99         2.01        23.01 
TCGA-66-2781 TCGA-66-2789 TCGA-66-2793 TCGA-66-2794 TCGA-68-A59J TCGA-77-6843 
        3.98         4.04        10.06        54.08        14.73        73.12 
TCGA-77-7140 TCGA-77-7335 TCGA-77-8008 TCGA-77-8136 TCGA-77-8145 TCGA-77-A5FZ 
       20.78        70.13        86.76        39.09         6.97       126.18 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6798 TCGA-85-7696 TCGA-85-7710 TCGA-85-8048 
       30.81        38.86         6.41        36.53         1.38        25.15 
TCGA-85-8052 TCGA-85-8071 TCGA-85-8276 TCGA-85-8350 TCGA-85-8355 TCGA-85-8481 
       24.13        14.07        34.52        22.45         2.01         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA 
       13.94        12.59        25.68        17.72        14.96        24.36 
TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED TCGA-92-8065 TCGA-94-7943 
       14.96         0.79        24.92        20.22         2.30        11.70 
TCGA-94-A4VJ TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-A53C TCGA-98-A53D 
       14.14        17.46        19.36        16.57        27.02        21.21 
TCGA-98-A53H TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HN TCGA-NC-A5HR 
       20.32        13.18        11.84         1.22        37.22        29.75 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52W TCGA-O2-A5IB 
        0.43        33.07         8.58        11.18 

  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                         154.32                          174.08 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                         19.000                          19.905 
[1] "0.0 - 154.3 (19.0)" "0.1 - 174.1 (19.9)"
[1] "hr=" "1.1"
D63V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(13Q12.11) MUTATED         0       49      105        1        41
  DEL PEAK 33(13Q12.11) WILD-TYPE       2       38       46        1        22
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(13Q12.11) MUTATED          62         2         51         12
  DEL PEAK 33(13Q12.11) WILD-TYPE        30         1         11          9
                                 vv
clus                              STAGE IV
  DEL PEAK 33(13Q12.11) MUTATED          4
  DEL PEAK 33(13Q12.11) WILD-TYPE        3
D63V3, multiclass
            clus
vv           DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                              49                              38
  STAGE IB                             105                              46
  STAGE II                               1                               1
  STAGE IIA                             41                              22
  STAGE IIB                             62                              30
  STAGE III                              2                               1
  STAGE IIIA                            51                              11
  STAGE IIIB                            12                               9
  STAGE IV                               4                               3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 33(13Q12.11) MUTATED    65 202  48  14
  DEL PEAK 33(13Q12.11) WILD-TYPE  46  88  21   9
D63V4, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  T1                            65                              46
  T2                           202                              88
  T3                            48                              21
  T4                            14                               9
[1] 4 2
[1] TRUE
[1] "dimension of 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   205  88  29   4
  DEL PEAK 33(13Q12.11) WILD-TYPE 107  43  10   1
D63V5, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  N0                           205                             107
  N1                            88                              43
  N2                            29                              10
  N3                             4                               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"
D63V6, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED   272   4
  DEL PEAK 33(13Q12.11) WILD-TYPE 132   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED    272    4
  DEL PEAK 33(13Q12.11) WILD-TYPE  132    3
   clus
vv  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  0                           272                             132
  1                             4                               3
[1] 2 2
[1] FALSE
D63V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    83 246
  DEL PEAK 33(13Q12.11) WILD-TYPE  44 120
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     83  246
  DEL PEAK 33(13Q12.11) WILD-TYPE   44  120
        clus
vv       DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  FEMALE                            83                              44
  MALE                             246                             120
[1] 2 2
[1] FALSE
D63V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 33(13Q12.11) MUTATED                                       8
  DEL PEAK 33(13Q12.11) WILD-TYPE                                     7
                                 vv
clus                              LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 33(13Q12.11) MUTATED                                         0
  DEL PEAK 33(13Q12.11) WILD-TYPE                                       1
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 33(13Q12.11) MUTATED                                        2
  DEL PEAK 33(13Q12.11) WILD-TYPE                                      4
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 33(13Q12.11) MUTATED                                         1
  DEL PEAK 33(13Q12.11) WILD-TYPE                                       0
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(13Q12.11) MUTATED                                                           318
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                         152
D63V9, multiclass
                                                             clus
vv                                                            DEL PEAK 33(13Q12.11) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           318
                                                             clus
vv                                                            DEL PEAK 33(13Q12.11) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             152
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    10 319
  DEL PEAK 33(13Q12.11) WILD-TYPE   3 161
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     10  319
  DEL PEAK 33(13Q12.11) WILD-TYPE    3  161
     clus
vv    DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  NO                             10                               3
  YES                           319                             161
[1] 2 2
[1] FALSE
D63V11, continuous
D63V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 33(13Q12.11) MUTATED   265  10   3  16
  DEL PEAK 33(13Q12.11) WILD-TYPE 129   2   1   6
D63V13, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  R0                           265                             129
  R1                            10                               2
  R2                             3                               1
  RX                            16                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(13Q12.11) MUTATED       4                        21   218
  DEL PEAK 33(13Q12.11) WILD-TYPE     5                        10   122
D63V14, multiclass
                           clus
vv                          DEL PEAK 33(13Q12.11) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               218
                           clus
vv                          DEL PEAK 33(13Q12.11) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                              10
  WHITE                                                 122
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V15, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED     7 191
  DEL PEAK 33(13Q12.11) WILD-TYPE   1 118
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED      7  191
  DEL PEAK 33(13Q12.11) WILD-TYPE    1  118
                        clus
vv                       DEL PEAK 33(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           191
                        clus
vv                       DEL PEAK 33(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             118
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 34(13Q14.2) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(13Q14.2) MUTATED   195 133
  DEL PEAK 34(13Q14.2) WILD-TYPE  86  63
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           328                            149 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           133                             63 
$`DEL PEAK 34(13Q14.2) MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 
       79.46         4.80        31.99         1.64        86.96         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2.79       154.32       119.54        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       60.89       122.43       119.80        43.23        31.63        88.11 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 
       33.93        10.82        32.19        21.99        14.93         4.31 
TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
        1.74        27.02        48.82        20.48        35.08        48.33 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       24.13         0.56        34.75        13.12        32.02        19.30 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
       11.77        31.73        64.93        63.55        44.25         0.79 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       79.20        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 
       16.64        22.06       133.74        98.01       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       14.07        54.44         1.55        27.02         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 
       36.62         6.94        44.19         2.63        31.50        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5927 TCGA-34-5928 
       32.88        31.27        65.23        67.79        30.94        18.15 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
        4.96         1.12        27.19         4.04        26.43        20.91 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 
        0.39         6.58         7.46         6.81         3.39        47.80 
TCGA-39-5022 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 
       55.20         1.71        24.33         1.94        27.39        35.64 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 
       17.06        40.21        22.49        38.66        33.11        18.38 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
       12.36        24.89        21.47        19.59         7.76        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-46-6025 TCGA-51-4079 TCGA-52-7622 
       13.38        11.77        11.61        10.65         0.39        28.34 
TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 
        5.46         8.75        27.45        28.96        18.25         2.04 
TCGA-56-6546 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 
        0.62         0.43         1.45         0.85         6.51         3.48 
TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 
       26.89        17.00        14.07         1.18        10.36        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 
       15.81        20.94        17.85        18.74         2.76         0.03 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       13.55        29.95        71.24        34.78        85.12        34.36 
TCGA-58-A46M TCGA-60-2696 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       35.24         3.58        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
       80.45        66.54        41.42         9.01        56.91        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       42.64         3.19        32.32        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI 
       26.83        11.77       102.67        70.62        66.61        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       59.97        45.57        11.34        25.28        89.29        78.28 
TCGA-63-A5MU TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 
       25.41        53.88        34.59        16.96        43.10         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
        2.01         0.92         0.99        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 
        0.99         2.01         2.01         7.07        19.00         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        2.01        19.00        12.03         3.98        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 
        1.97        25.97        40.01        22.98        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       30.02        10.06         4.01        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 
        6.94         8.02        13.35        16.18        29.56        75.09 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       11.18        89.98        20.78         0.49        42.28        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8128 
      106.95         0.16        46.78        15.75         6.51        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       82.92        12.59        53.92        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       26.40        27.39         9.63        54.41        65.49        35.90 
TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        0.33       132.36       117.57        22.29         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 
       42.08        27.62         9.67        12.99        34.95        31.30 
TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8070 
       32.91         1.15        29.95        18.94        19.04        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 
       14.07        16.87        10.09         0.76        13.22        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 
        5.29         3.09        32.71         0.72        14.63         0.10 
TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       15.62        19.33        19.73        12.56        16.21        15.85 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
       12.39         3.65         9.50         2.93        11.77        14.07 
TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 
       22.62         2.70         3.48         4.01         5.26        21.04 
TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 TCGA-94-A5I6 
        0.16         4.01         5.03        26.63        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8020 
       49.87        57.07        18.31        19.36         8.42         2.76 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53B 
       30.81        30.67        21.34        27.16         3.88         2.01 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
       18.58        20.71        12.89        16.11        13.18        13.41 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ 
        0.07        64.08         4.54        51.78        45.37        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
        4.21         2.89        39.85        30.58        24.00        14.73 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52Q 
       22.78        83.57        65.49         3.65        16.80         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89        11.18         0.20 

$`DEL PEAK 34(13Q14.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       12.20         7.46        75.75       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-5592 TCGA-18-5595 TCGA-21-1077 TCGA-21-1078 
       92.15        36.07        49.94        27.19        34.78        15.58 
TCGA-21-1079 TCGA-21-1081 TCGA-21-5784 TCGA-22-0944 TCGA-22-1005 TCGA-22-1012 
       31.73         9.34        41.69         7.33        64.21        14.10 
TCGA-22-4599 TCGA-22-4609 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-33-4532 
       38.17         9.57        14.63        54.28        71.34         7.63 
TCGA-33-4547 TCGA-33-4566 TCGA-33-6737 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL 
       79.53       174.08        19.76       110.99       118.36        27.16 
TCGA-34-2600 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       61.61        56.38         9.07        23.24        12.00        16.93 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4133 TCGA-37-4141 TCGA-39-5016 
        3.95         0.43         8.12         7.82         0.39        74.07 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 
       44.75        68.58        70.03        60.79        36.39        15.58 
TCGA-39-5037 TCGA-39-5039 TCGA-43-3394 TCGA-43-5670 TCGA-43-6771 TCGA-43-6773 
       35.70        17.88        27.02        27.91         5.46         3.81 
TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 
        2.93         9.73        14.20        12.03         9.99        13.91 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7810 TCGA-56-5897 TCGA-56-7221 TCGA-56-7223 
        0.39        29.95        30.35         0.10         0.99         0.99 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
        1.32         0.10        17.49         1.35        16.77         1.81 
TCGA-56-8623 TCGA-56-8626 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DR 
       22.75         9.93        19.23        13.32        21.04         0.13 
TCGA-56-A5DS TCGA-58-8387 TCGA-58-8392 TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 
        0.26        13.25        16.47        56.65        29.92        21.11 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2709 TCGA-60-2715 TCGA-60-2716 TCGA-63-A5MM 
       12.23        10.22        49.48        35.34        48.49        14.99 
TCGA-63-A5MT TCGA-63-A5MV TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2765 
       16.37        36.16         2.01        21.07         0.99         2.01 
TCGA-66-2766 TCGA-66-2770 TCGA-66-2789 TCGA-66-2794 TCGA-68-A59J TCGA-77-6843 
        1.02        23.01         4.04        54.08        14.73        73.12 
TCGA-77-6845 TCGA-77-8008 TCGA-77-8009 TCGA-77-8136 TCGA-77-8145 TCGA-77-A5FZ 
       23.28        86.76        53.95        39.09         6.97       126.18 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7710 
       30.81        38.86        11.97         6.41        36.53         1.38 
TCGA-85-8048 TCGA-85-8052 TCGA-85-8276 TCGA-85-8350 TCGA-85-8355 TCGA-85-8481 
       25.15        24.13        34.52        22.45         2.01         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA 
       13.94        12.59        25.68        17.72        14.96        24.36 
TCGA-85-A4QQ TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED TCGA-90-A59Q 
       18.18        14.96         0.79        24.92        20.22        10.59 
TCGA-92-8065 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-8170 TCGA-96-A4JL TCGA-98-A53A 
        2.30        11.70        14.14        17.46        16.57        18.15 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH TCGA-MF-A522 TCGA-NC-A5HH 
       27.02        21.21        20.32        19.10        11.84         1.22 
TCGA-NC-A5HN TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52W 
       37.22        29.75         0.43        33.07         8.58 

  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                        154.32                         174.08 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                         19.66                          17.72 
[1] "0.0 - 154.3 (19.7)" "0.1 - 174.1 (17.7)"
[1] "hr=" "1.1"
D64V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(13Q14.2) MUTATED         0       57      106        2        42
  DEL PEAK 34(13Q14.2) WILD-TYPE       2       30       45        0        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(13Q14.2) MUTATED          62         3         49         13
  DEL PEAK 34(13Q14.2) WILD-TYPE        30         0         13          8
                                vv
clus                             STAGE IV
  DEL PEAK 34(13Q14.2) MUTATED          4
  DEL PEAK 34(13Q14.2) WILD-TYPE        3
D64V3, multiclass
            clus
vv           DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                             57                             30
  STAGE IB                            106                             45
  STAGE II                              2                              0
  STAGE IIA                            42                             21
  STAGE IIB                            62                             30
  STAGE III                             3                              0
  STAGE IIIA                           49                             13
  STAGE IIIB                           13                              8
  STAGE IV                              4                              3
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 34(13Q14.2) MUTATED    73 204  48  15
  DEL PEAK 34(13Q14.2) WILD-TYPE  38  86  21   8
D64V4, multiclass
    clus
vv   DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  T1                           73                             38
  T2                          204                             86
  T3                           48                             21
  T4                           15                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2  N3
  DEL PEAK 34(13Q14.2) MUTATED   212  92  29   4
  DEL PEAK 34(13Q14.2) WILD-TYPE 100  39  10   1
D64V5, multiclass
    clus
vv   DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  N0                          212                            100
  N1                           92                             39
  N2                           29                             10
  N3                            4                              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"
D64V6, binary
                                cls
clus                               0   1
  DEL PEAK 34(13Q14.2) MUTATED   283   4
  DEL PEAK 34(13Q14.2) WILD-TYPE 121   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED    283    4
  DEL PEAK 34(13Q14.2) WILD-TYPE  121    3
   clus
vv  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  0                          283                            121
  1                            4                              3
[1] 2 2
[1] FALSE
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(13Q14.2) MUTATED    91 249
  DEL PEAK 34(13Q14.2) WILD-TYPE  36 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED     91  249
  DEL PEAK 34(13Q14.2) WILD-TYPE   36  117
        clus
vv       DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  FEMALE                           91                             36
  MALE                            249                            117
[1] 2 2
[1] FALSE
D64V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                                       7
  DEL PEAK 34(13Q14.2) WILD-TYPE                                     8
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                                         0
  DEL PEAK 34(13Q14.2) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 34(13Q14.2) MUTATED                                        2
  DEL PEAK 34(13Q14.2) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 34(13Q14.2) MUTATED                                         1
  DEL PEAK 34(13Q14.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(13Q14.2) MUTATED                                                           330
  DEL PEAK 34(13Q14.2) WILD-TYPE                                                         140
D64V9, multiclass
                                                             clus
vv                                                            DEL PEAK 34(13Q14.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          330
                                                             clus
vv                                                            DEL PEAK 34(13Q14.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            140
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, binary
                                cls
clus                               0   1
  DEL PEAK 34(13Q14.2) MUTATED    11 329
  DEL PEAK 34(13Q14.2) WILD-TYPE   2 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED     11  329
  DEL PEAK 34(13Q14.2) WILD-TYPE    2  151
     clus
vv    DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  NO                            11                              2
  YES                          329                            151
[1] 2 2
[1] FALSE
D64V11, continuous
D64V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(13Q14.2) MUTATED   271  10   3  16
  DEL PEAK 34(13Q14.2) WILD-TYPE 123   2   1   6
D64V13, multiclass
    clus
vv   DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  R0                          271                            123
  R1                           10                              2
  R2                            3                              1
  RX                           16                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(13Q14.2) MUTATED       4                        20   230
  DEL PEAK 34(13Q14.2) WILD-TYPE     5                        11   110
D64V14, multiclass
                           clus
vv                          DEL PEAK 34(13Q14.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           20
  WHITE                                              230
                           clus
vv                          DEL PEAK 34(13Q14.2) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V15, binary
                                cls
clus                               0   1
  DEL PEAK 34(13Q14.2) MUTATED     8 200
  DEL PEAK 34(13Q14.2) WILD-TYPE   0 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED      8  200
  DEL PEAK 34(13Q14.2) WILD-TYPE    0  109
                        clus
vv                       DEL PEAK 34(13Q14.2) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          200
                        clus
vv                       DEL PEAK 34(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                            109
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 35(14Q11.2) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(14Q11.2) MUTATED    89  78
  DEL PEAK 35(14Q11.2) WILD-TYPE 192 118
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                           167                            310 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                            78                            118 
$`DEL PEAK 35(14Q11.2) MUTATED`
TCGA-18-3416 TCGA-18-4086 TCGA-21-1071 TCGA-21-1083 TCGA-21-5784 TCGA-21-5786 
       31.99         2.79        46.88        43.23        41.69        33.93 
TCGA-22-0940 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 
       21.99        14.10        27.02        35.08        48.33         0.56 
TCGA-22-4601 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 
       34.75        63.55        14.63        44.25        71.34        79.20 
TCGA-22-5483 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4587 
       18.84        56.32        98.01        79.53       151.27        54.44 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASL TCGA-34-2596 
        4.70         0.30        36.62       110.99        27.16         2.63 
TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       61.61        31.50        28.96        16.93        30.94        18.15 
TCGA-34-5929 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 TCGA-37-4130 TCGA-37-4133 
        4.96        27.19        20.91         3.95         8.12         7.82 
TCGA-37-4135 TCGA-37-5819 TCGA-39-5016 TCGA-39-5024 TCGA-39-5030 TCGA-39-5035 
        6.81         3.39        74.07        70.03         1.94        15.58 
TCGA-39-5040 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6770 TCGA-43-7656 
       17.06        27.02        33.11        27.91        21.47        19.59 
TCGA-43-7657 TCGA-43-7658 TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 TCGA-46-6026 
        7.76        66.51         9.73        14.20         9.99        13.91 
TCGA-51-4079 TCGA-52-7809 TCGA-56-5897 TCGA-56-7582 TCGA-56-7822 TCGA-56-8307 
        0.39         5.46         0.10         0.85        17.49        26.89 
TCGA-56-8309 TCGA-56-A4BW TCGA-56-A4BY TCGA-58-8388 TCGA-58-8390 TCGA-58-A46K 
       14.07        19.23        17.85        13.55        29.95        34.36 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
       21.11         3.58        37.94        49.48        66.54         9.01 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH 
       56.91        50.33        26.83        11.77       102.67        66.61 
TCGA-63-A5MP TCGA-63-A5MT TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       25.28        16.37        16.96         1.02         2.01         0.92 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2766 TCGA-66-2769 TCGA-66-2773 TCGA-66-2777 
       43.99        21.01         1.02         7.07         3.02         2.01 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2793 TCGA-68-7757 TCGA-68-8250 
       25.97        40.01         4.04        10.06         6.94         8.02 
TCGA-68-8251 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 
       13.35        29.56        73.12        75.09        89.98         0.49 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8140 TCGA-77-8143 
        0.16        15.75         6.51        86.76        11.54        26.40 
TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH 
        0.33        22.29         5.92        42.08        27.62        38.86 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       11.97         6.41         1.15        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 
       19.04        24.13        31.56        16.87        10.09         0.76 
TCGA-85-8288 TCGA-85-8352 TCGA-85-8580 TCGA-85-A4JC TCGA-85-A511 TCGA-85-A53L 
       13.22         5.29        14.63        14.96        14.96        12.39 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A59Q TCGA-94-7033 
        9.50         2.93        11.77        20.22        10.59        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8491 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JL 
        0.16        11.70        26.63        16.14        57.07        16.57 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53J 
        8.42        30.81        30.67        21.34        18.15        20.71 
TCGA-J1-A4AH TCGA-LA-A446 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HJ TCGA-NC-A5HK 
       19.10        13.18         0.07        64.08        13.74         4.21 
TCGA-NC-A5HL TCGA-NK-A5CR TCGA-NK-A5CT TCGA-O2-A52Q TCGA-XC-AA0X 
        2.89        83.57        65.49         3.72         0.20 

$`DEL PEAK 35(14Q11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
       11.34        23.54        92.15        36.07         1.64        86.96 
TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1072 
        6.18       154.32        49.94        27.19       119.54        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       70.16        60.89        34.78        15.58        31.73       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5787 TCGA-21-A5DI 
        9.34       119.80        31.63        88.11        10.82        32.19 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1017 
        7.33        14.93         4.31        64.21         1.74        48.82 
TCGA-22-4591 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       20.48        24.13        38.17        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5478 TCGA-22-5479 
        9.57        11.77        31.73        64.93         0.79        54.28 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 
       11.74        30.12        62.86        16.64        22.06         7.63 
TCGA-33-4533 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 
      133.74       174.08       103.53        14.07         1.55        19.76 
TCGA-33-6738 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-34-2608 TCGA-34-2609 
       27.02         6.94        44.19       118.36        32.88        31.27 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        67.79        56.38         9.07        23.24        12.00 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
        1.12         4.04        26.43         0.43         0.39         6.58 
TCGA-37-4132 TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        7.46         0.39        47.80        44.75        68.58        55.20 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
       60.79         1.71        24.33        27.39        36.39        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-5668 
       35.70        17.88        40.21        22.49        38.66        18.38 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-8116 
       12.36        24.89         5.46         3.81        13.38        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-46-6025 TCGA-51-4080 TCGA-51-4081 
        2.93        11.61        12.03        10.65         0.39        29.95 
TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 
       28.34        30.35         8.75        27.45        28.96        18.25 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
        2.04         0.62         0.99         0.43         0.99         1.45 
TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-8308 TCGA-56-8503 
        1.32         6.51         0.10         3.48        17.00         1.35 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       16.77         1.81        22.75         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A4ZK 
       20.25        15.81        20.94        13.32        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8391 
        0.13         0.26         2.76         0.03        13.25        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       16.47        34.78        85.12        56.65        35.24        29.92 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       12.23        10.22        96.82        92.71        21.93        80.45 
TCGA-60-2711 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
       41.42        35.34        48.49        42.64         3.19        32.32 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
       29.85        35.90        23.57        70.62        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MU 
       45.57        14.99        11.34        89.29        78.28        25.41 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       36.16        53.88        34.59        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2756 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
        0.99         0.99        25.05         0.99         2.01         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        2.01        23.01        19.00        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 
       12.00        24.95         1.97        22.98        22.98         5.03 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
       30.02        54.08         4.01        49.05         2.73         6.64 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7142 
       16.18        14.73        23.28        11.18        20.78        42.28 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       70.13       106.95        46.78        53.95        37.81        82.92 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 
       12.59        53.92        39.09        17.72       104.09        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ 
        6.97         9.63        54.41        65.49        35.90       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GB TCGA-85-6175 TCGA-85-6561 
      132.36       117.57        42.41        30.81         9.67        12.99 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-8071 
       36.53        34.95        31.30        32.91         1.38        14.07 
TCGA-85-8276 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       34.52        22.45        16.77         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        0.72         7.76        13.94        12.59         0.10        15.62 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       25.68        19.33        17.72        24.36        18.18        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 
       12.56        16.21        15.85         0.79         3.65        24.92 
TCGA-90-7964 TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       14.07        22.62         2.70         3.48         4.01         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        2.30         4.01         5.03        14.14        17.69        49.87 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A538 TCGA-98-A539 
       18.31        17.46        19.36         2.76        27.16         3.88 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 
        2.01        27.02        21.21        20.32        18.58        12.89 
TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       16.11        13.41        11.84         4.54        51.78         1.22 
TCGA-NC-A5HI TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
       45.37        39.85        37.22        30.58        24.00        14.73 
TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N 
       29.75        22.78         3.65        16.80         0.43        33.07 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       12.72        43.89         8.58        11.18 

  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                        151.27                         174.08 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                        18.150                         19.745 
[1] "0.1 - 151.3 (18.1)" "0.0 - 174.1 (19.7)"
[1] "hr=" "1.4"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(14Q11.2) MUTATED         0       35       55        0        27
  DEL PEAK 35(14Q11.2) WILD-TYPE       2       52       96        2        36
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(14Q11.2) MUTATED          27         1         21          6
  DEL PEAK 35(14Q11.2) WILD-TYPE        65         2         41         15
                                vv
clus                             STAGE IV
  DEL PEAK 35(14Q11.2) MUTATED          0
  DEL PEAK 35(14Q11.2) WILD-TYPE        7
D65V3, multiclass
            clus
vv           DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                             35                             52
  STAGE IB                             55                             96
  STAGE II                              0                              2
  STAGE IIA                            27                             36
  STAGE IIB                            27                             65
  STAGE III                             1                              2
  STAGE IIIA                           21                             41
  STAGE IIIB                            6                             15
  STAGE IV                              0                              7
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 35(14Q11.2) MUTATED    46 101  20   5
  DEL PEAK 35(14Q11.2) WILD-TYPE  65 189  49  18
D65V4, multiclass
    clus
vv   DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  T1                           46                             65
  T2                          101                            189
  T3                           20                             49
  T4                            5                             18
[1] 4 2
[1] TRUE
[1] "dimension of 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   110  48  12   1
  DEL PEAK 35(14Q11.2) WILD-TYPE 202  83  27   4
D65V5, multiclass
    clus
vv   DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  N0                          110                            202
  N1                           48                             83
  N2                           12                             27
  N3                            1                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q11.2) MUTATED   142   0
  DEL PEAK 35(14Q11.2) WILD-TYPE 262   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED    142    0
  DEL PEAK 35(14Q11.2) WILD-TYPE  262    7
   clus
vv  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  0                          142                            262
  1                            0                              7
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q11.2) MUTATED    43 129
  DEL PEAK 35(14Q11.2) WILD-TYPE  84 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED     43  129
  DEL PEAK 35(14Q11.2) WILD-TYPE   84  237
        clus
vv       DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  FEMALE                           43                             84
  MALE                            129                            237
[1] 2 2
[1] FALSE
D65V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 35(14Q11.2) MUTATED                                       5
  DEL PEAK 35(14Q11.2) WILD-TYPE                                    10
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 35(14Q11.2) MUTATED                                         0
  DEL PEAK 35(14Q11.2) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 35(14Q11.2) MUTATED                                        0
  DEL PEAK 35(14Q11.2) WILD-TYPE                                      6
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 35(14Q11.2) MUTATED                                         1
  DEL PEAK 35(14Q11.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(14Q11.2) MUTATED                                                           166
  DEL PEAK 35(14Q11.2) WILD-TYPE                                                         304
D65V9, multiclass
                                                             clus
vv                                                            DEL PEAK 35(14Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          166
                                                             clus
vv                                                            DEL PEAK 35(14Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            304
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q11.2) MUTATED     5 167
  DEL PEAK 35(14Q11.2) WILD-TYPE   8 313
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED      5  167
  DEL PEAK 35(14Q11.2) WILD-TYPE    8  313
     clus
vv    DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  NO                             5                              8
  YES                          167                            313
[1] 2 2
[1] FALSE
D65V11, continuous
D65V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(14Q11.2) MUTATED   140   3   1   7
  DEL PEAK 35(14Q11.2) WILD-TYPE 254   9   3  15
D65V13, multiclass
    clus
vv   DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  R0                          140                            254
  R1                            3                              9
  R2                            1                              3
  RX                            7                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(14Q11.2) MUTATED       4                        13   118
  DEL PEAK 35(14Q11.2) WILD-TYPE     5                        18   222
D65V14, multiclass
                           clus
vv                          DEL PEAK 35(14Q11.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              118
                           clus
vv                          DEL PEAK 35(14Q11.2) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             18
  WHITE                                                222
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V15, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q11.2) MUTATED     2 110
  DEL PEAK 35(14Q11.2) WILD-TYPE   6 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED      2  110
  DEL PEAK 35(14Q11.2) WILD-TYPE    6  199
                        clus
vv                       DEL PEAK 35(14Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          110
                        clus
vv                       DEL PEAK 35(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            199
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 36(15Q11.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(15Q11.2) MUTATED    86  75
  DEL PEAK 36(15Q11.2) WILD-TYPE 195 121
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           161                            316 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                            75                            121 
$`DEL PEAK 36(15Q11.2) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3410 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
       12.20        75.75         4.80        11.34        92.15        31.99 
TCGA-18-3419 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1083 
        1.64        49.94       119.54        46.88        99.16        43.23 
TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1012 TCGA-22-1016 
       10.82        21.99         7.33        14.93        14.10        27.02 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-5471 
       48.82        48.33        24.13         0.56        38.17        31.73 
TCGA-22-5477 TCGA-22-5480 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4547 
       44.25        71.34        22.06         7.63       133.74        79.53 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-AAS8 
      103.53        14.07        54.44         1.55        19.76        36.62 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 TCGA-34-5929 
       44.19       118.36        27.16        61.61        31.50         4.96 
TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 
       27.19        26.43         3.95         7.82         0.39         3.39 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       47.80        74.07        68.58         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 TCGA-43-5668 
       27.39        36.39        17.06        22.49        38.66        18.38 
TCGA-43-5670 TCGA-43-7657 TCGA-43-A56V TCGA-46-6026 TCGA-51-4079 TCGA-52-7809 
       27.91         7.76        12.03        13.91         0.39         5.46 
TCGA-52-7810 TCGA-56-1622 TCGA-56-7580 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 
       30.35        28.96         1.32        17.49         3.48        26.89 
TCGA-56-8309 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A62T TCGA-58-8386 
       14.07        10.36        20.94        19.23         2.76         0.03 
TCGA-58-A46J TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 TCGA-60-2712 TCGA-60-2714 
       85.12        10.22        96.82        80.45         9.01        50.33 
TCGA-60-2720 TCGA-60-2723 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MI 
        3.19        35.90        11.77       102.67        66.61        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MS TCGA-63-A5MY TCGA-66-2737 TCGA-66-2742 
       59.97        45.57        78.28        34.59         2.01        21.07 
TCGA-66-2754 TCGA-66-2766 TCGA-66-2767 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 
        2.01         1.02         2.01        22.98         5.03        10.06 
TCGA-66-2794 TCGA-66-2800 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-7139 
       54.08        49.05        16.18        14.73        29.56        89.98 
TCGA-77-7141 TCGA-77-7337 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        0.49       106.95         6.51        53.95        37.81        82.92 
TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
        6.97        65.49         0.33        38.86         9.67        11.97 
TCGA-85-7696 TCGA-85-7843 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8352 
       36.53         1.15        16.87         0.76        13.22         5.29 
TCGA-85-8479 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 
        0.72        12.59        15.62        18.18        12.56        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 
        0.79        12.39         2.93        20.22        22.62         2.70 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8491 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF 
        5.26         2.30        26.63        11.84         0.07         4.54 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
       51.78        45.37        13.74         4.21         2.89        39.85 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX 
       37.22        30.58        24.00        14.73        83.57         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52W TCGA-O2-A5IB 
       33.07         3.72        12.72         8.58        11.18 

$`DEL PEAK 36(15Q11.2) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3411 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
        7.46        79.46       117.57        23.54        36.07        86.96 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1075 TCGA-21-1076 
        6.18         2.79       154.32        27.19        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       34.78        15.58        31.73       122.43         9.34       119.80 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-1002 
       31.63        88.11        41.69        33.93        32.19         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-4591 TCGA-22-4593 TCGA-22-4601 TCGA-22-4604 
       64.21         1.74        20.48        35.08        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 
       32.02        19.30         9.57        11.77        64.93        63.55 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
       14.63         0.79        54.28        79.20        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4566 
       30.12        62.86        56.32        16.64        98.01       174.08 
TCGA-33-4583 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD 
      151.27        27.02         4.70         0.30         6.94       110.99 
TCGA-34-2596 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
        2.63        28.96        32.88        31.27        65.23        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       56.38         9.07        23.24        12.00        16.93        30.94 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 
       18.15         1.12         4.04        20.91         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-39-5019 TCGA-39-5022 
        6.58         8.12         7.46         6.81        44.75        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
       70.03        60.79        15.58        35.64        35.70        17.88 
TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       40.21        27.02        33.11        12.36        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        5.46         3.81        19.59        66.51        13.38        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 TCGA-46-6025 
        2.93        11.61         9.73        14.20         9.99        10.65 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 
        0.39        29.95        28.34         8.75        27.45         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 
       18.25         2.04         0.62         0.99         0.43         0.99 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8308 TCGA-56-8503 
        1.45         0.85         6.51         0.10        17.00         1.35 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 
       16.77         1.81        22.75         1.18         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
       15.81        13.32        17.85        21.04        18.74         0.13 
TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        0.26        13.25        13.55        29.95        71.24        16.47 
TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       34.78        34.36        56.65        35.24        29.92        21.11 
TCGA-60-2696 TCGA-60-2697 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 
        3.58        12.23        37.94        92.71        21.93        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 
       66.54        41.42        56.91        35.34        48.49        42.64 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG TCGA-63-A5MM 
       32.32        29.85        23.57        26.83        70.62        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV 
       11.34        25.28        89.29        16.37        25.41        36.16 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 
       53.88        16.96        43.10         0.99         1.02         0.92 
TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        0.99        43.99        21.01        25.05         0.99         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         7.07        23.01        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2792 TCGA-66-2795 
       25.97        40.01        22.98         4.04        30.02         4.01 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-77-6843 
        2.73         6.64         6.94         8.02        13.35        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7142 TCGA-77-7335 
       75.09        23.28        11.18        20.78        42.28        70.13 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8131 TCGA-77-8133 
        0.16        46.78        15.75        86.76        12.59        53.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       39.09        17.72       104.09        11.54        26.40        27.39 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
        9.63        54.41        35.90       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
       22.29         5.92        42.41        42.08        30.81        27.62 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
       12.99         6.41        34.95        31.30        32.91         1.38 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       29.95        18.94        25.15        19.04        24.13        31.56 
TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
       14.07        34.52        10.09        22.45        16.77         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 
       32.71         2.01         7.76        14.63        13.94         0.10 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QR 
       25.68        19.33        17.72        14.96        24.36        19.73 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 
       16.21        15.85         3.65        24.92         9.50        11.77 
TCGA-90-7964 TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-94-7033 TCGA-94-7557 
       14.07        10.59         3.48         4.01        21.04         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
       11.70         4.01         5.03        14.14        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       49.87        57.07        18.31        17.46        19.36        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
        8.42         2.76        30.81        30.67        21.34        27.16 
TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
        3.88        18.15         2.01        27.02        21.21        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       18.58        20.71        19.10        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CT 
       13.41        64.08         1.22        29.75        22.78        65.49 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52V TCGA-XC-AA0X 
       16.80         0.43        43.89         0.20 

  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                        133.74                         174.08 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                         19.23                          19.07 
[1] "0.0 - 133.7 (19.2)" "0.1 - 174.1 (19.1)"
[1] "hr=" "1.2"
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(15Q11.2) MUTATED         2       24       42        0        21
  DEL PEAK 36(15Q11.2) WILD-TYPE       0       63      109        2        42
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(15Q11.2) MUTATED          34         3         28          8
  DEL PEAK 36(15Q11.2) WILD-TYPE        58         0         34         13
                                vv
clus                             STAGE IV
  DEL PEAK 36(15Q11.2) MUTATED          3
  DEL PEAK 36(15Q11.2) WILD-TYPE        4
D66V3, multiclass
            clus
vv           DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             24                             63
  STAGE IB                             42                            109
  STAGE II                              0                              2
  STAGE IIA                            21                             42
  STAGE IIB                            34                             58
  STAGE III                             3                              0
  STAGE IIIA                           28                             34
  STAGE IIIB                            8                             13
  STAGE IV                              3                              4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 36(15Q11.2) MUTATED    30 101  25   9
  DEL PEAK 36(15Q11.2) WILD-TYPE  81 189  44  14
D66V4, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  T1                           30                             81
  T2                          101                            189
  T3                           25                             44
  T4                            9                             14
[1] 4 2
[1] TRUE
[1] "dimension of 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(15Q11.2) MUTATED    90  51  20   2
  DEL PEAK 36(15Q11.2) WILD-TYPE 222  80  19   3
D66V5, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  N0                           90                            222
  N1                           51                             80
  N2                           20                             19
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED   133   3
  DEL PEAK 36(15Q11.2) WILD-TYPE 271   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED    133    3
  DEL PEAK 36(15Q11.2) WILD-TYPE  271    4
   clus
vv  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  0                          133                            271
  1                            3                              4
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED    50 115
  DEL PEAK 36(15Q11.2) WILD-TYPE  77 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED     50  115
  DEL PEAK 36(15Q11.2) WILD-TYPE   77  251
        clus
vv       DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  FEMALE                           50                             77
  MALE                            115                            251
[1] 2 2
[1] FALSE
D66V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 36(15Q11.2) MUTATED                                       3
  DEL PEAK 36(15Q11.2) WILD-TYPE                                    12
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 36(15Q11.2) MUTATED                                         0
  DEL PEAK 36(15Q11.2) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 36(15Q11.2) MUTATED                                        2
  DEL PEAK 36(15Q11.2) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 36(15Q11.2) MUTATED                                         1
  DEL PEAK 36(15Q11.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(15Q11.2) MUTATED                                                           159
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                         311
D66V9, multiclass
                                                             clus
vv                                                            DEL PEAK 36(15Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          159
                                                             clus
vv                                                            DEL PEAK 36(15Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            311
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED     6 159
  DEL PEAK 36(15Q11.2) WILD-TYPE   7 321
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED      6  159
  DEL PEAK 36(15Q11.2) WILD-TYPE    7  321
     clus
vv    DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  NO                             6                              7
  YES                          159                            321
[1] 2 2
[1] FALSE
D66V11, continuous
D66V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(15Q11.2) MUTATED   130   5   2   6
  DEL PEAK 36(15Q11.2) WILD-TYPE 264   7   2  16
D66V13, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  R0                          130                            264
  R1                            5                              7
  R2                            2                              2
  RX                            6                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(15Q11.2) MUTATED       5                        13   111
  DEL PEAK 36(15Q11.2) WILD-TYPE     4                        18   229
D66V14, multiclass
                           clus
vv                          DEL PEAK 36(15Q11.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              111
                           clus
vv                          DEL PEAK 36(15Q11.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             18
  WHITE                                                229
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V15, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED     2  99
  DEL PEAK 36(15Q11.2) WILD-TYPE   6 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED      2   99
  DEL PEAK 36(15Q11.2) WILD-TYPE    6  210
                        clus
vv                       DEL PEAK 36(15Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           99
                        clus
vv                       DEL PEAK 36(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            210
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 37(15Q21.1) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(15Q21.1) MUTATED    91  73
  DEL PEAK 37(15Q21.1) WILD-TYPE 190 123
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                           164                            313 
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                            73                            123 
$`DEL PEAK 37(15Q21.1) MUTATED`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3412 TCGA-18-3416 TCGA-18-3419 TCGA-18-5592 
       12.20        75.75        11.34        31.99         1.64        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1080 TCGA-21-5786 TCGA-21-5787 
      119.54        46.88        99.16       122.43        33.93        10.82 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
        7.33        14.93        14.10        27.02        48.82        20.48 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-5471 TCGA-22-5477 
       48.33        24.13         0.56        38.17        31.73        44.25 
TCGA-22-5480 TCGA-33-4533 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
       71.34       133.74       103.53        14.07        54.44         1.55 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
       36.62         6.94       110.99        44.19       118.36        27.16 
TCGA-34-2600 TCGA-34-2604 TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 
       61.61        31.50         4.96        27.19        26.43         3.95 
TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 
        7.82         0.39         3.39        47.80        74.07        68.58 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5040 
        1.71        24.33         1.94        27.39        36.39        17.06 
TCGA-43-2578 TCGA-43-2581 TCGA-43-5668 TCGA-43-5670 TCGA-43-7657 TCGA-43-8116 
       22.49        38.66        18.38        27.91         7.76        11.77 
TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-52-7810 
       12.03         9.99        10.65        13.91         0.39        30.35 
TCGA-52-7812 TCGA-56-7580 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
       27.45         1.32        17.49         3.48        26.89        14.07 
TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A62T TCGA-58-8386 
       10.36        15.81        20.94        19.23         2.76         0.03 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 TCGA-60-2712 TCGA-60-2714 TCGA-60-2720 
       10.22        96.82        80.45         9.01        50.33         3.19 
TCGA-60-2723 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML 
       35.90        11.77       102.67        66.61        59.97        45.57 
TCGA-63-A5MS TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2737 TCGA-66-2742 TCGA-66-2754 
       78.28        53.88        34.59         2.01        21.07         2.01 
TCGA-66-2756 TCGA-66-2766 TCGA-66-2767 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 
        0.99         1.02         2.01        22.98         5.03        10.06 
TCGA-66-2794 TCGA-66-2800 TCGA-68-8250 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 
       54.08        49.05         8.02        16.18        14.73        29.56 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7337 TCGA-77-8007 TCGA-77-8009 
       23.28        89.98         0.49       106.95         6.51        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G6 
       37.81        82.92         6.97        65.49         0.33        22.29 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7843 TCGA-85-8072 
       38.86         9.67        11.97        36.53         1.15        16.87 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8479 TCGA-85-8584 TCGA-85-8666 
       34.52         0.76        13.22         0.72        12.59        15.62 
TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 
       25.68        18.18        12.56        14.96        12.39         3.65 
TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-8064 TCGA-92-8065 TCGA-94-8491 
        2.93        20.22        22.62         5.26         2.30        26.63 
TCGA-96-A4JK TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       19.36        11.84         0.07         4.54        51.78        45.37 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
        4.21         2.89        39.85        37.22        30.58        24.00 
TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       14.73        83.57         3.65        33.07         3.72        12.72 
TCGA-O2-A52W TCGA-O2-A5IB 
        8.58        11.18 

$`DEL PEAK 37(15Q21.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
        7.46        79.46         4.80       117.57        23.54        92.15 
TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
       36.07        86.96         6.18         2.79       154.32        27.19 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 
       70.16        60.89        34.78        15.58        31.73         9.34 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI 
      119.80        43.23        31.63        88.11        41.69        32.19 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 TCGA-22-4601 
       21.99         4.31        64.21         1.74        35.08        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 
       13.12        32.02        19.30         9.57        11.77        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 
       63.55        14.63         0.79        54.28        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 
       18.84        30.12        62.86        56.32        16.64        22.06 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-6737 
        7.63        98.01        79.53       174.08       151.27        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-34-2596 TCGA-34-2605 TCGA-34-2608 
       27.02         4.70         0.30         2.63        28.96        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       31.27        65.23        67.79        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 
       12.00        16.93        30.94        18.15         1.12         4.04 
TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       20.91         0.43         0.39         6.58         8.12         7.46 
TCGA-37-4135 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5035 
        6.81        44.75        55.20        70.03        60.79        15.58 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 
       35.64        35.70        17.88        40.21        27.02        33.11 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       12.36        24.89        21.47         5.46         3.81        19.59 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
       66.51        13.38         2.93        11.61         9.73        14.20 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-1622 
        0.39        29.95        28.34         5.46         8.75        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
        0.10        18.25         2.04         0.62         0.99         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8308 
        0.99         1.45         0.85         6.51         0.10        17.00 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 
        1.35        16.77         1.81        22.75         1.18         9.93 
TCGA-56-8628 TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
       20.25        13.32        17.85        21.04        18.74         0.13 
TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        0.26        13.25        13.55        29.95        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
       34.78        85.12        34.36        56.65        35.24        29.92 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       21.11         3.58        12.23        37.94        92.71        21.93 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 
       49.48        66.54        41.42        56.91        35.34        48.49 
TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG 
       42.64        32.32        29.85        23.57        26.83        70.62 
TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT 
       58.65        14.99        11.34        25.28        89.29        16.37 
TCGA-63-A5MU TCGA-63-A5MV TCGA-66-2727 TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 
       25.41        36.16        16.96        43.10         0.99         1.02 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        0.92        43.99        21.01        25.05         0.99         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        2.01         7.07        23.01        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       19.00        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2792 TCGA-66-2795 
       25.97        40.01        22.98         4.04        30.02         4.01 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-77-6843 TCGA-77-6844 
        2.73         6.64         6.94        13.35        73.12        75.09 
TCGA-77-7138 TCGA-77-7140 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 
       11.18        20.78        42.28        70.13         0.16        46.78 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       15.75        86.76        12.59        53.92        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 
      104.09        11.54        26.40        27.39         9.63        54.41 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 
       35.90       126.18       132.36       117.57         5.92        42.41 
TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 
       42.08        30.81        27.62        12.99         6.41        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       31.30        32.91         1.38        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 TCGA-85-8350 
       19.04        24.13        31.56        14.07        10.09        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 
       16.77         5.29         3.09        32.71         2.01         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC 
       14.63        13.94         0.10        19.33        17.72        14.96 
TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 TCGA-90-6837 
       24.36        19.73        16.21        15.85         0.79        24.92 
TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
        9.50        11.77        14.07        10.59         2.70         3.48 
TCGA-92-8063 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        4.01        21.04         0.16        11.70         4.01         5.03 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
       14.14        16.14        17.69        49.87        57.07        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       17.46        16.57         8.42         2.76        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       21.34        27.16         3.88        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       21.21        20.32        18.58        20.71        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HJ 
       16.11        13.18        13.41        64.08         1.22        13.74 
TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52V 
       29.75        22.78        65.49        16.80         0.43        43.89 
TCGA-XC-AA0X 
        0.20 

  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                        133.74                         174.08 
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                        19.295                         19.040 
[1] "0.0 - 133.7 (19.3)" "0.1 - 174.1 (19.0)"
[1] "hr=" "1.1"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(15Q21.1) MUTATED         2       27       41        0        22
  DEL PEAK 37(15Q21.1) WILD-TYPE       0       60      110        2        41
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(15Q21.1) MUTATED          34         3         27          9
  DEL PEAK 37(15Q21.1) WILD-TYPE        58         0         35         12
                                vv
clus                             STAGE IV
  DEL PEAK 37(15Q21.1) MUTATED          3
  DEL PEAK 37(15Q21.1) WILD-TYPE        4
D67V3, multiclass
            clus
vv           DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             27                             60
  STAGE IB                             41                            110
  STAGE II                              0                              2
  STAGE IIA                            22                             41
  STAGE IIB                            34                             58
  STAGE III                             3                              0
  STAGE IIIA                           27                             35
  STAGE IIIB                            9                             12
  STAGE IV                              3                              4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 37(15Q21.1) MUTATED    33 100  25  10
  DEL PEAK 37(15Q21.1) WILD-TYPE  78 190  44  13
D67V4, multiclass
    clus
vv   DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  T1                           33                             78
  T2                          100                            190
  T3                           25                             44
  T4                           10                             13
[1] 4 2
[1] TRUE
[1] "dimension of 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(15Q21.1) MUTATED    93  51  21   2
  DEL PEAK 37(15Q21.1) WILD-TYPE 219  80  18   3
D67V5, multiclass
    clus
vv   DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  N0                           93                            219
  N1                           51                             80
  N2                           21                             18
  N3                            2                              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"
D67V6, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q21.1) MUTATED   133   3
  DEL PEAK 37(15Q21.1) WILD-TYPE 271   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q21.1) MUTATED    133    3
  DEL PEAK 37(15Q21.1) WILD-TYPE  271    4
   clus
vv  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  0                          133                            271
  1                            3                              4
[1] 2 2
[1] FALSE
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q21.1) MUTATED    48 120
  DEL PEAK 37(15Q21.1) WILD-TYPE  79 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q21.1) MUTATED     48  120
  DEL PEAK 37(15Q21.1) WILD-TYPE   79  246
        clus
vv       DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  FEMALE                           48                             79
  MALE                            120                            246
[1] 2 2
[1] FALSE
D67V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 37(15Q21.1) MUTATED                                       2
  DEL PEAK 37(15Q21.1) WILD-TYPE                                    13
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 37(15Q21.1) MUTATED                                         0
  DEL PEAK 37(15Q21.1) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 37(15Q21.1) MUTATED                                        2
  DEL PEAK 37(15Q21.1) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 37(15Q21.1) MUTATED                                         1
  DEL PEAK 37(15Q21.1) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(15Q21.1) MUTATED                                                           163
  DEL PEAK 37(15Q21.1) WILD-TYPE                                                         307
D67V9, multiclass
                                                             clus
vv                                                            DEL PEAK 37(15Q21.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  2
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          163
                                                             clus
vv                                                            DEL PEAK 37(15Q21.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            307
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q21.1) MUTATED     6 162
  DEL PEAK 37(15Q21.1) WILD-TYPE   7 318
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q21.1) MUTATED      6  162
  DEL PEAK 37(15Q21.1) WILD-TYPE    7  318
     clus
vv    DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  NO                             6                              7
  YES                          162                            318
[1] 2 2
[1] FALSE
D67V11, continuous
D67V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(15Q21.1) MUTATED   133   4   2   6
  DEL PEAK 37(15Q21.1) WILD-TYPE 261   8   2  16
D67V13, multiclass
    clus
vv   DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  R0                          133                            261
  R1                            4                              8
  R2                            2                              2
  RX                            6                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(15Q21.1) MUTATED       4                        16   112
  DEL PEAK 37(15Q21.1) WILD-TYPE     5                        15   228
D67V14, multiclass
                           clus
vv                          DEL PEAK 37(15Q21.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              112
                           clus
vv                          DEL PEAK 37(15Q21.1) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                228
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V15, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q21.1) MUTATED     3 101
  DEL PEAK 37(15Q21.1) WILD-TYPE   5 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q21.1) MUTATED      3  101
  DEL PEAK 37(15Q21.1) WILD-TYPE    5  208
                        clus
vv                       DEL PEAK 37(15Q21.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          101
                        clus
vv                       DEL PEAK 37(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            208
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 38(16P13.3) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(16P13.3) MUTATED   109  68
  DEL PEAK 38(16P13.3) WILD-TYPE 172 128
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                           177                            300 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            68                            128 
$`DEL PEAK 38(16P13.3) MUTATED`
TCGA-18-3410 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 
        4.80        92.15        36.07        86.96       154.32        49.94 
TCGA-21-1070 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 TCGA-21-1082 
      119.54        70.16        60.89        34.78       122.43       119.80 
TCGA-21-5786 TCGA-22-0940 TCGA-22-1002 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 
       33.93        21.99         4.31        14.10        48.33        24.13 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 
       38.17        13.12        11.77         0.79        71.34        11.74 
TCGA-22-5485 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4582 TCGA-33-4587 TCGA-33-6737 
       30.12        22.06       133.74       103.53        54.44        19.76 
TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2609 
        6.94        44.19       118.36        27.16         2.63        31.27 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-8455 
        9.07        23.24        16.93        30.94        18.15         4.04 
TCGA-34-A5IX TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5027 
       20.91         3.39        47.80        74.07        68.58        60.79 
TCGA-39-5028 TCGA-39-5040 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 
        1.71        17.06        27.02        27.91        12.36        19.59 
TCGA-43-7657 TCGA-43-8116 TCGA-43-8118 TCGA-43-A56U TCGA-51-4080 TCGA-52-7622 
        7.76        11.77         2.93        14.20         0.39        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 TCGA-56-7579 
        5.46        30.35        27.45        28.96         2.04         1.45 
TCGA-56-7580 TCGA-56-7822 TCGA-56-8307 TCGA-56-8503 TCGA-56-8629 TCGA-56-A49D 
        1.32        17.49        26.89         1.35        15.81        20.94 
TCGA-56-A4BX TCGA-56-A4BY TCGA-58-8386 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
       13.32        17.85         0.03        16.47        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-60-2695 TCGA-60-2708 TCGA-60-2719 TCGA-60-2720 
       34.36        56.65        21.11        80.45        42.64         3.19 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH 
       35.90        23.57        26.83        11.77       102.67        66.61 
TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       45.57        25.28        53.88        34.59        16.96        43.10 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 
        1.02         2.01         0.92        43.99        21.01         0.99 
TCGA-66-2766 TCGA-66-2773 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-66-2787 
        1.02         3.02         3.98        12.00        25.97        40.01 
TCGA-66-2792 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 
       30.02        49.05         6.64        13.35        14.73        29.56 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7142 TCGA-77-8130 TCGA-77-8136 TCGA-77-8140 
       23.28        89.98        42.28        82.92        39.09        11.54 
TCGA-77-8143 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G7 TCGA-77-A5GF 
       26.40        65.49        35.90         0.33         5.92        27.62 
TCGA-77-A5GH TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 
       38.86         6.41        31.30        32.91         1.15        18.94 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
       24.13        31.56        10.09        16.77         5.29         3.09 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4CN 
        2.01         0.72        14.63         0.10        25.68        19.33 
TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE 
       14.96        19.73        12.39         3.65         2.93        22.62 
TCGA-92-7340 TCGA-92-8064 TCGA-94-7557 TCGA-94-8035 TCGA-96-7544 TCGA-96-8169 
        2.70         5.26         0.16         4.01        49.87        18.31 
TCGA-96-A4JK TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53I TCGA-J1-A4AH 
       19.36        21.34         3.88        18.15        18.58        19.10 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HG TCGA-NC-A5HJ 
       12.89        16.11        13.41         0.07        51.78        13.74 
TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CT TCGA-O2-A52N 
        4.21        37.22        30.58        22.78        65.49        33.07 
TCGA-O2-A52S TCGA-O2-A52W TCGA-O2-A5IB 
       12.72         8.58        11.18 

$`DEL PEAK 38(16P13.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75        79.46       117.57        11.34 
TCGA-18-3414 TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 TCGA-18-4086 TCGA-18-5595 
       23.54        31.99         1.64         6.18         2.79        27.19 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1083 
       46.88        99.16        15.58        31.73         9.34        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 
       31.63        88.11        41.69        10.82        32.19         7.33 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 
       14.93        64.21         1.74        27.02        48.82        20.48 
TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       35.08         0.56        34.75        32.02        19.30         9.57 
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
       31.73        64.93        63.55        14.63        44.25        54.28 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 
       79.20        18.84        62.86        56.32        16.64         7.63 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 
       98.01        79.53       174.08       151.27        14.07         1.55 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-34-2600 
       27.02         4.70         0.30        36.62       110.99        61.61 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       31.50        28.96        32.88        65.23        67.79        56.38 
TCGA-34-5240 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 
       12.00         4.96         1.12        27.19        26.43         3.95 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        0.43         0.39         6.58         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 
        6.81         0.39        44.75        55.20        70.03        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        27.39        36.39        15.58        35.64        35.70 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 
       17.88        40.21        22.49        38.66        33.11        18.38 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7658 TCGA-43-8115 
       24.89        21.47         5.46         3.81        66.51        13.38 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       11.61         9.73        12.03         9.99        10.65        13.91 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7811 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 
        0.39        29.95         8.75         0.10        18.25         0.62 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
        0.99         0.43         0.99         0.85         6.51         0.10 
TCGA-56-8304 TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 
        3.48        17.00        14.07        16.77         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4ZJ 
        1.18        10.36         9.93        20.25        19.23        21.04 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 
       18.74         0.13         0.26         2.76        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 
       29.95        71.24        35.24        29.92         3.58        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 
       10.22        96.82        37.94        92.71        21.93        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       66.54        41.42         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2721 TCGA-60-2722 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
       48.49        32.32        29.85        70.62        58.65        59.97 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       14.99        11.34        89.29        78.28        16.37        25.41 
TCGA-63-A5MV TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 TCGA-66-2759 
       36.16         2.01        21.07         0.99         0.99        25.05 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
        2.01         2.01         2.01         7.07        23.01        19.00 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 
        2.01        19.00        12.03        24.95         1.97        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
        4.04        22.98         5.03        10.06        54.08         4.01 
TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 
        2.73         6.94         8.02        16.18        73.12        75.09 
TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       11.18        20.78         0.49        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
       46.78        15.75         6.51        86.76        53.95        37.81 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 
       12.59        53.92        17.72       104.09        27.39         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
        9.63        54.41       126.18       132.36       117.57        22.29 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       42.41        42.08        30.81         9.67        11.97        12.99 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 
       36.53        34.95         1.38        29.95        25.15        19.04 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       14.07        16.87        34.52         0.76        13.22        22.45 
TCGA-85-8354 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4JB 
       32.71         7.76        13.94        12.59        15.62        17.72 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       24.36        18.18        12.56        16.21        15.85        14.96 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
        0.79        24.92         9.50        11.77        14.07        20.22 
TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
       10.59         3.48         4.01         2.30        21.04        11.70 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7545 
        5.03        26.63        14.14        16.14        17.69        57.07 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       17.46        16.57         8.42         2.76        30.81        30.67 
TCGA-98-A538 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J 
       27.16         2.01        27.02        21.21        20.32        20.71 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI 
       13.18        11.84        64.08         4.54         1.22        45.37 
TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NK-A5CR 
        2.89        39.85        24.00        14.73        29.75        83.57 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
        3.65        16.80         0.43         3.72        43.89         0.20 

  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                        154.32                         174.08 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                        20.910                         18.315 
[1] "0.0 - 154.3 (20.9)" "0.1 - 174.1 (18.3)"
[1] "hr=" "1.1"
D68V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 38(16P13.3) MUTATED         2       30       58        0        23
  DEL PEAK 38(16P13.3) WILD-TYPE       0       57       93        2        40
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(16P13.3) MUTATED          36         2         27          3
  DEL PEAK 38(16P13.3) WILD-TYPE        56         1         35         18
                                vv
clus                             STAGE IV
  DEL PEAK 38(16P13.3) MUTATED          3
  DEL PEAK 38(16P13.3) WILD-TYPE        4
D68V3, multiclass
            clus
vv           DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             30                             57
  STAGE IB                             58                             93
  STAGE II                              0                              2
  STAGE IIA                            23                             40
  STAGE IIB                            36                             56
  STAGE III                             2                              1
  STAGE IIIA                           27                             35
  STAGE IIIB                            3                             18
  STAGE IV                              3                              4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 38(16P13.3) MUTATED    33 111  32   8
  DEL PEAK 38(16P13.3) WILD-TYPE  78 179  37  15
D68V4, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  T1                           33                             78
  T2                          111                            179
  T3                           32                             37
  T4                            8                             15
[1] 4 2
[1] TRUE
[1] "dimension of 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(16P13.3) MUTATED   120  49  14   0
  DEL PEAK 38(16P13.3) WILD-TYPE 192  82  25   5
D68V5, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  N0                          120                            192
  N1                           49                             82
  N2                           14                             25
  N3                            0                              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"
D68V6, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED   152   3
  DEL PEAK 38(16P13.3) WILD-TYPE 252   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED    152    3
  DEL PEAK 38(16P13.3) WILD-TYPE  252    4
   clus
vv  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  0                          152                            252
  1                            3                              4
[1] 2 2
[1] FALSE
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED    50 134
  DEL PEAK 38(16P13.3) WILD-TYPE  77 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED     50  134
  DEL PEAK 38(16P13.3) WILD-TYPE   77  232
        clus
vv       DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  FEMALE                           50                             77
  MALE                            134                            232
[1] 2 2
[1] FALSE
D68V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 38(16P13.3) MUTATED                                       8
  DEL PEAK 38(16P13.3) WILD-TYPE                                     7
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 38(16P13.3) MUTATED                                         0
  DEL PEAK 38(16P13.3) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 38(16P13.3) MUTATED                                        2
  DEL PEAK 38(16P13.3) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 38(16P13.3) MUTATED                                         1
  DEL PEAK 38(16P13.3) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(16P13.3) MUTATED                                                           173
  DEL PEAK 38(16P13.3) WILD-TYPE                                                         297
D68V9, multiclass
                                                             clus
vv                                                            DEL PEAK 38(16P13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          173
                                                             clus
vv                                                            DEL PEAK 38(16P13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            297
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED     5 179
  DEL PEAK 38(16P13.3) WILD-TYPE   8 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED      5  179
  DEL PEAK 38(16P13.3) WILD-TYPE    8  301
     clus
vv    DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  NO                             5                              8
  YES                          179                            301
[1] 2 2
[1] FALSE
D68V11, continuous
D68V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(16P13.3) MUTATED   151   1   0   7
  DEL PEAK 38(16P13.3) WILD-TYPE 243  11   4  15
D68V13, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  R0                          151                            243
  R1                            1                             11
  R2                            0                              4
  RX                            7                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(16P13.3) MUTATED       2                        15   124
  DEL PEAK 38(16P13.3) WILD-TYPE     7                        16   216
D68V14, multiclass
                           clus
vv                          DEL PEAK 38(16P13.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           15
  WHITE                                              124
                           clus
vv                          DEL PEAK 38(16P13.3) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             16
  WHITE                                                216
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V15, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED     3 116
  DEL PEAK 38(16P13.3) WILD-TYPE   5 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED      3  116
  DEL PEAK 38(16P13.3) WILD-TYPE    5  193
                        clus
vv                       DEL PEAK 38(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          116
                        clus
vv                       DEL PEAK 38(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            193
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 39(16Q23.1) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(16Q23.1) MUTATED   124  72
  DEL PEAK 39(16Q23.1) WILD-TYPE 157 124
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           196                            281 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                            72                            124 
$`DEL PEAK 39(16Q23.1) MUTATED`
TCGA-18-3410 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-4083 TCGA-18-5592 
        4.80        92.15        31.99         1.64         6.18        49.94 
TCGA-21-1070 TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-21-5787 TCGA-22-0940 
      119.54        60.89       122.43        43.23        10.82        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
        7.33         4.31        14.10        48.33        24.13        38.17 
TCGA-22-4604 TCGA-22-5473 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5489 
       13.12        63.55         0.79        71.34        79.20        62.86 
TCGA-33-4533 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-33-6737 TCGA-33-AASI 
      133.74        79.53       151.27        14.07        19.76        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2604 TCGA-34-2609 TCGA-34-5231 
      118.36        27.16         2.63        31.50        31.27        65.23 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5927 TCGA-34-5929 TCGA-34-8455 TCGA-34-A5IX 
        9.07        23.24        30.94         4.96         4.04        20.91 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
       47.80        74.07        44.75        70.03        60.79         1.71 
TCGA-39-5030 TCGA-39-5040 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 
        1.94        17.06        22.49        27.02        33.11        18.38 
TCGA-43-5670 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
       27.91         7.76        66.51        11.77         9.73        14.20 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       10.65        13.91         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7730 
       30.35         0.99         0.43         1.45         1.32         6.51 
TCGA-56-7822 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8626 
       17.49        26.89        17.00        14.07         1.35         9.93 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       20.94        13.32        17.85         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
       29.95        71.24        16.47        34.78        85.12        56.65 
TCGA-58-A46M TCGA-60-2695 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2714 
       35.24        21.11        66.54        41.42        56.91        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MH 
       42.64         3.19        35.90        26.83       102.67        66.61 
TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 
       58.65        45.57        34.59        16.96        43.10         1.02 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 
        0.92        43.99        25.05         0.99         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2778 TCGA-66-2782 TCGA-66-2786 TCGA-66-2787 
        7.07        23.01        19.00        12.00        25.97        40.01 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 
        4.04        22.98        30.02        10.06        49.05         6.64 
TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       13.35        14.73        29.56        89.98         0.49        42.28 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8136 TCGA-77-8139 TCGA-77-8143 TCGA-77-8150 
       46.78        15.75        39.09       104.09        26.40        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 
       65.49         0.33        38.86        12.99         6.41        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 TCGA-85-8071 TCGA-85-8352 
       31.30        32.91        29.95        18.94        14.07         5.29 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN 
        3.09         2.01        14.63         0.10        15.62        19.33 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A5B5 
       17.72        14.96        19.73        12.56        16.21         3.65 
TCGA-90-7766 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-8064 TCGA-92-8065 
        9.50         2.93        20.22        22.62         5.26         2.30 
TCGA-94-7557 TCGA-94-8035 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-8169 TCGA-96-A4JK 
        0.16         4.01        14.14        16.14        18.31        19.36 
TCGA-96-A4JL TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53I TCGA-J1-A4AH 
       16.57        27.16         3.88        18.15        18.58        19.10 
TCGA-LA-A7SW TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
       13.41        51.78        13.74         4.21         2.89        37.22 
TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT 
       30.58        14.73        29.75        22.78        83.57        65.49 
TCGA-O2-A52N TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07         8.58        11.18         0.20 

$`DEL PEAK 39(16Q23.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75        79.46       117.57        11.34 
TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
       23.54        36.07        86.96         2.79       154.32        27.19 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       46.88        99.16        70.16        34.78        15.58        31.73 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 
        9.34       119.80        31.63        88.11        41.69        33.93 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 
       32.19        14.93        64.21         1.74        27.02        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 
       20.48        35.08         0.56        34.75        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 
        9.57        11.77        31.73        64.93        14.63        44.25 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 
       54.28        11.74        18.84        30.12        56.32        16.64 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4587 
       22.06         7.63        98.01       174.08       103.53        54.44 
TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
        1.55        27.02         4.70         0.30        36.62         6.94 
TCGA-33-AASD TCGA-34-2600 TCGA-34-2605 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 
      110.99        61.61        28.96        32.88        67.79        56.38 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 
       12.00        16.93        18.15         1.12        27.19        26.43 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        3.95         0.43         0.39         6.58         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 
        7.82         6.81         0.39         3.39        68.58        55.20 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
       24.33        27.39        36.39        15.58        35.64        35.70 
TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       17.88        40.21        38.66        12.36        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8118 TCGA-43-A474 
        5.46         3.81        19.59        13.38         2.93        11.61 
TCGA-43-A56V TCGA-46-3768 TCGA-51-4080 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
       12.03         9.99         0.39         8.75        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7223 TCGA-56-7582 
        0.10        18.25         2.04         0.62         0.99         0.85 
TCGA-56-7731 TCGA-56-8304 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
        0.10         3.48        16.77         1.81        22.75         1.18 
TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A4ZK 
       10.36        20.25        15.81        19.23        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-A46K TCGA-58-A46N TCGA-60-2696 
        0.13         0.26         2.76        34.36        29.92         3.58 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       12.23        10.22        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2712 TCGA-60-2715 TCGA-60-2716 TCGA-60-2721 
       80.45        49.48         9.01        35.34        48.49        32.32 
TCGA-60-2722 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5MM 
       29.85        23.57        11.77        70.62        59.97        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU 
       11.34        25.28        89.29        78.28        16.37        25.41 
TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
       36.16        53.88         2.01        21.07         0.99         2.01 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2771 TCGA-66-2773 
        0.99        21.01         2.01         1.02        19.00         3.02 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 
        2.01        12.03         3.98        24.95         1.97        22.98 
TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 
        5.03        54.08         4.01         2.73         6.94         8.02 
TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 
       16.18        73.12        75.09        23.28        11.18        20.78 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
       70.13       106.95         0.16         6.51        86.76        53.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 
       37.81        82.92        12.59        53.92        17.72        11.54 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
       27.39         6.97         9.63        35.90       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
      117.57        22.29         5.92        42.41        42.08        30.81 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7710 TCGA-85-7843 
       27.62         9.67        11.97        36.53         1.38         1.15 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 
       25.15        19.04        24.13        31.56        16.87        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 
       10.09         0.76        13.22        22.45        16.77        32.71 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4PA 
        0.72         7.76        13.94        12.59        25.68        24.36 
TCGA-85-A4QQ TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       18.18        15.85        14.96         0.79        12.39        24.92 
TCGA-90-7769 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       11.77        14.07        10.59         2.70         3.48         4.01 
TCGA-94-7033 TCGA-94-7943 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 
       21.04        11.70         5.03        26.63        17.69        49.87 
TCGA-96-7545 TCGA-96-8170 TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 
       57.07        17.46         8.42         2.76        30.81        30.67 
TCGA-98-8023 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J 
       21.34         2.01        27.02        21.21        20.32        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       12.89        16.11        13.18        11.84         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HM TCGA-NC-A5HP TCGA-NK-A5CX 
        4.54         1.22        45.37        39.85        24.00         3.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       16.80         0.43         3.72        12.72        43.89 

  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                        151.27                         174.08 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                        19.345                         19.000 
[1] "0.0 - 151.3 (19.3)" "0.1 - 174.1 (19.0)"
[1] "hr=" "1.2"
D69V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(16Q23.1) MUTATED         2       32       60        0        26
  DEL PEAK 39(16Q23.1) WILD-TYPE       0       55       91        2        37
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(16Q23.1) MUTATED          42         1         30          7
  DEL PEAK 39(16Q23.1) WILD-TYPE        50         2         32         14
                                vv
clus                             STAGE IV
  DEL PEAK 39(16Q23.1) MUTATED          2
  DEL PEAK 39(16Q23.1) WILD-TYPE        5
D69V3, multiclass
            clus
vv           DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             32                             55
  STAGE IB                             60                             91
  STAGE II                              0                              2
  STAGE IIA                            26                             37
  STAGE IIB                            42                             50
  STAGE III                             1                              2
  STAGE IIIA                           30                             32
  STAGE IIIB                            7                             14
  STAGE IV                              2                              5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 39(16Q23.1) MUTATED    39 121  35   9
  DEL PEAK 39(16Q23.1) WILD-TYPE  72 169  34  14
D69V4, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  T1                           39                             72
  T2                          121                            169
  T3                           35                             34
  T4                            9                             14
[1] 4 2
[1] TRUE
[1] "dimension of 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(16Q23.1) MUTATED   131  52  16   3
  DEL PEAK 39(16Q23.1) WILD-TYPE 181  79  23   2
D69V5, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  N0                          131                            181
  N1                           52                             79
  N2                           16                             23
  N3                            3                              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"
D69V6, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED   170   2
  DEL PEAK 39(16Q23.1) WILD-TYPE 234   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED    170    2
  DEL PEAK 39(16Q23.1) WILD-TYPE  234    5
   clus
vv  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  0                          170                            234
  1                            2                              5
[1] 2 2
[1] FALSE
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED    59 145
  DEL PEAK 39(16Q23.1) WILD-TYPE  68 221
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED     59  145
  DEL PEAK 39(16Q23.1) WILD-TYPE   68  221
        clus
vv       DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  FEMALE                           59                             68
  MALE                            145                            221
[1] 2 2
[1] FALSE
D69V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 39(16Q23.1) MUTATED                                       7
  DEL PEAK 39(16Q23.1) WILD-TYPE                                     8
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 39(16Q23.1) MUTATED                                         0
  DEL PEAK 39(16Q23.1) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 39(16Q23.1) MUTATED                                        0
  DEL PEAK 39(16Q23.1) WILD-TYPE                                      6
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 39(16Q23.1) MUTATED                                         0
  DEL PEAK 39(16Q23.1) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(16Q23.1) MUTATED                                                           197
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                         273
D69V9, multiclass
                                                             clus
vv                                                            DEL PEAK 39(16Q23.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          197
                                                             clus
vv                                                            DEL PEAK 39(16Q23.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            273
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED     8 196
  DEL PEAK 39(16Q23.1) WILD-TYPE   5 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED      8  196
  DEL PEAK 39(16Q23.1) WILD-TYPE    5  284
     clus
vv    DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  NO                             8                              5
  YES                          196                            284
[1] 2 2
[1] FALSE
D69V11, continuous
D69V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(16Q23.1) MUTATED   160   5   2   7
  DEL PEAK 39(16Q23.1) WILD-TYPE 234   7   2  15
D69V13, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  R0                          160                            234
  R1                            5                              7
  R2                            2                              2
  RX                            7                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(16Q23.1) MUTATED       3                        16   140
  DEL PEAK 39(16Q23.1) WILD-TYPE     6                        15   200
D69V14, multiclass
                           clus
vv                          DEL PEAK 39(16Q23.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              140
                           clus
vv                          DEL PEAK 39(16Q23.1) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V15, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED     2 131
  DEL PEAK 39(16Q23.1) WILD-TYPE   6 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED      2  131
  DEL PEAK 39(16Q23.1) WILD-TYPE    6  178
                        clus
vv                       DEL PEAK 39(16Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          131
                        clus
vv                       DEL PEAK 39(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            178
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 40(17P11.2) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(17P11.2) MUTATED   153 107
  DEL PEAK 40(17P11.2) WILD-TYPE 128  89
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           260                            217 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           107                             89 
$`DEL PEAK 40(17P11.2) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       12.20         7.46         4.80        11.34        23.54        92.15 
TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 
       31.99         1.64        86.96         2.79       154.32       119.54 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       46.88        70.16        34.78       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 
       88.11        10.82        32.19         7.33         1.74        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 
       27.02        20.48        24.13         0.56        38.17        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 TCGA-22-5477 
       32.02        19.30         9.57        11.77        64.93        44.25 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       71.34        79.20        18.84        62.86        56.32        16.64 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       22.06         7.63        79.53       103.53       151.27        14.07 
TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       54.44         4.70         0.30        36.62         6.94       110.99 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2604 TCGA-34-2608 TCGA-34-5240 
      118.36        27.16        61.61        31.50        32.88        12.00 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       27.19         4.04        26.43        20.91         3.95         0.43 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5029 
        7.82         6.81         0.39         3.39        74.07        24.33 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-5670 TCGA-43-6143 
       36.39        15.58        17.06        40.21        27.91        12.36 
TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 
       19.59        66.51        13.38        11.77        11.61         9.73 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-52-7622 
       14.20        12.03        10.65        13.91         0.39        28.34 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 
       27.45        28.96         0.10        18.25         0.99         1.32 
TCGA-56-7582 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
        0.85        17.49         3.48        26.89        14.07         1.35 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.18        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       17.85        21.04         2.76         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 
       29.95        71.24        34.78        56.65        35.24        21.11 
TCGA-60-2696 TCGA-60-2703 TCGA-60-2706 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 
        3.58        96.82        92.71         9.01        56.91        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
       42.64         3.19        32.32        29.85        35.90        26.83 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ 
       11.77       102.67        70.62        66.61        58.65        59.97 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2742 
       16.37        36.16        53.88        34.59        16.96        21.07 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        1.02         2.01        43.99        21.01        25.05         0.99 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 
        1.02         2.01         2.01         7.07        19.00         3.02 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
        2.01        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 
       25.97        22.98         4.04         5.03        10.06         4.01 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 
        6.94        13.35        14.73        29.56        75.09        23.28 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 
       89.98         0.49        42.28       106.95         0.16        15.75 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
       86.76        53.95        37.81        82.92        12.59        53.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 
       39.09        17.72       104.09        11.54         6.97         9.63 
TCGA-77-8150 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5GB 
       54.41        35.90       132.36       117.57        22.29        30.81 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 TCGA-85-7843 TCGA-85-7844 TCGA-85-8070 
       38.86        11.97        34.95         1.15        29.95        31.56 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8479 TCGA-85-8584 TCGA-85-A4CL 
       34.52         0.76        13.22         0.72        12.59        25.68 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 
       17.72        14.96        18.18        16.21        15.85         0.79 
TCGA-85-A53L TCGA-90-7767 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 
       12.39         2.93        14.07        20.22         3.48         4.01 
TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 
        2.30        21.04         4.01        26.63        14.14        16.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK TCGA-98-8021 
       17.69        49.87        57.07        17.46        19.36        30.81 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I 
       30.67        27.16         3.88        18.15         2.01        18.58 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK 
       12.89        16.11         4.54        51.78        45.37         4.21 
TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR 
        2.89        39.85        30.58        24.00        14.73        29.75 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q 
       83.57        65.49         3.65        16.80        33.07         3.72 
TCGA-O2-A52V TCGA-XC-AA0X 
       43.89         0.20 

$`DEL PEAK 40(17P11.2) WILD-TYPE`
TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3417 TCGA-18-4083 TCGA-18-5592 
       75.75        79.46       117.57        36.07         6.18        49.94 
TCGA-18-5595 TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 
       27.19        99.16        60.89        15.58        31.73       122.43 
TCGA-21-1081 TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 
        9.34        41.69        33.93        21.99        14.93         4.31 
TCGA-22-1005 TCGA-22-1017 TCGA-22-4593 TCGA-22-4594 TCGA-22-4601 TCGA-22-5471 
       64.21        48.82        35.08        48.33        34.75        31.73 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 
       63.55        14.63         0.79        54.28        11.74        30.12 
TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
      133.74        98.01       174.08         1.55        19.76        27.02 
TCGA-33-AASI TCGA-34-2596 TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
       44.19         2.63        28.96        31.27        65.23        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       56.38         9.07        23.24        16.93        30.94        18.15 
TCGA-34-5929 TCGA-34-7107 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        4.96         1.12         0.39         6.58         8.12         7.46 
TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
       47.80        44.75        68.58        55.20        70.03        60.79 
TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
        1.71         1.94        27.39        35.64        35.70        17.88 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 
       22.49        38.66        27.02        33.11        18.38        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-8118 TCGA-46-3768 
       21.47         5.46         3.81         7.76         2.93         9.99 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-6545 
        0.39        29.95         5.46        30.35         8.75         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 
        0.62         0.99         0.43         1.45         6.51         0.10 
TCGA-56-8308 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-A4BW TCGA-56-A4BX 
       17.00        16.77         1.81        22.75        19.23        13.32 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K 
       18.74         0.13         0.26        16.47        85.12        34.36 
TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 
       29.92        12.23        10.22        37.94        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2715 TCGA-60-2716 TCGA-60-2724 
       49.48        66.54        41.42        35.34        48.49        23.57 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       45.57        14.99        11.34        25.28        89.29        78.28 
TCGA-63-A5MU TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 
       25.41        43.10         2.01         0.99         0.92         0.99 
TCGA-66-2765 TCGA-66-2770 TCGA-66-2778 TCGA-66-2787 TCGA-66-2790 TCGA-66-2792 
        2.01        23.01        19.00        40.01        22.98        30.02 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-A59I 
       54.08        49.05         2.73         6.64         8.02        16.18 
TCGA-77-6843 TCGA-77-7138 TCGA-77-7140 TCGA-77-7335 TCGA-77-7463 TCGA-77-8007 
       73.12        11.18        20.78        70.13        46.78         6.51 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G7 
       26.40        27.39        65.49         0.33       126.18         5.92 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 
       42.41        42.08        27.62         9.67        12.99         6.41 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 
       36.53        31.30        32.91         1.38        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8350 
       19.04        24.13        14.07        16.87        10.09        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 
       16.77         5.29         3.09        32.71         2.01         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4PA 
       14.63        13.94         0.10        15.62        19.33        24.36 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A511 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 
       19.73        12.56        14.96         3.65        24.92         9.50 
TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 TCGA-94-7557 
       11.77        22.62        10.59         2.70         5.26         0.16 
TCGA-94-7943 TCGA-94-8490 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       11.70         5.03        18.31        16.57         8.42         2.76 
TCGA-98-8023 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53J TCGA-J1-A4AH 
       21.34        27.02        21.21        20.32        20.71        19.10 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HH 
       13.18        13.41        11.84         0.07        64.08         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HN TCGA-NC-A5HT TCGA-NK-A7XE TCGA-O2-A52S TCGA-O2-A52W 
       13.74        37.22        22.78         0.43        12.72         8.58 
TCGA-O2-A5IB 
       11.18 

  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                        154.32                         174.08 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                         18.92                          19.23 
[1] "0.0 - 154.3 (18.9)" "0.1 - 174.1 (19.2)"
[1] "hr=" "1.1"
D70V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(17P11.2) MUTATED         1       50       77        1        39
  DEL PEAK 40(17P11.2) WILD-TYPE       1       37       74        1        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(17P11.2) MUTATED          48         1         34         12
  DEL PEAK 40(17P11.2) WILD-TYPE        44         2         28          9
                                vv
clus                             STAGE IV
  DEL PEAK 40(17P11.2) MUTATED          5
  DEL PEAK 40(17P11.2) WILD-TYPE        2
D70V3, multiclass
            clus
vv           DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             50                             37
  STAGE IB                             77                             74
  STAGE II                              1                              1
  STAGE IIA                            39                             24
  STAGE IIB                            48                             44
  STAGE III                             1                              2
  STAGE IIIA                           34                             28
  STAGE IIIB                           12                              9
  STAGE IV                              5                              2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 40(17P11.2) MUTATED    63 159  37   9
  DEL PEAK 40(17P11.2) WILD-TYPE  48 131  32  14
D70V4, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  T1                           63                             48
  T2                          159                            131
  T3                           37                             32
  T4                            9                             14
[1] 4 2
[1] TRUE
[1] "dimension of 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   168  68  24   4
  DEL PEAK 40(17P11.2) WILD-TYPE 144  63  15   1
D70V5, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  N0                          168                            144
  N1                           68                             63
  N2                           24                             15
  N3                            4                              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"
D70V6, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED   218   5
  DEL PEAK 40(17P11.2) WILD-TYPE 186   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED    218    5
  DEL PEAK 40(17P11.2) WILD-TYPE  186    2
   clus
vv  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  0                          218                            186
  1                            5                              2
[1] 2 2
[1] FALSE
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED    64 204
  DEL PEAK 40(17P11.2) WILD-TYPE  63 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED     64  204
  DEL PEAK 40(17P11.2) WILD-TYPE   63  162
        clus
vv       DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  FEMALE                           64                             63
  MALE                            204                            162
[1] 2 2
[1] FALSE
D70V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                                      10
  DEL PEAK 40(17P11.2) WILD-TYPE                                     5
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                                         1
  DEL PEAK 40(17P11.2) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 40(17P11.2) MUTATED                                        2
  DEL PEAK 40(17P11.2) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 40(17P11.2) MUTATED                                         1
  DEL PEAK 40(17P11.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(17P11.2) MUTATED                                                           254
  DEL PEAK 40(17P11.2) WILD-TYPE                                                         216
D70V9, multiclass
                                                             clus
vv                                                            DEL PEAK 40(17P11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          254
                                                             clus
vv                                                            DEL PEAK 40(17P11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            216
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED    10 258
  DEL PEAK 40(17P11.2) WILD-TYPE   3 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED     10  258
  DEL PEAK 40(17P11.2) WILD-TYPE    3  222
     clus
vv    DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  NO                            10                              3
  YES                          258                            222
[1] 2 2
[1] FALSE
D70V11, continuous
D70V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(17P11.2) MUTATED   225   6   2   9
  DEL PEAK 40(17P11.2) WILD-TYPE 169   6   2  13
D70V13, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  R0                          225                            169
  R1                            6                              6
  R2                            2                              2
  RX                            9                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(17P11.2) MUTATED       5                        15   180
  DEL PEAK 40(17P11.2) WILD-TYPE     4                        16   160
D70V14, multiclass
                           clus
vv                          DEL PEAK 40(17P11.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           15
  WHITE                                              180
                           clus
vv                          DEL PEAK 40(17P11.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             16
  WHITE                                                160
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V15, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED     4 160
  DEL PEAK 40(17P11.2) WILD-TYPE   4 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED      4  160
  DEL PEAK 40(17P11.2) WILD-TYPE    4  149
                        clus
vv                       DEL PEAK 40(17P11.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          160
                        clus
vv                       DEL PEAK 40(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            149
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 41(17Q11.2) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(17Q11.2) MUTATED    82  46
  DEL PEAK 41(17Q11.2) WILD-TYPE 199 150
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           128                            349 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                            46                            150 
$`DEL PEAK 41(17Q11.2) MUTATED`
TCGA-18-3410 TCGA-18-3414 TCGA-18-3416 TCGA-21-1070 TCGA-21-1082 TCGA-21-5786 
        4.80        23.54        31.99       119.54       119.80        33.93 
TCGA-21-A5DI TCGA-22-1011 TCGA-22-1016 TCGA-22-4595 TCGA-22-4596 TCGA-22-4607 
       32.19         1.74        27.02        24.13         0.56        19.30 
TCGA-22-5472 TCGA-22-5478 TCGA-22-5492 TCGA-33-4583 TCGA-33-4587 TCGA-33-AASD 
       64.93         0.79        16.64       151.27        54.44       110.99 
TCGA-33-AASI TCGA-34-2600 TCGA-34-2604 TCGA-34-5239 TCGA-34-5241 TCGA-34-8454 
       44.19        61.61        31.50        23.24        16.93        27.19 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3789 TCGA-37-4141 TCGA-39-5029 TCGA-39-5035 
        4.04        20.91         0.43         0.39        24.33        15.58 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6770 TCGA-43-7656 
       22.49        38.66        33.11        27.91        21.47        19.59 
TCGA-43-A56U TCGA-43-A56V TCGA-46-6025 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 
       14.20        12.03        10.65        30.35        27.45         0.10 
TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 
       18.25         0.99         1.32        17.49         1.35         1.18 
TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4ZJ TCGA-56-A62T TCGA-58-8386 
       10.36        20.25        20.94        21.04         2.76         0.03 
TCGA-58-8391 TCGA-58-8393 TCGA-60-2695 TCGA-60-2696 TCGA-60-2706 TCGA-60-2713 
       71.24        34.78        21.11         3.58        92.71        56.91 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 
       50.33        42.64         3.19        32.32        35.90        23.57 
TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI TCGA-66-2753 TCGA-66-2763 TCGA-66-2769 
       70.62        66.61        58.65         1.02         0.99         7.07 
TCGA-66-2771 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       19.00        12.03        12.00        24.95         1.97        25.97 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2793 TCGA-66-2794 TCGA-68-8250 TCGA-68-8251 
       22.98         4.04        10.06        54.08         8.02        13.35 
TCGA-68-A59J TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 
       14.73        86.76        82.92        12.59        39.09        17.72 
TCGA-77-8144 TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5GB TCGA-77-A5GH 
       27.39        54.41       132.36        22.29        30.81        38.86 
TCGA-85-7697 TCGA-85-7950 TCGA-85-8287 TCGA-85-8352 TCGA-85-8479 TCGA-85-A4JB 
       34.95        18.94         0.76         5.29         0.72        17.72 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       14.96        18.18        16.21         0.79        12.39         3.65 
TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-8491 
       20.22         4.01         2.30        21.04         0.16        26.63 
TCGA-94-A5I6 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-L3-A4E7 
       17.69         2.76        30.81        30.67        27.16        12.89 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HQ TCGA-NK-A5CT 
        4.54        51.78         4.21        39.85        14.73        65.49 
TCGA-NK-A5CX TCGA-O2-A52Q 
        3.65         3.72 

$`DEL PEAK 41(17Q11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 
       12.20         7.46        75.75        79.46       117.57        11.34 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 
       92.15        36.07         1.64        86.96         6.18         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
      154.32        49.94        27.19        46.88        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       60.89        34.78        15.58        31.73       122.43         9.34 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 
       43.23        31.63        88.11        41.69        10.82        21.99 
TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1017 
        7.33        14.93         4.31        64.21        14.10        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       20.48        35.08        48.33        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 
       32.02         9.57        11.77        31.73        63.55        14.63 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
       44.25        54.28        71.34        79.20        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
       30.12        62.86        56.32        22.06         7.63       133.74 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 
       98.01        79.53       174.08       103.53        14.07         1.55 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       19.76        27.02         4.70         0.30        36.62         6.94 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
      118.36        27.16         2.63        28.96        32.88        31.27 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 TCGA-34-5927 
       65.23        67.79        56.38         9.07        12.00        30.94 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-37-3783 TCGA-37-3792 
       18.15         4.96         1.12        26.43         3.95         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 
        6.58         8.12         7.46         7.82         6.81         3.39 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
       47.80        74.07        44.75        68.58        55.20        70.03 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
       60.79         1.71         1.94        27.39        36.39        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-5668 
       35.70        17.88        17.06        40.21        27.02        18.38 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 
       12.36        24.89         5.46         3.81         7.76        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-46-3768 
       13.38        11.77         2.93        11.61         9.73         9.99 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       13.91         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7811 TCGA-56-1622 TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 
        8.75        28.96         2.04         0.62         0.99         0.43 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 
        1.45         0.85         6.51         0.10         3.48        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8626 
       17.00        14.07        16.77         1.81        22.75         9.93 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR 
       15.81        19.23        13.32        17.85        18.74         0.13 
TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 TCGA-58-A46J 
        0.26        13.25        13.55        29.95        16.47        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 
       34.36        56.65        35.24        29.92        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       96.82        37.94        21.93        80.45        49.48        66.54 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2716 TCGA-60-2722 TCGA-60-2725 
       41.42         9.01        35.34        48.49        29.85        26.83 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
       11.77       102.67        59.97        45.57        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV 
       25.28        89.29        78.28        16.37        25.41        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       53.88        34.59        16.96        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        0.99         2.01         0.92         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 
       25.05         2.01         1.02         2.01         2.01        23.01 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 TCGA-66-2787 TCGA-66-2790 
        3.02         2.01        19.00         3.98        40.01        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
        5.03        30.02         4.01        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
        6.94        16.18        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       11.18        89.98        20.78         0.49        42.28        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 
      106.95         0.16        46.78        15.75         6.51        53.95 
TCGA-77-8128 TCGA-77-8133 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 
       37.81        53.92       104.09        11.54        26.40         6.97 
TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 
        9.63        65.49        35.90         0.33       126.18       117.57 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 
        5.92        42.41        42.08        27.62         9.67        11.97 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
       12.99         6.41        36.53        31.30        32.91         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
        1.15        29.95        25.15        19.04        24.13        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 
       14.07        16.87        34.52        10.09        13.22        22.45 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 
       16.77         3.09        32.71         2.01         7.76        14.63 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       13.94        12.59         0.10        15.62        25.68        19.33 
TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-90-6837 
       24.36        19.73        12.56        15.85        14.96        24.92 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q 
        9.50         2.93        11.77        14.07        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 
        2.70         3.48         5.26        11.70         4.01         5.03 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
       14.14        16.14        49.87        57.07        18.31        17.46 
TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53A 
       19.36        16.57         8.42        21.34         3.88        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
        2.01        27.02        21.21        20.32        18.58        20.71 
TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
       19.10        16.11        13.18        13.41        11.84         0.07 
TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN 
       64.08         1.22        45.37        13.74         2.89        37.22 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5D1 
       30.58        24.00        29.75        22.78        83.57        16.80 
TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
        0.43        33.07        12.72        43.89         8.58        11.18 
TCGA-XC-AA0X 
        0.20 

  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                          0.03                           0.07 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                        151.27                         174.08 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                        20.235                         18.840 
[1] "0.0 - 151.3 (20.2)" "0.1 - 174.1 (18.8)"
[1] "hr=" "1.1"
D71V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(17Q11.2) MUTATED         0       25       44        0        10
  DEL PEAK 41(17Q11.2) WILD-TYPE       2       62      107        2        53
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(17Q11.2) MUTATED          19         1         22          7
  DEL PEAK 41(17Q11.2) WILD-TYPE        73         2         40         14
                                vv
clus                             STAGE IV
  DEL PEAK 41(17Q11.2) MUTATED          3
  DEL PEAK 41(17Q11.2) WILD-TYPE        4
D71V3, multiclass
            clus
vv           DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                             25                             62
  STAGE IB                             44                            107
  STAGE II                              0                              2
  STAGE IIA                            10                             53
  STAGE IIB                            19                             73
  STAGE III                             1                              2
  STAGE IIIA                           22                             40
  STAGE IIIB                            7                             14
  STAGE IV                              3                              4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 41(17Q11.2) MUTATED    29  70  25   7
  DEL PEAK 41(17Q11.2) WILD-TYPE  82 220  44  16
D71V4, multiclass
    clus
vv   DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  T1                           29                             82
  T2                           70                            220
  T3                           25                             44
  T4                            7                             16
[1] 4 2
[1] TRUE
[1] "dimension of 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(17Q11.2) MUTATED    91  20  14   2
  DEL PEAK 41(17Q11.2) WILD-TYPE 221 111  25   3
D71V5, multiclass
    clus
vv   DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  N0                           91                            221
  N1                           20                            111
  N2                           14                             25
  N3                            2                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q11.2) MUTATED   103   3
  DEL PEAK 41(17Q11.2) WILD-TYPE 301   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED    103    3
  DEL PEAK 41(17Q11.2) WILD-TYPE  301    4
   clus
vv  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  0                          103                            301
  1                            3                              4
[1] 2 2
[1] FALSE
D71V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q11.2) MUTATED    37  94
  DEL PEAK 41(17Q11.2) WILD-TYPE  90 272
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED     37   94
  DEL PEAK 41(17Q11.2) WILD-TYPE   90  272
        clus
vv       DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  FEMALE                           37                             90
  MALE                             94                            272
[1] 2 2
[1] FALSE
D71V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 41(17Q11.2) MUTATED                                       2
  DEL PEAK 41(17Q11.2) WILD-TYPE                                    13
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 41(17Q11.2) MUTATED                                         0
  DEL PEAK 41(17Q11.2) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 41(17Q11.2) MUTATED                                        1
  DEL PEAK 41(17Q11.2) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 41(17Q11.2) MUTATED                                         1
  DEL PEAK 41(17Q11.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(17Q11.2) MUTATED                                                           127
  DEL PEAK 41(17Q11.2) WILD-TYPE                                                         343
D71V9, multiclass
                                                             clus
vv                                                            DEL PEAK 41(17Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  2
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          127
                                                             clus
vv                                                            DEL PEAK 41(17Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            343
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V10, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q11.2) MUTATED     2 129
  DEL PEAK 41(17Q11.2) WILD-TYPE  11 351
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED      2  129
  DEL PEAK 41(17Q11.2) WILD-TYPE   11  351
     clus
vv    DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  NO                             2                             11
  YES                          129                            351
[1] 2 2
[1] FALSE
D71V11, continuous
D71V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(17Q11.2) MUTATED   102   2   1   9
  DEL PEAK 41(17Q11.2) WILD-TYPE 292  10   3  13
D71V13, multiclass
    clus
vv   DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  R0                          102                            292
  R1                            2                             10
  R2                            1                              3
  RX                            9                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(17Q11.2) MUTATED       3                        12    82
  DEL PEAK 41(17Q11.2) WILD-TYPE     6                        19   258
D71V14, multiclass
                           clus
vv                          DEL PEAK 41(17Q11.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                               82
                           clus
vv                          DEL PEAK 41(17Q11.2) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             19
  WHITE                                                258
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V15, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q11.2) MUTATED     3  84
  DEL PEAK 41(17Q11.2) WILD-TYPE   5 225
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED      3   84
  DEL PEAK 41(17Q11.2) WILD-TYPE    5  225
                        clus
vv                       DEL PEAK 41(17Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           84
                        clus
vv                       DEL PEAK 41(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            225
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 42(17Q25.3) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(17Q25.3) MUTATED    62  34
  DEL PEAK 42(17Q25.3) WILD-TYPE 219 162
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                            96                            381 
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                            34                            162 
$`DEL PEAK 42(17Q25.3) MUTATED`
TCGA-18-3415 TCGA-18-3421 TCGA-21-1070 TCGA-21-1075 TCGA-21-A5DI TCGA-22-1011 
       92.15        86.96       119.54        70.16        32.19         1.74 
TCGA-22-1016 TCGA-22-5472 TCGA-22-5482 TCGA-33-4538 TCGA-33-4583 TCGA-33-A4WN 
       27.02        64.93        11.74        98.01       151.27         4.70 
TCGA-34-2600 TCGA-34-5241 TCGA-34-5929 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       61.61        16.93         4.96        20.91         3.95         0.43 
TCGA-37-3792 TCGA-37-5819 TCGA-39-5029 TCGA-43-2581 TCGA-43-5670 TCGA-43-A56U 
        0.39         3.39        24.33        38.66        27.91        14.20 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7810 TCGA-56-5898 TCGA-56-7580 TCGA-56-7822 
        0.39        28.34        30.35        18.25         1.32        17.49 
TCGA-56-8503 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4ZJ TCGA-56-A5DR 
        1.35         1.18         9.93        20.25        21.04         0.13 
TCGA-58-8388 TCGA-58-8393 TCGA-60-2695 TCGA-60-2696 TCGA-60-2708 TCGA-60-2714 
       13.55        34.78        21.11         3.58        80.45        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5ML 
       42.64         3.19        32.32        70.62        66.61        45.57 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 
       12.03        12.00        24.95         1.97        25.97         4.04 
TCGA-66-2790 TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7337 
       22.98        14.73        29.56        75.09        23.28       106.95 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8144 TCGA-77-8150 
       37.81        82.92        12.59        17.72        27.39        54.41 
TCGA-77-A5G1 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-7697 TCGA-85-7710 TCGA-85-7844 
      132.36        30.81        38.86        34.95         1.38        29.95 
TCGA-85-7950 TCGA-85-8070 TCGA-85-8287 TCGA-85-8288 TCGA-85-8355 TCGA-85-8479 
       18.94        31.56         0.76        13.22         2.01         0.72 
TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A50Z TCGA-92-8063 TCGA-94-7557 TCGA-94-8035 
       17.72        18.18        16.21         4.01         0.16         4.01 
TCGA-94-A5I6 TCGA-96-7544 TCGA-98-8021 TCGA-98-A538 TCGA-L3-A4E7 TCGA-LA-A7SW 
       17.69        49.87        30.81        27.16        12.89        13.41 
TCGA-MF-A522 TCGA-NC-A5HK TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       11.84         4.21        22.78        65.49         3.65        16.80 

$`DEL PEAK 42(17Q25.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-4083 
       11.34        23.54        31.99        36.07         1.64         6.18 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 
        2.79       154.32        49.94        27.19        46.88        99.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       60.89        34.78        15.58        31.73       122.43         9.34 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 
      119.80        43.23        31.63        88.11        41.69        33.93 
TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
       10.82        21.99         7.33        14.93         4.31        64.21 
TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
       14.10        48.82        20.48        35.08        48.33        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
        0.56        38.17        34.75        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
        9.57        11.77        31.73        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 
        0.79        54.28        71.34        79.20        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
       62.86        56.32        16.64        22.06         7.63       133.74 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
       79.53       174.08       103.53        14.07        54.44         1.55 
TCGA-33-6737 TCGA-33-6738 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       19.76        27.02         0.30        36.62         6.94       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 
       44.19       118.36        27.16         2.63        31.50        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       32.88        31.27        65.23        67.79        56.38         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 
       23.24        12.00        30.94        18.15         1.12        27.19 
TCGA-34-8455 TCGA-34-8456 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        4.04        26.43         6.58         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        6.81         0.39        47.80        74.07        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 
       55.20        70.03        60.79         1.71         1.94        27.39 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 
       36.39        15.58        35.64        35.70        17.88        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-6143 
       40.21        22.49        27.02        33.11        18.38        12.36 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 
       24.89        21.47         5.46         3.81        19.59         7.76 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
       66.51        13.38        11.77         2.93        11.61         9.73 
TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 
       12.03         9.99        10.65        13.91         0.39        29.95 
TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
        5.46         8.75        27.45        28.96         0.10         2.04 
TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
        0.62         0.99         0.43         0.99         1.45         0.85 
TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        6.51         0.10         3.48        26.89        17.00        14.07 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D 
       16.77         1.81        22.75        10.36        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       19.23        13.32        17.85        18.74         0.26         2.76 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J 
        0.03        13.25        29.95        71.24        16.47        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 
       34.36        56.65        35.24        29.92        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 
       96.82        37.94        92.71        21.93        49.48        66.54 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2722 
       41.42         9.01        56.91        35.34        48.49        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MI 
       35.90        23.57        26.83        11.77       102.67        58.65 
TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       59.97        14.99        11.34        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       16.37        25.41        36.16        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       43.10         2.01        21.07         0.99         1.02         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        0.92         0.99        43.99        21.01        25.05         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
        2.01         1.02         2.01         2.01         7.07        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 TCGA-66-2787 
       19.00         3.02         2.01        19.00         3.98        40.01 
TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 
       22.98         5.03        30.02        10.06        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       49.05         2.73         6.64         6.94         8.02        13.35 
TCGA-68-A59I TCGA-77-6843 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 
       16.18        73.12        11.18        89.98        20.78         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       42.28        70.13         0.16        46.78        15.75         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 
       86.76        53.95        53.92        39.09       104.09        11.54 
TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
       26.40         6.97         9.63        65.49        35.90         0.33 
TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
      126.18       117.57        22.29         5.92        42.41        42.08 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       27.62         9.67        11.97        12.99         6.41        36.53 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
       31.30        32.91         1.15        25.15        19.04        24.13 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 
       14.07        16.87        34.52        10.09        22.45        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
        5.29         3.09        32.71         7.76        14.63        13.94 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC 
       12.59         0.10        15.62        25.68        19.33        14.96 
TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       24.36        19.73        12.56        15.85        14.96         0.79 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
       12.39         3.65        24.92         9.50         2.93        11.77 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
       14.07        20.22        22.62        10.59         2.70         3.48 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-8490 TCGA-94-8491 
        5.26         2.30        21.04        11.70         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I4 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
       14.14        16.14        57.07        18.31        17.46        19.36 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 TCGA-98-8023 TCGA-98-A539 
       16.57         8.42         2.76        30.67        21.34         3.88 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I 
       18.15         2.01        27.02        21.21        20.32        18.58 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HD TCGA-NC-A5HE 
       20.71        19.10        16.11        13.18         0.07        64.08 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL 
        4.54        51.78         1.22        45.37        13.74         2.89 
TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR 
       39.85        37.22        30.58        24.00        14.73        29.75 
TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       83.57         0.43        33.07         3.72        12.72        43.89 
TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
        8.58        11.18         0.20 

  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                          0.13                           0.03 
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                        151.27                         174.08 
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                         20.58                          19.04 
[1] "0.1 - 151.3 (20.6)" "0.0 - 174.1 (19.0)"
[1] "hr=" "1.3"
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(17Q25.3) MUTATED         0       19       36        0         7
  DEL PEAK 42(17Q25.3) WILD-TYPE       2       68      115        2        56
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(17Q25.3) MUTATED          23         0         13          3
  DEL PEAK 42(17Q25.3) WILD-TYPE        69         3         49         18
                                vv
clus                             STAGE IV
  DEL PEAK 42(17Q25.3) MUTATED          0
  DEL PEAK 42(17Q25.3) WILD-TYPE        7
D72V3, multiclass
            clus
vv           DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  STAGE I                               0                              2
  STAGE IA                             19                             68
  STAGE IB                             36                            115
  STAGE II                              0                              2
  STAGE IIA                             7                             56
  STAGE IIB                            23                             69
  STAGE III                             0                              3
  STAGE IIIA                           13                             49
  STAGE IIIB                            3                             18
  STAGE IV                              0                              7
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 42(17Q25.3) MUTATED    24  55  20   2
  DEL PEAK 42(17Q25.3) WILD-TYPE  87 235  49  21
D72V4, multiclass
    clus
vv   DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  T1                           24                             87
  T2                           55                            235
  T3                           20                             49
  T4                            2                             21
[1] 4 2
[1] TRUE
[1] "dimension of 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(17Q25.3) MUTATED    71  20   6   2
  DEL PEAK 42(17Q25.3) WILD-TYPE 241 111  33   3
D72V5, multiclass
    clus
vv   DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  N0                           71                            241
  N1                           20                            111
  N2                            6                             33
  N3                            2                              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"
D72V6, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q25.3) MUTATED    85   0
  DEL PEAK 42(17Q25.3) WILD-TYPE 319   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q25.3) MUTATED     85    0
  DEL PEAK 42(17Q25.3) WILD-TYPE  319    7
   clus
vv  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  0                           85                            319
  1                            0                              7
[1] 2 2
[1] FALSE
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q25.3) MUTATED    22  79
  DEL PEAK 42(17Q25.3) WILD-TYPE 105 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q25.3) MUTATED     22   79
  DEL PEAK 42(17Q25.3) WILD-TYPE  105  287
        clus
vv       DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  FEMALE                           22                            105
  MALE                             79                            287
[1] 2 2
[1] FALSE
D72V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 42(17Q25.3) MUTATED                                       4
  DEL PEAK 42(17Q25.3) WILD-TYPE                                    11
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 42(17Q25.3) MUTATED                                         0
  DEL PEAK 42(17Q25.3) WILD-TYPE                                       1
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 42(17Q25.3) MUTATED                                        1
  DEL PEAK 42(17Q25.3) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 42(17Q25.3) MUTATED                                         0
  DEL PEAK 42(17Q25.3) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(17Q25.3) MUTATED                                                            96
  DEL PEAK 42(17Q25.3) WILD-TYPE                                                         374
D72V9, multiclass
                                                             clus
vv                                                            DEL PEAK 42(17Q25.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  4
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           96
                                                             clus
vv                                                            DEL PEAK 42(17Q25.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   11
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            374
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q25.3) MUTATED     3  98
  DEL PEAK 42(17Q25.3) WILD-TYPE  10 382
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q25.3) MUTATED      3   98
  DEL PEAK 42(17Q25.3) WILD-TYPE   10  382
     clus
vv    DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  NO                             3                             10
  YES                           98                            382
[1] 2 2
[1] FALSE
D72V11, continuous
D72V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(17Q25.3) MUTATED    81   1   1   6
  DEL PEAK 42(17Q25.3) WILD-TYPE 313  11   3  16
D72V13, multiclass
    clus
vv   DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  R0                           81                            313
  R1                            1                             11
  R2                            1                              3
  RX                            6                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(17Q25.3) MUTATED       0                         7    70
  DEL PEAK 42(17Q25.3) WILD-TYPE     9                        24   270
D72V14, multiclass
                           clus
vv                          DEL PEAK 42(17Q25.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               70
                           clus
vv                          DEL PEAK 42(17Q25.3) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                             24
  WHITE                                                270
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V15, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q25.3) MUTATED     3  67
  DEL PEAK 42(17Q25.3) WILD-TYPE   5 242
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q25.3) MUTATED      3   67
  DEL PEAK 42(17Q25.3) WILD-TYPE    5  242
                        clus
vv                       DEL PEAK 42(17Q25.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       DEL PEAK 42(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            242
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 43(18Q23) MUTATION ANALYSIS
D73V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 43(18Q23) MUTATED   138  88
  DEL PEAK 43(18Q23) WILD-TYPE 143 108
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                         226                          251 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                          88                          108 
$`DEL PEAK 43(18Q23) MUTATED`
TCGA-18-3412 TCGA-18-3414 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 
       11.34        23.54        31.99        36.07        86.96         2.79 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 
      119.54        46.88        31.73       122.43        43.23        31.63 
TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1016 TCGA-22-1017 
       33.93        10.82        32.19        14.93        27.02        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4613 
       20.48        35.08        24.13        38.17        34.75        11.77 
TCGA-22-5471 TCGA-22-5473 TCGA-22-5491 TCGA-22-5492 TCGA-33-4533 TCGA-33-4538 
       31.73        63.55        56.32        16.64       133.74        98.01 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4589 TCGA-33-6737 
       79.53       174.08       103.53       151.27         1.55        19.76 
TCGA-33-6738 TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
       27.02         0.30         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-5231 TCGA-34-5236 
       27.16        31.50        28.96        32.88        65.23         9.07 
TCGA-34-5241 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4130 
       16.93        27.19         4.04        20.91         0.39         8.12 
TCGA-37-4133 TCGA-39-5016 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5036 
        7.82        74.07        60.79         1.71        24.33        35.64 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 TCGA-43-5670 TCGA-43-6770 
       40.21        22.49        27.02        18.38        27.91        21.47 
TCGA-43-7656 TCGA-43-8116 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-52-7810 
       19.59        11.77         9.99        10.65         0.39        30.35 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7221 TCGA-56-7222 
       27.45        28.96         0.10         2.04         0.99         0.43 
TCGA-56-7223 TCGA-56-7730 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
        0.99         6.51        17.49         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8624 TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BY 
        1.35         1.18         9.93        15.81        19.23        17.85 
TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8386 TCGA-58-A46K TCGA-58-A46M 
       18.74         0.13         2.76         0.03        34.36        35.24 
TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 
       10.22        92.71        21.93        80.45        50.33        42.64 
TCGA-60-2720 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5MP 
        3.19        11.77       102.67        66.61        59.97        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MW TCGA-66-2734 
       89.29        78.28        16.37        25.41        53.88        43.10 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 
        2.01         0.99         1.02        21.01         0.99         2.01 
TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 
        1.02         2.01        19.00         3.02        12.03         3.98 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
        1.97        40.01        22.98         5.03        30.02        54.08 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59J TCGA-77-6842 TCGA-77-6845 
       49.05         2.73         6.94        14.73        29.56        23.28 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 
        0.49        42.28       106.95        82.92        12.59        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 TCGA-77-8154 
       17.72       104.09        11.54        27.39         9.63        35.90 
TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-6175 
        0.33       132.36       117.57        22.29        42.41         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       11.97        12.99         6.41        36.53        34.95        31.30 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 
        1.15        29.95        18.94        19.04        14.07        16.87 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       34.52        10.09         0.76         5.29         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JC 
        2.01         0.72        12.59         0.10        15.62        14.96 
TCGA-85-A4QQ TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 
       18.18        15.85        14.96        12.39         3.65         9.50 
TCGA-90-7769 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-7033 
       11.77        20.22         3.48         4.01         5.26        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8491 TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-8169 
        0.16        11.70        26.63        16.14        17.69        18.31 
TCGA-96-8170 TCGA-96-A4JK TCGA-98-7454 TCGA-98-8020 TCGA-98-8022 TCGA-98-8023 
       17.46        19.36         8.42         2.76        30.67        21.34 
TCGA-98-A538 TCGA-98-A539 TCGA-98-A53B TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A524 
       27.16         3.88         2.01        20.71        19.10        16.11 
TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       13.41         0.07        64.08        51.78         1.22        45.37 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ 
        4.21         2.89        39.85        37.22        24.00        14.73 
TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-O2-A52N TCGA-O2-A52Q 
       29.75        16.80        33.07         3.72 

$`DEL PEAK 43(18Q23) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
       12.20         7.46        75.75        79.46         4.80       117.57 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4083 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
       92.15         1.64         6.18       154.32        49.94        27.19 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 
       99.16        70.16        60.89        34.78        15.58         9.34 
TCGA-21-1082 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
      119.80        88.11        41.69        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4594 TCGA-22-4596 TCGA-22-4604 
       64.21         1.74        14.10        48.33         0.56        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5472 TCGA-22-5474 TCGA-22-5477 
       32.02        19.30         9.57        64.93        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
        0.79        54.28        71.34        79.20        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4586 TCGA-33-4587 
       30.12        62.86        22.06         7.63        14.07        54.44 
TCGA-33-A4WN TCGA-33-AAS8 TCGA-34-2596 TCGA-34-2600 TCGA-34-2609 TCGA-34-5232 
        4.70        36.62         2.63        61.61        31.27        67.79 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       56.38        23.24        12.00        30.94        18.15         4.96 
TCGA-34-7107 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 
        1.12        26.43         3.95         0.43         6.58         7.46 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
        6.81         0.39         3.39        47.80        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
       55.20        70.03         1.94        27.39        36.39        15.58 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 
       35.70        17.88        17.06        38.66        33.11        12.36 
TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 
       24.89         5.46         3.81         7.76        66.51        13.38 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 
        2.93        11.61         9.73        14.20        12.03        13.91 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 
        0.39        29.95        28.34         5.46         8.75        18.25 
TCGA-56-6546 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-8308 
        0.62         1.45         1.32         0.85         0.10        17.00 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D 
       16.77         1.81        22.75        10.36        20.25        20.94 
TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
       13.32        21.04         0.26        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N 
       71.24        16.47        34.78        85.12        56.65        29.92 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 
       21.11         3.58        12.23        96.82        37.94        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 
       66.54        41.42         9.01        56.91        35.34        48.49 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MG 
       32.32        29.85        35.90        23.57        26.83        70.62 
TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MV TCGA-63-A5MY 
       58.65        45.57        14.99        11.34        36.16        34.59 
TCGA-66-2727 TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
       16.96        21.07         2.01         0.92         0.99        43.99 
TCGA-66-2759 TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 TCGA-66-2778 
       25.05         2.01         7.07        23.01         2.01        19.00 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2793 
       12.00        24.95        25.97        22.98         4.04        10.06 
TCGA-66-2795 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-77-6843 
        4.01         6.64         8.02        13.35        16.18        73.12 
TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7335 TCGA-77-7338 
       75.09        11.18        89.98        20.78        70.13         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
       46.78        15.75         6.51        86.76        53.95        37.81 
TCGA-77-8133 TCGA-77-8143 TCGA-77-8145 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5FZ 
       53.92        26.40         6.97        54.41        65.49       126.18 
TCGA-77-A5G7 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-7699 
        5.92        42.08        30.81        27.62        38.86        32.91 
TCGA-85-7710 TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8288 TCGA-85-8350 
        1.38        25.15        24.13        31.56        13.22        22.45 
TCGA-85-8351 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4CN 
       16.77         7.76        14.63        13.94        25.68        19.33 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A513 
       17.72        24.36        19.73        12.56        16.21         0.79 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       24.92         2.93        14.07        22.62        10.59         2.70 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 
        2.30         4.01         5.03        14.14        49.87        57.07 
TCGA-96-A4JL TCGA-98-8021 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H 
       16.57        30.81        18.15        27.02        21.21        20.32 
TCGA-98-A53I TCGA-L3-A4E7 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HJ 
       18.58        12.89        13.18        11.84         4.54        13.74 
TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE 
       30.58        22.78        83.57        65.49         3.65         0.43 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89         8.58        11.18         0.20 

  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                        0.03                         0.10 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                      174.08                       154.32 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                       19.07                        19.30 
[1] "0.0 - 174.1 (19.1)" "0.1 - 154.3 (19.3)"
[1] "hr=" "1.1"
D73V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(18Q23) MUTATED         1       36       72        0        29
  DEL PEAK 43(18Q23) WILD-TYPE       1       51       79        2        34
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(18Q23) MUTATED          48         1         32          5
  DEL PEAK 43(18Q23) WILD-TYPE        44         2         30         16
                              vv
clus                           STAGE IV
  DEL PEAK 43(18Q23) MUTATED          5
  DEL PEAK 43(18Q23) WILD-TYPE        2
D73V3, multiclass
            clus
vv           DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  STAGE I                             1                            1
  STAGE IA                           36                           51
  STAGE IB                           72                           79
  STAGE II                            0                            2
  STAGE IIA                          29                           34
  STAGE IIB                          48                           44
  STAGE III                           1                            2
  STAGE IIIA                         32                           30
  STAGE IIIB                          5                           16
  STAGE IV                            5                            2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  DEL PEAK 43(18Q23) MUTATED    47 137  39   8
  DEL PEAK 43(18Q23) WILD-TYPE  64 153  30  15
D73V4, multiclass
    clus
vv   DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  T1                         47                           64
  T2                        137                          153
  T3                         39                           30
  T4                          8                           15
[1] 4 2
[1] TRUE
[1] "dimension of 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(18Q23) MUTATED   142  66  18   1
  DEL PEAK 43(18Q23) WILD-TYPE 170  65  21   4
D73V5, multiclass
    clus
vv   DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  N0                        142                          170
  N1                         66                           65
  N2                         18                           21
  N3                          1                            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 43(18Q23) MUTATED   188   5
  DEL PEAK 43(18Q23) WILD-TYPE 216   2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED    188    5
  DEL PEAK 43(18Q23) WILD-TYPE  216    2
   clus
vv  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  0                        188                          216
  1                          5                            2
[1] 2 2
[1] FALSE
D73V7, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED    45 186
  DEL PEAK 43(18Q23) WILD-TYPE  82 180
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED     45  186
  DEL PEAK 43(18Q23) WILD-TYPE   82  180
        clus
vv       DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  FEMALE                         45                           82
  MALE                          186                          180
[1] 2 2
[1] FALSE
D73V8, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 43(18Q23) MUTATED                                       6
  DEL PEAK 43(18Q23) WILD-TYPE                                     9
                              vv
clus                           LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 43(18Q23) MUTATED                                         0
  DEL PEAK 43(18Q23) WILD-TYPE                                       1
                              vv
clus                           LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 43(18Q23) MUTATED                                        3
  DEL PEAK 43(18Q23) WILD-TYPE                                      3
                              vv
clus                           LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 43(18Q23) MUTATED                                         0
  DEL PEAK 43(18Q23) WILD-TYPE                                       1
                              vv
clus                           LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(18Q23) MUTATED                                                           222
  DEL PEAK 43(18Q23) WILD-TYPE                                                         248
D73V9, multiclass
                                                             clus
vv                                                            DEL PEAK 43(18Q23) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        222
                                                             clus
vv                                                            DEL PEAK 43(18Q23) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          248
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED     6 225
  DEL PEAK 43(18Q23) WILD-TYPE   7 255
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED      6  225
  DEL PEAK 43(18Q23) WILD-TYPE    7  255
     clus
vv    DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  NO                           6                            7
  YES                        225                          255
[1] 2 2
[1] FALSE
D73V11, continuous
D73V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 43(18Q23) MUTATED   187   4   1  13
  DEL PEAK 43(18Q23) WILD-TYPE 207   8   3   9
D73V13, multiclass
    clus
vv   DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  R0                        187                          207
  R1                          4                            8
  R2                          1                            3
  RX                         13                            9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(18Q23) MUTATED       4                        16   159
  DEL PEAK 43(18Q23) WILD-TYPE     5                        15   181
D73V14, multiclass
                           clus
vv                          DEL PEAK 43(18Q23) MUTATED
  ASIAN                                              4
  BLACK OR AFRICAN AMERICAN                         16
  WHITE                                            159
                           clus
vv                          DEL PEAK 43(18Q23) WILD-TYPE
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           15
  WHITE                                              181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V15, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED     5 142
  DEL PEAK 43(18Q23) WILD-TYPE   3 167
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED      5  142
  DEL PEAK 43(18Q23) WILD-TYPE    3  167
                        clus
vv                       DEL PEAK 43(18Q23) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        142
                        clus
vv                       DEL PEAK 43(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          167
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 44(19P13.3) MUTATION ANALYSIS
D74V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(19P13.3) MUTATED   139  86
  DEL PEAK 44(19P13.3) WILD-TYPE 142 110
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           225                            252 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            86                            110 
$`DEL PEAK 44(19P13.3) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3411 TCGA-18-3412 TCGA-18-3417 TCGA-18-5592 
        7.46        79.46       117.57        11.34        36.07        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 
      119.54        46.88        34.78       122.43         9.34        43.23 
TCGA-21-5783 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 
       88.11        10.82        32.19        21.99         4.31        64.21 
TCGA-22-1012 TCGA-22-4591 TCGA-22-4594 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 
       14.10        20.48        48.33        34.75        32.02        19.30 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5481 TCGA-22-5483 TCGA-22-5492 TCGA-22-A5C4 
       14.63         0.79        79.20        18.84        16.64        22.06 
TCGA-33-4532 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6737 
        7.63        79.53       103.53        14.07        54.44        19.76 
TCGA-33-6738 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2604 
       27.02         6.94       110.99        44.19        27.16        31.50 
TCGA-34-2608 TCGA-34-5236 TCGA-34-5241 TCGA-34-5928 TCGA-34-5929 TCGA-34-8456 
       32.88         9.07        16.93        18.15         4.96        26.43 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        0.43         0.39         6.58         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
        6.81         0.39         3.39        47.80        44.75        68.58 
TCGA-39-5029 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
       24.33        36.39        15.58        35.64        35.70        17.06 
TCGA-43-2576 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
       40.21        22.49        27.02        33.11        18.38        27.91 
TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-7657 TCGA-43-8115 TCGA-43-A56V 
       12.36        21.47        19.59         7.76        13.38        12.03 
TCGA-46-6025 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
       10.65         0.39        29.95         5.46        30.35         8.75 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 
       28.96         0.10        18.25         0.62         0.43         0.99 
TCGA-56-7579 TCGA-56-7730 TCGA-56-7822 TCGA-56-8624 TCGA-56-8629 TCGA-56-A49D 
        1.45         6.51        17.49         1.18        15.81        20.94 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR TCGA-56-A62T TCGA-58-8388 TCGA-58-8390 
       21.04        18.74         0.13         2.76        13.55        29.95 
TCGA-58-8393 TCGA-58-A46L TCGA-60-2696 TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 
       34.78        56.65         3.58        10.22        92.71        21.93 
TCGA-60-2711 TCGA-60-2714 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-63-A5MB 
       41.42        50.33         3.19        29.85        35.90       102.67 
TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       58.65        25.28        89.29        78.28        16.37        36.16 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 
       34.59        16.96        43.10         1.02         2.01         0.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
       21.01        25.05         1.02         2.01         7.07        19.00 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
        2.01        12.03         3.98        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-66-2795 
       25.97        22.98         4.04        22.98        10.06         4.01 
TCGA-68-7756 TCGA-68-8250 TCGA-68-A59I TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 
        6.64         8.02        16.18        73.12        23.28        11.18 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8136 
        0.16        46.78        86.76        53.95        82.92        39.09 
TCGA-77-8138 TCGA-77-8144 TCGA-77-8145 TCGA-77-8156 TCGA-77-A5G1 TCGA-85-6560 
       17.72        27.39         6.97         0.33       132.36        11.97 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       36.53        34.95        31.30        32.91         1.38         1.15 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       31.56        14.07        16.87        34.52        10.09         0.76 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 TCGA-85-8584 
       22.45        16.77         5.29        32.71         0.72        12.59 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A510 TCGA-85-A53L 
        0.10        25.68        17.72        14.96        15.85        12.39 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 
       14.07        20.22        22.62        10.59         3.48         4.01 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8490 TCGA-94-A4VJ 
        2.30        21.04         0.16        11.70         5.03        14.14 
TCGA-94-A5I6 TCGA-96-8169 TCGA-98-8020 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A 
       17.69        18.31         2.76        27.16         3.88        18.15 
TCGA-98-A53B TCGA-98-A53J TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD 
        2.01        20.71        13.18        13.41        11.84         0.07 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HM 
       51.78        45.37        13.74         4.21         2.89        39.85 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       37.22        24.00        14.73        65.49         3.65        16.80 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-XC-AA0X 
       33.07         3.72         0.20 

$`DEL PEAK 44(19P13.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3410 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 
       12.20        75.75         4.80        23.54        92.15        31.99 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
        1.64        86.96         6.18         2.79       154.32        27.19 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 
       99.16        70.16        60.89        15.58        31.73       119.80 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1000 TCGA-22-1011 
       31.63        41.69        33.93         7.33        14.93         1.74 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
       27.02        48.82        35.08        24.13         0.56        38.17 
TCGA-22-4604 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
       13.12         9.57        11.77        31.73        64.93        63.55 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
       44.25        54.28        71.34        11.74        30.12        62.86 
TCGA-22-5491 TCGA-33-4533 TCGA-33-4538 TCGA-33-4566 TCGA-33-4583 TCGA-33-4589 
       56.32       133.74        98.01       174.08       151.27         1.55 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 
        4.70         0.30        36.62       118.36         2.63        61.61 
TCGA-34-2605 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
       28.96        31.27        65.23        67.79        56.38        23.24 
TCGA-34-5240 TCGA-34-5927 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX 
       12.00        30.94         1.12        27.19         4.04        20.91 
TCGA-37-3783 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
        3.95        74.07        55.20        70.03        60.79         1.71 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5039 TCGA-43-2581 TCGA-43-6647 TCGA-43-6771 
        1.94        27.39        17.88        38.66        24.89         5.46 
TCGA-43-6773 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 
        3.81        66.51        11.77         2.93        11.61         9.73 
TCGA-43-A56U TCGA-46-3768 TCGA-46-6026 TCGA-51-4080 TCGA-52-7622 TCGA-52-7812 
       14.20         9.99        13.91         0.39        28.34        27.45 
TCGA-56-6545 TCGA-56-7221 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-8304 
        2.04         0.99         1.32         0.85         0.10         3.48 
TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
       26.89        17.00        14.07         1.35        16.77         1.81 
TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX 
       22.75        10.36         9.93        20.25        19.23        13.32 
TCGA-56-A4BY TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8391 TCGA-58-8392 
       17.85         0.26         0.03        13.25        71.24        16.47 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 
       85.12        34.36        35.24        29.92        21.11        12.23 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2712 
       96.82        37.94        80.45        49.48        66.54         9.01 
TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2721 TCGA-60-2724 
       56.91        35.34        48.49        42.64        32.32        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML 
       26.83        11.77        70.62        66.61        59.97        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MU TCGA-63-A5MW TCGA-66-2737 TCGA-66-2742 
       14.99        11.34        25.41        53.88         2.01        21.07 
TCGA-66-2744 TCGA-66-2755 TCGA-66-2757 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
        0.99         0.92        43.99         0.99         2.01         2.01 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2778 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 
       23.01         3.02        19.00        40.01         5.03        30.02 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J 
       54.08        49.05         2.73         6.94        13.35        14.73 
TCGA-77-6842 TCGA-77-6844 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
       29.56        75.09        89.98        20.78         0.49        42.28 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 
       70.13       106.95        15.75         6.51        37.81        12.59 
TCGA-77-8133 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 
       53.92       104.09        11.54        26.40         9.63        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       65.49        35.90       126.18       117.57        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       42.41        42.08        30.81        27.62        38.86         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
       12.99         6.41        29.95        18.94        25.15        19.04 
TCGA-85-8052 TCGA-85-8288 TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 
       24.13        13.22         3.09         2.01         7.76        14.63 
TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       13.94        15.62        19.33        24.36        18.18        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 
       12.56        16.21        14.96         0.79         3.65        24.92 
TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-92-7340 TCGA-92-8064 TCGA-94-8035 
        9.50         2.93        11.77         2.70         5.26         4.01 
TCGA-94-8491 TCGA-94-A5I4 TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JK 
       26.63        16.14        49.87        57.07        17.46        19.36 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53C 
       16.57         8.42        30.81        30.67        21.34        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
       21.21        20.32        18.58        19.10        12.89        16.11 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HO TCGA-NC-A5HR TCGA-NC-A5HT 
       64.08         4.54         1.22        30.58        29.75        22.78 
TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       83.57         0.43        12.72        43.89         8.58        11.18 

  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                        132.36                         174.08 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                         17.72                          21.09 
[1] "0.1 - 132.4 (17.7)" "0.0 - 174.1 (21.1)"
[1] "hr=" "1.1"
D74V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(19P13.3) MUTATED         1       37       72        0        31
  DEL PEAK 44(19P13.3) WILD-TYPE       1       50       79        2        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(19P13.3) MUTATED          38         1         35          9
  DEL PEAK 44(19P13.3) WILD-TYPE        54         2         27         12
                                vv
clus                             STAGE IV
  DEL PEAK 44(19P13.3) MUTATED          3
  DEL PEAK 44(19P13.3) WILD-TYPE        4
D74V3, multiclass
            clus
vv           DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             37                             50
  STAGE IB                             72                             79
  STAGE II                              0                              2
  STAGE IIA                            31                             32
  STAGE IIB                            38                             54
  STAGE III                             1                              2
  STAGE IIIA                           35                             27
  STAGE IIIB                            9                             12
  STAGE IV                              3                              4
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 44(19P13.3) MUTATED    50 138  32   9
  DEL PEAK 44(19P13.3) WILD-TYPE  61 152  37  14
D74V4, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  T1                           50                             61
  T2                          138                            152
  T3                           32                             37
  T4                            9                             14
[1] 4 2
[1] TRUE
[1] "dimension of 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(19P13.3) MUTATED   152  51  23   2
  DEL PEAK 44(19P13.3) WILD-TYPE 160  80  16   3
D74V5, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  N0                          152                            160
  N1                           51                             80
  N2                           23                             16
  N3                            2                              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"
D74V6, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED   188   3
  DEL PEAK 44(19P13.3) WILD-TYPE 216   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED    188    3
  DEL PEAK 44(19P13.3) WILD-TYPE  216    4
   clus
vv  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  0                          188                            216
  1                            3                              4
[1] 2 2
[1] FALSE
D74V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED    53 176
  DEL PEAK 44(19P13.3) WILD-TYPE  74 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     53  176
  DEL PEAK 44(19P13.3) WILD-TYPE   74  190
        clus
vv       DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  FEMALE                           53                             74
  MALE                            176                            190
[1] 2 2
[1] FALSE
D74V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                                       7
  DEL PEAK 44(19P13.3) WILD-TYPE                                     8
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                                         1
  DEL PEAK 44(19P13.3) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 44(19P13.3) MUTATED                                        3
  DEL PEAK 44(19P13.3) WILD-TYPE                                      3
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                                         1
  DEL PEAK 44(19P13.3) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(19P13.3) MUTATED                                                           217
  DEL PEAK 44(19P13.3) WILD-TYPE                                                         253
D74V9, multiclass
                                                             clus
vv                                                            DEL PEAK 44(19P13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          217
                                                             clus
vv                                                            DEL PEAK 44(19P13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            253
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED     6 223
  DEL PEAK 44(19P13.3) WILD-TYPE   7 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      6  223
  DEL PEAK 44(19P13.3) WILD-TYPE    7  257
     clus
vv    DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  NO                             6                              7
  YES                          223                            257
[1] 2 2
[1] FALSE
D74V11, continuous
D74V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(19P13.3) MUTATED   180   6   1  10
  DEL PEAK 44(19P13.3) WILD-TYPE 214   6   3  12
D74V13, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  R0                          180                            214
  R1                            6                              6
  R2                            1                              3
  RX                           10                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(19P13.3) MUTATED       3                        20   153
  DEL PEAK 44(19P13.3) WILD-TYPE     6                        11   187
D74V14, multiclass
                           clus
vv                          DEL PEAK 44(19P13.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           20
  WHITE                                              153
                           clus
vv                          DEL PEAK 44(19P13.3) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V15, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED     3 148
  DEL PEAK 44(19P13.3) WILD-TYPE   5 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      3  148
  DEL PEAK 44(19P13.3) WILD-TYPE    5  161
                        clus
vv                       DEL PEAK 44(19P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          148
                        clus
vv                       DEL PEAK 44(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            161
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 45(19Q13.32) MUTATION ANALYSIS
D75V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 45(19Q13.32) MUTATED    91  47
  DEL PEAK 45(19Q13.32) WILD-TYPE 190 149
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                            138                             339 
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                             47                             149 
$`DEL PEAK 45(19Q13.32) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 TCGA-18-3416 
       12.20        79.46         4.80       117.57        11.34        31.99 
TCGA-18-5592 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 TCGA-22-0944 TCGA-22-1005 
       49.94        60.89        34.78       122.43         7.33        64.21 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4595 TCGA-22-4607 TCGA-22-4613 TCGA-22-5478 
       48.82        48.33        24.13        19.30        11.77         0.79 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4586 TCGA-33-AASB TCGA-33-AASI TCGA-34-2600 
        7.63        98.01        14.07         6.94        44.19        61.61 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-37-4129 TCGA-37-4133 
       16.93        30.94         4.96         1.12         6.58         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 TCGA-39-5036 TCGA-43-3394 TCGA-43-6770 
        6.81         0.39        74.07        35.64        27.02        21.47 
TCGA-43-7657 TCGA-43-8116 TCGA-43-A474 TCGA-46-6026 TCGA-51-4081 TCGA-52-7809 
        7.76        11.77        11.61        13.91        29.95         5.46 
TCGA-52-7810 TCGA-56-5897 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7822 
       30.35         0.10         0.99         0.43         1.45        17.49 
TCGA-56-8308 TCGA-56-8622 TCGA-56-A4BX TCGA-56-A62T TCGA-58-8386 TCGA-58-8392 
       17.00         1.81        13.32         2.76         0.03        16.47 
TCGA-58-A46L TCGA-60-2695 TCGA-60-2696 TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 
       56.65        21.11         3.58        10.22        92.71        21.93 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2726 TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MS 
       50.33        42.64        11.77        45.57        25.28        78.28 
TCGA-66-2727 TCGA-66-2753 TCGA-66-2766 TCGA-66-2777 TCGA-66-2781 TCGA-66-2783 
       16.96         1.02         1.02         2.01         3.98        24.95 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-77-6845 
       30.02        54.08        49.05         2.73         6.64        23.28 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7463 TCGA-77-8128 TCGA-77-8143 
        0.49        42.28         0.16        46.78        37.81        26.40 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G8 
       27.39         9.63        65.49        35.90         0.33        42.41 
TCGA-77-A5GA TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7843 
       42.08        11.97        12.99        36.53        34.95         1.15 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 
       18.94        25.15        31.56        14.07        16.87         0.76 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL 
       16.77         3.09         2.01        12.59         0.10        25.68 
TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A53L TCGA-90-A4ED TCGA-92-7341 TCGA-94-7557 
       14.96        19.73        12.39        20.22         3.48         0.16 
TCGA-94-7943 TCGA-94-8490 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8021 
       11.70         5.03        16.14        57.07        19.36        30.81 
TCGA-98-A539 TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
        3.88        20.71        16.11        13.18        13.41        11.84 
TCGA-NC-A5HD TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        0.07        51.78        45.37        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-XC-AA0X 
       37.22        24.00        29.75        16.80         3.72         0.20 

$`DEL PEAK 45(19Q13.32) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
        7.46        75.75        23.54        92.15        36.07         1.64 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 TCGA-21-1070 
       86.96         6.18         2.79       154.32        27.19       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 
       46.88        99.16        70.16        15.58        31.73         9.34 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 
      119.80        43.23        31.63        88.11        41.69        33.93 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1011 
       10.82        32.19        21.99        14.93         4.31         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 
       14.10        27.02        20.48        35.08         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 
       34.75        13.12        32.02         9.57        31.73        64.93 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
       63.55        14.63        44.25        54.28        71.34        79.20 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       11.74        18.84        30.12        62.86        56.32        16.64 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       22.06       133.74        79.53       174.08       103.53       151.27 
TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       54.44         1.55        19.76        27.02         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2604 
       36.62       110.99       118.36        27.16         2.63        31.50 
TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       28.96        32.88        31.27        65.23        67.79        56.38 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 
        9.07        23.24        12.00        18.15        27.19         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 
       26.43        20.91         3.95         0.43         0.39         8.12 
TCGA-37-4132 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        7.46         3.39        47.80        44.75        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       70.03        60.79         1.71        24.33         1.94        27.39 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
       36.39        15.58        35.70        17.88        17.06        40.21 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
       22.49        38.66        33.11        18.38        27.91        12.36 
TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-7658 TCGA-43-8115 
       24.89         5.46         3.81        19.59        66.51        13.38 
TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 
        2.93         9.73        14.20        12.03         9.99        10.65 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
        0.39         0.39        28.34         8.75        27.45        28.96 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 
       18.25         2.04         0.62         0.99         1.32         0.85 
TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
        6.51         0.10         3.48        26.89        14.07         1.35 
TCGA-56-8504 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
       16.77        22.75         1.18        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       15.81        20.94        19.23        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        0.13         0.26        13.25        13.55        29.95        71.24 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 
       34.78        85.12        34.36        35.24        29.92        12.23 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 
       96.82        37.94        80.45        49.48        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2721 
        9.01        56.91        35.34        48.49         3.19        32.32 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MG 
       29.85        35.90        23.57        26.83       102.67        70.62 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR 
       66.61        58.65        59.97        14.99        11.34        89.29 
TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 
       16.37        25.41        36.16        53.88        34.59        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
        2.01        21.07         0.99         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
       43.99        21.01        25.05         0.99         2.01         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 
        2.01         7.07        23.01        19.00         3.02        19.00 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
       12.03        12.00         1.97        25.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 TCGA-68-7757 
        4.04        22.98         5.03        10.06         4.01         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 
        8.02        13.35        16.18        14.73        29.56        73.12 
TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7335 TCGA-77-7337 
       75.09        11.18        89.98        20.78        70.13       106.95 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 
       15.75         6.51        86.76        53.95        82.92        12.59 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 
       53.92        39.09        17.72       104.09        11.54         6.97 
TCGA-77-8150 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       54.41       126.18       132.36       117.57        22.29         5.92 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6798 TCGA-85-7698 
       30.81        27.62        38.86         9.67         6.41        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8276 
       32.91         1.38        29.95        19.04        24.13        34.52 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 
       10.09        13.22        22.45         5.29        32.71         0.72 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
        7.76        14.63        13.94        15.62        19.33        17.72 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       24.36        18.18        12.56        16.21        15.85        14.96 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
        0.79         3.65        24.92         9.50         2.93        11.77 
TCGA-90-7964 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 
       14.07        22.62        10.59         2.70         4.01         5.26 
TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        2.30        21.04         4.01        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 
       49.87        18.31        17.46        16.57         8.42         2.76 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.67        21.34        27.16        18.15         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-NC-A5HE 
       21.21        20.32        18.58        19.10        12.89        64.08 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT 
        4.54         1.22        39.85        30.58        14.73        22.78 
TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52S 
       83.57        65.49         3.65         0.43        33.07        12.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
       43.89         8.58        11.18 

  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                           0.03                            0.10 
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                         122.43                          174.08 
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                          16.62                           20.78 
[1] "0.0 - 122.4 (16.6)" "0.1 - 174.1 (20.8)"
[1] "hr=" "1"  
D75V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(19Q13.32) MUTATED         0       24       45        1        22
  DEL PEAK 45(19Q13.32) WILD-TYPE       2       63      106        1        41
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(19Q13.32) MUTATED          25         1         16          5
  DEL PEAK 45(19Q13.32) WILD-TYPE        67         2         46         16
                                 vv
clus                              STAGE IV
  DEL PEAK 45(19Q13.32) MUTATED          2
  DEL PEAK 45(19Q13.32) WILD-TYPE        5
D75V3, multiclass
            clus
vv           DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  STAGE I                                0                               2
  STAGE IA                              24                              63
  STAGE IB                              45                             106
  STAGE II                               1                               1
  STAGE IIA                             22                              41
  STAGE IIB                             25                              67
  STAGE III                              1                               2
  STAGE IIIA                            16                              46
  STAGE IIIB                             5                              16
  STAGE IV                               2                               5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 45(19Q13.32) MUTATED    31  86  22   5
  DEL PEAK 45(19Q13.32) WILD-TYPE  80 204  47  18
D75V4, multiclass
    clus
vv   DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  T1                            31                              80
  T2                            86                             204
  T3                            22                              47
  T4                             5                              18
[1] 4 2
[1] TRUE
[1] "dimension of 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(19Q13.32) MUTATED    96  33  11   1
  DEL PEAK 45(19Q13.32) WILD-TYPE 216  98  28   4
D75V5, multiclass
    clus
vv   DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  N0                            96                             216
  N1                            33                              98
  N2                            11                              28
  N3                             1                               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"
D75V6, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.32) MUTATED   120   2
  DEL PEAK 45(19Q13.32) WILD-TYPE 284   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.32) MUTATED    120    2
  DEL PEAK 45(19Q13.32) WILD-TYPE  284    5
   clus
vv  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  0                           120                             284
  1                             2                               5
[1] 2 2
[1] FALSE
D75V7, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.32) MUTATED    29 115
  DEL PEAK 45(19Q13.32) WILD-TYPE  98 251
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.32) MUTATED     29  115
  DEL PEAK 45(19Q13.32) WILD-TYPE   98  251
        clus
vv       DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  FEMALE                            29                              98
  MALE                             115                             251
[1] 2 2
[1] FALSE
D75V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 45(19Q13.32) MUTATED                                       8
  DEL PEAK 45(19Q13.32) WILD-TYPE                                     7
                                 vv
clus                              LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 45(19Q13.32) MUTATED                                         0
  DEL PEAK 45(19Q13.32) WILD-TYPE                                       1
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 45(19Q13.32) MUTATED                                        2
  DEL PEAK 45(19Q13.32) WILD-TYPE                                      4
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 45(19Q13.32) MUTATED                                         0
  DEL PEAK 45(19Q13.32) WILD-TYPE                                       1
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(19Q13.32) MUTATED                                                           134
  DEL PEAK 45(19Q13.32) WILD-TYPE                                                         336
D75V9, multiclass
                                                             clus
vv                                                            DEL PEAK 45(19Q13.32) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           134
                                                             clus
vv                                                            DEL PEAK 45(19Q13.32) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             336
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.32) MUTATED     5 139
  DEL PEAK 45(19Q13.32) WILD-TYPE   8 341
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.32) MUTATED      5  139
  DEL PEAK 45(19Q13.32) WILD-TYPE    8  341
     clus
vv    DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  NO                              5                               8
  YES                           139                             341
[1] 2 2
[1] FALSE
D75V11, continuous
D75V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 45(19Q13.32) MUTATED   108   4   2  10
  DEL PEAK 45(19Q13.32) WILD-TYPE 286   8   2  12
D75V13, multiclass
    clus
vv   DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  R0                           108                             286
  R1                             4                               8
  R2                             2                               2
  RX                            10                              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(19Q13.32) MUTATED       2                        11    98
  DEL PEAK 45(19Q13.32) WILD-TYPE     7                        20   242
D75V14, multiclass
                           clus
vv                          DEL PEAK 45(19Q13.32) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                                98
                           clus
vv                          DEL PEAK 45(19Q13.32) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              20
  WHITE                                                 242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V15, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.32) MUTATED     2  88
  DEL PEAK 45(19Q13.32) WILD-TYPE   6 221
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.32) MUTATED      2   88
  DEL PEAK 45(19Q13.32) WILD-TYPE    6  221
                        clus
vv                       DEL PEAK 45(19Q13.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            88
                        clus
vv                       DEL PEAK 45(19Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             221
[1] 2 2
[1] FALSE

Clustering(76) Variable = DEL PEAK 46(21Q11.2) MUTATION ANALYSIS
D76V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 46(21Q11.2) MUTATED   137  95
  DEL PEAK 46(21Q11.2) WILD-TYPE 144 101
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           232                            245 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                            95                            101 
$`DEL PEAK 46(21Q11.2) MUTATED`
TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-4721 
       75.75        11.34        23.54        92.15        31.99       154.32 
TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1083 
      119.54        99.16        70.16        60.89        31.73        43.23 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 
       33.93        10.82        21.99         7.33         4.31        14.10 
TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 
       27.02        48.82        20.48        35.08        48.33        38.17 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       11.77        63.55        14.63        44.25         0.79        54.28 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-22-A5C4 
       71.34        79.20        11.74        18.84        56.32        22.06 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 
        7.63        98.01        79.53        14.07        54.44         1.55 
TCGA-33-6737 TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 
       19.76        36.62         6.94        44.19        27.16         2.63 
TCGA-34-2604 TCGA-34-5231 TCGA-34-5234 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 
       31.50        65.23        56.38        30.94        18.15         1.12 
TCGA-34-8455 TCGA-34-8456 TCGA-37-3792 TCGA-37-4130 TCGA-37-5819 TCGA-39-5016 
        4.04        26.43         0.39         8.12         3.39        74.07 
TCGA-39-5019 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 
       44.75        24.33        27.39        36.39        35.64        35.70 
TCGA-39-5039 TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 
       17.88        33.11        18.38        24.89         5.46        19.59 
TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       12.03         9.99        13.91         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 TCGA-56-6546 TCGA-56-7222 
        5.46        30.35         0.10        18.25         0.62         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-56-8503 
        0.99         1.45         1.32         0.85        17.49         1.35 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A62T TCGA-58-8386 
       15.81        20.94        13.32        21.04         2.76         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 TCGA-60-2703 TCGA-60-2707 
       13.25        13.55        29.95        16.47        96.82        21.93 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2719 TCGA-60-2721 TCGA-60-2723 
       41.42         9.01        35.34        42.64        32.32        35.90 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN 
       26.83        11.77       102.67        59.97        45.57        11.34 
TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 
       25.28        78.28        36.16        53.88        34.59        43.10 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
       21.07         0.99         1.02         2.01         0.92        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2771 
       21.01        25.05         0.99         2.01         1.02        19.00 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-66-2788 
        2.01        12.03         3.98        12.00        25.97        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 
        5.03        30.02        10.06         4.01         2.73         6.64 
TCGA-68-8250 TCGA-68-8251 TCGA-77-6842 TCGA-77-7138 TCGA-77-7140 TCGA-77-7335 
        8.02        13.35        29.56        11.18        20.78        70.13 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8128 TCGA-77-8136 TCGA-77-8140 
       46.78        15.75        86.76        37.81        39.09        11.54 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        6.97         9.63        54.41        65.49        35.90         0.33 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
      117.57        22.29        27.62        38.86        11.97         6.41 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 TCGA-85-8048 TCGA-85-8070 TCGA-85-8071 
       36.53        31.30         1.15        25.15        31.56        14.07 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 
       34.52         0.76        22.45        16.77         5.29        32.71 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
        2.01         7.76         0.10        15.62        25.68        19.33 
TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L 
       14.96        19.73        16.21        15.85        14.96        12.39 
TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
        3.65         9.50         2.93        11.77        20.22        22.62 
TCGA-92-7341 TCGA-92-8064 TCGA-94-7557 TCGA-94-7943 TCGA-94-8490 TCGA-94-8491 
        3.48         5.26         0.16        11.70         5.03        26.63 
TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       16.14        17.69        19.36        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A539 TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-NC-A5HD 
       27.16         3.88        18.58        20.71        16.11         0.07 
TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP 
        1.22        13.74         4.21        39.85        37.22        24.00 
TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52N 
       14.73        83.57        65.49         3.65        16.80        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W 
        3.72        12.72        43.89         8.58 

$`DEL PEAK 46(21Q11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3417 
       12.20         7.46        79.46         4.80       117.57        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 
        1.64        86.96         6.18         2.79        49.94        27.19 
TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       46.88        34.78        15.58       122.43         9.34       119.80 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1005 
       31.63        88.11        41.69        32.19        14.93        64.21 
TCGA-22-1011 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
        1.74        24.13         0.56        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 TCGA-22-5485 TCGA-22-5489 
       19.30         9.57        31.73        64.93        30.12        62.86 
TCGA-22-5492 TCGA-33-4533 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-6738 
       16.64       133.74       174.08       103.53       151.27        27.02 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASJ TCGA-34-2600 TCGA-34-2605 
        4.70         0.30       110.99       118.36        61.61        28.96 
TCGA-34-2608 TCGA-34-2609 TCGA-34-5232 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       32.88        31.27        67.79         9.07        23.24        12.00 
TCGA-34-5241 TCGA-34-5929 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       16.93         4.96        27.19        20.91         3.95         0.43 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 
        6.58         7.46         7.82         6.81         0.39        47.80 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
       68.58        55.20        70.03        60.79         1.71         1.94 
TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
       15.58        17.06        40.21        22.49        38.66        27.02 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 
       27.91        12.36        21.47         3.81         7.76        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
       13.38        11.77         2.93        11.61         9.73        14.20 
TCGA-46-6025 TCGA-51-4079 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 
       10.65         0.39         8.75        27.45        28.96         2.04 
TCGA-56-7221 TCGA-56-7730 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 
        0.99         6.51         0.10         3.48        26.89        17.00 
TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07        16.77         1.81        22.75         1.18        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR 
        9.93        20.25        19.23        17.85        18.74         0.13 
TCGA-56-A5DS TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
        0.26        71.24        34.78        85.12        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 
       35.24        29.92        21.11         3.58        12.23        10.22 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       37.94        92.71        80.45        49.48        66.54        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2724 TCGA-63-A5MG 
       50.33        48.49         3.19        29.85        23.57        70.62 
TCGA-63-A5MH TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MU 
       66.61        58.65        14.99        89.29        16.37        25.41 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2756 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       16.96         2.01         0.99         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2778 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
       23.01         3.02        19.00        24.95         1.97        40.01 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 TCGA-66-2800 TCGA-68-7757 TCGA-68-A59I 
        4.04        22.98        54.08        49.05         6.94        16.18 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
       14.73        73.12        75.09        23.28        89.98         0.49 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8009 TCGA-77-8130 
       42.28       106.95         0.16         6.51        53.95        82.92 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 TCGA-77-8144 
       12.59        53.92        17.72       104.09        26.40        27.39 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB 
      126.18       132.36         5.92        42.41        42.08        30.81 
TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
        9.67        12.99        34.95        32.91         1.38        29.95 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8277 TCGA-85-8288 
       18.94        19.04        24.13        16.87        10.09        13.22 
TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB 
        3.09         0.72        14.63        13.94        12.59        17.72 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 TCGA-90-7964 
       24.36        18.18        12.56         0.79        24.92        14.07 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-8035 
       10.59         2.70         4.01         2.30        21.04         4.01 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
       14.14        49.87        57.07        18.31        17.46        16.57 
TCGA-98-7454 TCGA-98-8020 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53D 
        8.42         2.76        18.15         2.01        27.02        21.21 
TCGA-98-A53H TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.32        19.10        12.89        13.18        13.41        11.84 
TCGA-NC-A5HE TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HO 
       64.08         4.54        51.78        45.37         2.89        30.58 
TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A7XE TCGA-O2-A5IB TCGA-XC-AA0X 
       29.75        22.78         0.43        11.18         0.20 

  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                        154.32                         174.08 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                        19.475                         19.000 
[1] "0.0 - 154.3 (19.5)" "0.1 - 174.1 (19.0)"
[1] "hr=" "1.1"
D76V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(21Q11.2) MUTATED         2       43       69        2        38
  DEL PEAK 46(21Q11.2) WILD-TYPE       0       44       82        0        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(21Q11.2) MUTATED          45         2         28          6
  DEL PEAK 46(21Q11.2) WILD-TYPE        47         1         34         15
                                vv
clus                             STAGE IV
  DEL PEAK 46(21Q11.2) MUTATED          5
  DEL PEAK 46(21Q11.2) WILD-TYPE        2
D76V3, multiclass
            clus
vv           DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  STAGE I                               2                              0
  STAGE IA                             43                             44
  STAGE IB                             69                             82
  STAGE II                              2                              0
  STAGE IIA                            38                             25
  STAGE IIB                            45                             47
  STAGE III                             2                              1
  STAGE IIIA                           28                             34
  STAGE IIIB                            6                             15
  STAGE IV                              5                              2
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 46(21Q11.2) MUTATED    54 144  33  10
  DEL PEAK 46(21Q11.2) WILD-TYPE  57 146  36  13
D76V4, multiclass
    clus
vv   DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  T1                           54                             57
  T2                          144                            146
  T3                           33                             36
  T4                           10                             13
[1] 4 2
[1] TRUE
[1] "dimension of 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(21Q11.2) MUTATED   150  70  18   1
  DEL PEAK 46(21Q11.2) WILD-TYPE 162  61  21   4
D76V5, multiclass
    clus
vv   DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  N0                          150                            162
  N1                           70                             61
  N2                           18                             21
  N3                            1                              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"
D76V6, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED   201   5
  DEL PEAK 46(21Q11.2) WILD-TYPE 203   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED    201    5
  DEL PEAK 46(21Q11.2) WILD-TYPE  203    2
   clus
vv  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  0                          201                            203
  1                            5                              2
[1] 2 2
[1] FALSE
D76V7, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED    51 190
  DEL PEAK 46(21Q11.2) WILD-TYPE  76 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED     51  190
  DEL PEAK 46(21Q11.2) WILD-TYPE   76  176
        clus
vv       DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  FEMALE                           51                             76
  MALE                            190                            176
[1] 2 2
[1] FALSE
D76V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 46(21Q11.2) MUTATED                                       6
  DEL PEAK 46(21Q11.2) WILD-TYPE                                     9
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 46(21Q11.2) MUTATED                                         1
  DEL PEAK 46(21Q11.2) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 46(21Q11.2) MUTATED                                        2
  DEL PEAK 46(21Q11.2) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 46(21Q11.2) MUTATED                                         1
  DEL PEAK 46(21Q11.2) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(21Q11.2) MUTATED                                                           231
  DEL PEAK 46(21Q11.2) WILD-TYPE                                                         239
D76V9, multiclass
                                                             clus
vv                                                            DEL PEAK 46(21Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          231
                                                             clus
vv                                                            DEL PEAK 46(21Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            239
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V10, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED     4 237
  DEL PEAK 46(21Q11.2) WILD-TYPE   9 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED      4  237
  DEL PEAK 46(21Q11.2) WILD-TYPE    9  243
     clus
vv    DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  NO                             4                              9
  YES                          237                            243
[1] 2 2
[1] FALSE
D76V11, continuous
D76V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 46(21Q11.2) MUTATED   194   5   1  10
  DEL PEAK 46(21Q11.2) WILD-TYPE 200   7   3  12
D76V13, multiclass
    clus
vv   DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  R0                          194                            200
  R1                            5                              7
  R2                            1                              3
  RX                           10                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(21Q11.2) MUTATED       3                        14   162
  DEL PEAK 46(21Q11.2) WILD-TYPE     6                        17   178
D76V14, multiclass
                           clus
vv                          DEL PEAK 46(21Q11.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              162
                           clus
vv                          DEL PEAK 46(21Q11.2) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             17
  WHITE                                                178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V15, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED     6 144
  DEL PEAK 46(21Q11.2) WILD-TYPE   2 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED      6  144
  DEL PEAK 46(21Q11.2) WILD-TYPE    2  165
                        clus
vv                       DEL PEAK 46(21Q11.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          144
                        clus
vv                       DEL PEAK 46(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            165
[1] 2 2
[1] FALSE

Clustering(77) Variable = DEL PEAK 47(21Q22.3) MUTATION ANALYSIS
D77V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 47(21Q22.3) MUTATED   160 103
  DEL PEAK 47(21Q22.3) WILD-TYPE 121  93
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                           263                            214 
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                           103                             93 
$`DEL PEAK 47(21Q22.3) MUTATED`
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 
       75.75       117.57        11.34        23.54        92.15        31.99 
TCGA-18-3417 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 TCGA-21-1072 
       36.07         6.18         2.79       154.32       119.54        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 
       70.16        60.89        31.73        43.23        88.11        33.93 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
       10.82         7.33         4.31        14.10        27.02        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4604 TCGA-22-4609 
       20.48        35.08        48.33        38.17        13.12         9.57 
TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       11.77        31.73        63.55        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-22-5492 
       54.28        71.34        11.74        18.84        56.32        16.64 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 
        7.63        98.01        79.53       103.53        14.07         1.55 
TCGA-33-AAS8 TCGA-33-AASI TCGA-33-AASL TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
       36.62        44.19        27.16        31.50        28.96        32.88 
TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 
        9.07        16.93        30.94        18.15         1.12         4.04 
TCGA-34-8456 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 
       26.43         0.43         0.39         8.12         7.82         6.81 
TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 
        3.39        74.07        44.75        60.79        24.33        27.39 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 TCGA-43-2578 
       36.39        35.64        35.70        17.88        40.21        22.49 
TCGA-43-3920 TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 
       33.11        18.38        24.89         5.46        19.59         7.76 
TCGA-43-8116 TCGA-43-8118 TCGA-43-A56V TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 
       11.77         2.93        12.03        10.65        13.91         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 
       29.95        28.34         5.46        30.35        28.96         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       18.25         2.04         0.62         0.43         0.99         1.45 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-8503 TCGA-56-8629 
        1.32         0.85         6.51        17.49         1.35        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZJ TCGA-56-A62T TCGA-58-8386 
       20.94        19.23        13.32        21.04         2.76         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 TCGA-58-A46K TCGA-60-2698 
       13.25        13.55        29.95        16.47        34.36        10.22 
TCGA-60-2703 TCGA-60-2707 TCGA-60-2708 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 
       96.82        21.93        80.45        41.42         9.01        56.91 
TCGA-60-2715 TCGA-60-2719 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 
       35.34        42.64        32.32        29.85        35.90        26.83 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP 
       11.77       102.67        58.65        45.57        11.34        25.28 
TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       78.28        36.16        53.88        34.59        16.96        43.10 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2758 TCGA-66-2759 
       21.07         1.02         2.01         0.92        21.01        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 TCGA-66-2771 
        0.99         2.01         1.02         2.01         7.07        19.00 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 
        2.01        12.03         3.98        12.00         1.97        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
       40.01        22.98        22.98         5.03        30.02        10.06 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 
        4.01        49.05         2.73         6.64         8.02        13.35 
TCGA-77-6842 TCGA-77-7141 TCGA-77-7335 TCGA-77-7463 TCGA-77-8008 TCGA-77-8009 
       29.56         0.49        70.13        46.78        86.76        53.95 
TCGA-77-8128 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       37.81         6.97         9.63        54.41        65.49        35.90 
TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH 
        0.33       117.57        22.29         5.92        27.62        38.86 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 TCGA-85-8048 
       12.99         6.41        36.53        31.30         1.15        25.15 
TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8350 
       19.04        31.56        14.07        34.52         0.76        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       16.77         5.29        32.71         2.01         0.72         7.76 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QR 
        0.10        15.62        25.68        19.33        14.96        19.73 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7766 
       16.21        15.85        14.96        12.39         3.65         9.50 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 
       11.77        20.22        22.62         3.48         5.26        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
        0.16        11.70        26.63        14.14        16.14        17.69 
TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
       19.36        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HD 
       18.58        20.71        12.89        16.11        13.18         0.07 
TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HN 
       64.08         1.22        13.74         4.21        39.85        37.22 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       24.00        14.73        83.57        65.49         3.65        16.80 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A52W TCGA-O2-A5IB 
        3.72        12.72        43.89         8.58        11.18 

$`DEL PEAK 47(21Q22.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3419 TCGA-18-3421 
       12.20         7.46        79.46         4.80         1.64        86.96 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 
       49.94        27.19        46.88        34.78        15.58       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-21-A5DI TCGA-22-0940 
        9.34       119.80        31.63        41.69        32.19        21.99 
TCGA-22-1000 TCGA-22-1005 TCGA-22-1011 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 
       14.93        64.21         1.74        24.13         0.56        34.75 
TCGA-22-4605 TCGA-22-4607 TCGA-22-5472 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 
       32.02        19.30        64.93        79.20        30.12        62.86 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-6737 
       22.06       133.74       174.08       151.27        54.44        19.76 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ 
       27.02         4.70         0.30         6.94       110.99       118.36 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
        2.63        61.61        31.27        65.23        67.79        56.38 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5929 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 
       23.24        12.00         4.96        27.19        20.91         3.95 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4141 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 
        6.58         7.46         0.39        47.80        68.58        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 
       70.03         1.71         1.94        15.58        17.06        38.66 
TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6773 TCGA-43-7658 
       27.02        27.91        12.36        21.47         3.81        66.51 
TCGA-43-8115 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 TCGA-51-4079 
       13.38        11.61         9.73        14.20         9.99         0.39 
TCGA-52-7811 TCGA-52-7812 TCGA-56-7221 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 
        8.75        27.45         0.99         0.10         3.48        26.89 
TCGA-56-8308 TCGA-56-8309 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
       17.00        14.07        16.77         1.81        22.75         1.18 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR 
       10.36         9.93        20.25        17.85        18.74         0.13 
TCGA-56-A5DS TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M 
        0.26        71.24        34.78        85.12        56.65        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2704 TCGA-60-2706 
       29.92        21.11         3.58        12.23        37.94        92.71 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2724 
       49.48        66.54        50.33        48.49         3.19        23.57 
TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MT 
       70.62        66.61        59.97        14.99        89.29        16.37 
TCGA-63-A5MU TCGA-66-2737 TCGA-66-2744 TCGA-66-2756 TCGA-66-2757 TCGA-66-2768 
       25.41         2.01         0.99         0.99        43.99         2.01 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2778 TCGA-66-2783 TCGA-66-2789 TCGA-66-2794 
       23.01         3.02        19.00        24.95         4.04        54.08 
TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
        6.94        16.18        14.73        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 
       11.18        89.98        20.78        42.28       106.95         0.16 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       15.75         6.51        82.92        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-A5FZ 
       17.72       104.09        11.54        26.40        27.39       126.18 
TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-85-6175 TCGA-85-6560 
      132.36        42.41        42.08        30.81         9.67        11.97 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 
       34.95        32.91         1.38        29.95        18.94        24.13 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8288 TCGA-85-8353 TCGA-85-8580 TCGA-85-8582 
       16.87        10.09        13.22         3.09        14.63        13.94 
TCGA-85-8584 TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A513 
       12.59        17.72        24.36        18.18        12.56         0.79 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7964 TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
       24.92         2.93        14.07        10.59         2.70         4.01 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
        2.30         4.01         5.03        49.87        57.07        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-A53A TCGA-98-A53B 
       17.46        16.57         8.42         2.76        18.15         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-J1-A4AH TCGA-LA-A7SW TCGA-MF-A522 
       27.02        21.21        20.32        19.10        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HR 
        4.54        51.78        45.37         2.89        30.58        29.75 
TCGA-NC-A5HT TCGA-NK-A7XE TCGA-O2-A52N TCGA-XC-AA0X 
       22.78         0.43        33.07         0.20 

  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                          0.03                           0.10 
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                        154.32                         174.08 
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                        18.840                         20.005 
[1] "0.0 - 154.3 (18.8)" "0.1 - 174.1 (20.0)"
[1] "hr=" "1.1"
D77V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(21Q22.3) MUTATED         1       51       85        2        37
  DEL PEAK 47(21Q22.3) WILD-TYPE       1       36       66        0        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(21Q22.3) MUTATED          45         3         31         12
  DEL PEAK 47(21Q22.3) WILD-TYPE        47         0         31          9
                                vv
clus                             STAGE IV
  DEL PEAK 47(21Q22.3) MUTATED          6
  DEL PEAK 47(21Q22.3) WILD-TYPE        1
D77V3, multiclass
            clus
vv           DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             51                             36
  STAGE IB                             85                             66
  STAGE II                              2                              0
  STAGE IIA                            37                             26
  STAGE IIB                            45                             47
  STAGE III                             3                              0
  STAGE IIIA                           31                             31
  STAGE IIIB                           12                              9
  STAGE IV                              6                              1
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 47(21Q22.3) MUTATED    60 167  33  14
  DEL PEAK 47(21Q22.3) WILD-TYPE  51 123  36   9
D77V4, multiclass
    clus
vv   DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  T1                           60                             51
  T2                          167                            123
  T3                           33                             36
  T4                           14                              9
[1] 4 2
[1] TRUE
[1] "dimension of 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(21Q22.3) MUTATED   176  71  22   2
  DEL PEAK 47(21Q22.3) WILD-TYPE 136  60  17   3
D77V5, multiclass
    clus
vv   DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  N0                          176                            136
  N1                           71                             60
  N2                           22                             17
  N3                            2                              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"
D77V6, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q22.3) MUTATED   231   6
  DEL PEAK 47(21Q22.3) WILD-TYPE 173   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q22.3) MUTATED    231    6
  DEL PEAK 47(21Q22.3) WILD-TYPE  173    1
   clus
vv  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  0                          231                            173
  1                            6                              1
[1] 2 2
[1] FALSE
D77V7, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q22.3) MUTATED    56 218
  DEL PEAK 47(21Q22.3) WILD-TYPE  71 148
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q22.3) MUTATED     56  218
  DEL PEAK 47(21Q22.3) WILD-TYPE   71  148
        clus
vv       DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  FEMALE                           56                             71
  MALE                            218                            148
[1] 2 2
[1] FALSE
D77V8, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 47(21Q22.3) MUTATED                                       7
  DEL PEAK 47(21Q22.3) WILD-TYPE                                     8
                                vv
clus                             LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 47(21Q22.3) MUTATED                                         1
  DEL PEAK 47(21Q22.3) WILD-TYPE                                       0
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 47(21Q22.3) MUTATED                                        3
  DEL PEAK 47(21Q22.3) WILD-TYPE                                      3
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 47(21Q22.3) MUTATED                                         0
  DEL PEAK 47(21Q22.3) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(21Q22.3) MUTATED                                                           263
  DEL PEAK 47(21Q22.3) WILD-TYPE                                                         207
D77V9, multiclass
                                                             clus
vv                                                            DEL PEAK 47(21Q22.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          263
                                                             clus
vv                                                            DEL PEAK 47(21Q22.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            207
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V10, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q22.3) MUTATED     7 267
  DEL PEAK 47(21Q22.3) WILD-TYPE   6 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q22.3) MUTATED      7  267
  DEL PEAK 47(21Q22.3) WILD-TYPE    6  213
     clus
vv    DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  NO                             7                              6
  YES                          267                            213
[1] 2 2
[1] FALSE
D77V11, continuous
D77V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 47(21Q22.3) MUTATED   218   7   2  12
  DEL PEAK 47(21Q22.3) WILD-TYPE 176   5   2  10
D77V13, multiclass
    clus
vv   DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  R0                          218                            176
  R1                            7                              5
  R2                            2                              2
  RX                           12                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 47(21Q22.3) MUTATED       3                        14   186
  DEL PEAK 47(21Q22.3) WILD-TYPE     6                        17   154
D77V14, multiclass
                           clus
vv                          DEL PEAK 47(21Q22.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              186
                           clus
vv                          DEL PEAK 47(21Q22.3) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             17
  WHITE                                                154
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V15, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q22.3) MUTATED     6 165
  DEL PEAK 47(21Q22.3) WILD-TYPE   2 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q22.3) MUTATED      6  165
  DEL PEAK 47(21Q22.3) WILD-TYPE    2  144
                        clus
vv                       DEL PEAK 47(21Q22.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          165
                        clus
vv                       DEL PEAK 47(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            144
[1] 2 2
[1] FALSE

Clustering(78) Variable = DEL PEAK 48(22Q11.21) MUTATION ANALYSIS
D78V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 48(22Q11.21) MUTATED    52  39
  DEL PEAK 48(22Q11.21) WILD-TYPE 229 157
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                             91                             386 
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                             39                             157 
$`DEL PEAK 48(22Q11.21) MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-18-3417 TCGA-18-4083 TCGA-21-1071 TCGA-21-1080 
        7.46        31.99        36.07         6.18        46.88       122.43 
TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1016 TCGA-22-4594 TCGA-22-4601 
       10.82        32.19        21.99        27.02        48.33        34.75 
TCGA-22-5471 TCGA-22-5480 TCGA-22-A5C4 TCGA-33-4583 TCGA-33-4587 TCGA-33-6737 
       31.73        71.34        22.06       151.27        54.44        19.76 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASL TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
       36.62         6.94        27.16         0.39         6.58         7.46 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5035 TCGA-39-5040 TCGA-43-2578 TCGA-43-2581 
       47.80        74.07        15.58        17.06        22.49        38.66 
TCGA-43-6771 TCGA-43-7656 TCGA-43-A56V TCGA-52-7812 TCGA-56-6546 TCGA-56-7222 
        5.46        19.59        12.03        27.45         0.62         0.43 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-58-A46M TCGA-60-2698 TCGA-63-A5MN 
        3.48        26.89        14.07        35.24        10.22        11.34 
TCGA-63-A5MP TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 
       25.28        16.96         1.02         2.01        43.99        21.01 
TCGA-66-2759 TCGA-66-2766 TCGA-66-2771 TCGA-66-2778 TCGA-66-2782 TCGA-66-2785 
       25.05         1.02        19.00        19.00        12.00         1.97 
TCGA-66-2790 TCGA-66-2793 TCGA-66-2795 TCGA-68-8250 TCGA-68-A59I TCGA-77-6843 
       22.98        10.06         4.01         8.02        16.18        73.12 
TCGA-77-7138 TCGA-77-8139 TCGA-77-8150 TCGA-85-6560 TCGA-85-8049 TCGA-85-8072 
       11.18       104.09        54.41        11.97        19.04        16.87 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A53L TCGA-90-A4ED 
       12.59         0.10        15.62        25.68        12.39        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-98-7454 
       22.62        10.59         4.01         2.30         4.01         8.42 
TCGA-98-8023 TCGA-98-A53B TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HJ TCGA-NC-A5HL 
       21.34         2.01        11.84        64.08        13.74         2.89 
TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 
       39.85        30.58        14.73        65.49         3.65        16.80 
TCGA-O2-A52W 
        8.58 

$`DEL PEAK 48(22Q11.21) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
       12.20        75.75        79.46         4.80       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       23.54        92.15         1.64        86.96         2.79       154.32 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
       49.94        27.19       119.54        99.16        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
       34.78        15.58        31.73         9.34       119.80        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1000 
       31.63        88.11        41.69        33.93         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 
        4.31        64.21         1.74        14.10        48.82        20.48 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 
       35.08        24.13         0.56        38.17        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 
       19.30         9.57        11.77        64.93        63.55        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
       44.25         0.79        54.28        79.20        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 
       30.12        62.86        56.32        16.64         7.63       133.74 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 
       98.01        79.53       174.08       103.53        14.07         1.55 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
       27.02         4.70         0.30       110.99        44.19       118.36 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 
        2.63        61.61        31.50        28.96        32.88        31.27 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        67.79        56.38         9.07        23.24        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       16.93        30.94        18.15         4.96         1.12        27.19 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 
        4.04        26.43        20.91         3.95         0.43         8.12 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 
        7.82         6.81         0.39         3.39        44.75        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       55.20        70.03        60.79         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-2576 
       27.39        36.39        35.64        35.70        17.88        40.21 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       27.02        33.11        18.38        27.91        12.36        24.89 
TCGA-43-6770 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
       21.47         3.81         7.76        66.51        13.38        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 TCGA-46-6025 
        2.93        11.61         9.73        14.20         9.99        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       13.91         0.39         0.39        29.95        28.34         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
       30.35         8.75        28.96         0.10        18.25         2.04 
TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
        0.99         0.99         1.45         1.32         0.85         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8308 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
        0.10        17.49        17.00         1.35        16.77         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75         1.18        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       20.94        19.23        13.32        17.85        21.04        18.74 
TCGA-56-A5DR TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        0.13         0.26         2.76         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       29.95        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2703 
       56.65        29.92        21.11         3.58        12.23        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       37.94        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       41.42         9.01        56.91        50.33        35.34        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       42.64         3.19        32.32        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MI 
       26.83        11.77       102.67        70.62        66.61        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
       59.97        45.57        14.99        89.29        78.28        16.37 
TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 
       25.41        36.16        53.88        34.59        43.10         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 
       21.07         0.99         0.92         0.99         0.99         2.01 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
        2.01         2.01         7.07        23.01         3.02         2.01 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 
       12.03         3.98        24.95        25.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 
        4.04         5.03        30.02        54.08        49.05         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 
        6.64         6.94        13.35        14.73        29.56        75.09 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       23.28        89.98        20.78         0.49        42.28        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
      106.95         0.16        46.78        15.75         6.51        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       53.95        37.81        82.92        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 
       17.72        11.54        26.40        27.39         6.97         9.63 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       65.49        35.90         0.33       126.18       132.36       117.57 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF 
       22.29         5.92        42.41        42.08        30.81        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       38.86         9.67        12.99         6.41        36.53        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
       31.30        32.91         1.38         1.15        29.95        18.94 
TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 
       25.15        24.13        31.56        14.07        34.52        10.09 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
        0.76        13.22        22.45        16.77         5.29         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       32.71         2.01         0.72         7.76        14.63        13.94 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       19.33        17.72        14.96        24.36        18.18        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 
       12.56        16.21        15.85        14.96         0.79         3.65 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-92-7340 
       24.92         9.50         2.93        11.77        14.07         2.70 
TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-8490 
        3.48         5.26        21.04         0.16        11.70         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-7545 
       26.63        14.14        16.14        17.69        49.87        57.07 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8020 TCGA-98-8021 
       18.31        17.46        19.36        16.57         2.76        30.81 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D 
       30.67        27.16         3.88        18.15        27.02        21.21 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 
       20.32        18.58        20.71        19.10        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HD TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       13.18        13.41         0.07         4.54        51.78         1.22 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NC-A5HT 
       45.37         4.21        37.22        24.00        29.75        22.78 
TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       83.57         0.43        33.07         3.72        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                         151.27                          174.08 
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                         16.960                          19.545 
[1] "0.1 - 151.3 (17.0)" "0.0 - 174.1 (19.5)"
[1] "hr=" "1.2"
D78V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 48(22Q11.21) MUTATED         1       17       22        0        15
  DEL PEAK 48(22Q11.21) WILD-TYPE       1       70      129        2        48
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(22Q11.21) MUTATED          16         0         16          3
  DEL PEAK 48(22Q11.21) WILD-TYPE        76         3         46         18
                                 vv
clus                              STAGE IV
  DEL PEAK 48(22Q11.21) MUTATED          2
  DEL PEAK 48(22Q11.21) WILD-TYPE        5
D78V3, multiclass
            clus
vv           DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  STAGE I                                1                               1
  STAGE IA                              17                              70
  STAGE IB                              22                             129
  STAGE II                               0                               2
  STAGE IIA                             15                              48
  STAGE IIB                             16                              76
  STAGE III                              0                               3
  STAGE IIIA                            16                              46
  STAGE IIIB                             3                              18
  STAGE IV                               2                               5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 48(22Q11.21) MUTATED    21  55  14   3
  DEL PEAK 48(22Q11.21) WILD-TYPE  90 235  55  20
D78V4, multiclass
    clus
vv   DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  T1                            21                              90
  T2                            55                             235
  T3                            14                              55
  T4                             3                              20
[1] 4 2
[1] TRUE
[1] "dimension of 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(22Q11.21) MUTATED    56  25  11   1
  DEL PEAK 48(22Q11.21) WILD-TYPE 256 106  28   4
D78V5, multiclass
    clus
vv   DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  N0                            56                             256
  N1                            25                             106
  N2                            11                              28
  N3                             1                               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"
D78V6, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q11.21) MUTATED    71   2
  DEL PEAK 48(22Q11.21) WILD-TYPE 333   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q11.21) MUTATED     71    2
  DEL PEAK 48(22Q11.21) WILD-TYPE  333    5
   clus
vv  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  0                            71                             333
  1                             2                               5
[1] 2 2
[1] FALSE
D78V7, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q11.21) MUTATED    23  70
  DEL PEAK 48(22Q11.21) WILD-TYPE 104 296
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q11.21) MUTATED     23   70
  DEL PEAK 48(22Q11.21) WILD-TYPE  104  296
        clus
vv       DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  FEMALE                            23                             104
  MALE                              70                             296
[1] 2 2
[1] FALSE
D78V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 48(22Q11.21) MUTATED                                       2
  DEL PEAK 48(22Q11.21) WILD-TYPE                                    13
                                 vv
clus                              LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 48(22Q11.21) MUTATED                                         0
  DEL PEAK 48(22Q11.21) WILD-TYPE                                       1
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 48(22Q11.21) MUTATED                                        1
  DEL PEAK 48(22Q11.21) WILD-TYPE                                      5
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 48(22Q11.21) MUTATED                                         1
  DEL PEAK 48(22Q11.21) WILD-TYPE                                       0
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 48(22Q11.21) MUTATED                                                            89
  DEL PEAK 48(22Q11.21) WILD-TYPE                                                         381
D78V9, multiclass
                                                             clus
vv                                                            DEL PEAK 48(22Q11.21) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   2
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            89
                                                             clus
vv                                                            DEL PEAK 48(22Q11.21) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             381
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q11.21) MUTATED     4  89
  DEL PEAK 48(22Q11.21) WILD-TYPE   9 391
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q11.21) MUTATED      4   89
  DEL PEAK 48(22Q11.21) WILD-TYPE    9  391
     clus
vv    DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  NO                              4                               9
  YES                            89                             391
[1] 2 2
[1] FALSE
D78V11, continuous
D78V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 48(22Q11.21) MUTATED    71   1   2   4
  DEL PEAK 48(22Q11.21) WILD-TYPE 323  11   2  18
D78V13, multiclass
    clus
vv   DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  R0                            71                             323
  R1                             1                              11
  R2                             2                               2
  RX                             4                              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 48(22Q11.21) MUTATED       2                         8    60
  DEL PEAK 48(22Q11.21) WILD-TYPE     7                        23   280
D78V14, multiclass
                           clus
vv                          DEL PEAK 48(22Q11.21) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                60
                           clus
vv                          DEL PEAK 48(22Q11.21) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              23
  WHITE                                                 280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V15, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q11.21) MUTATED     1  54
  DEL PEAK 48(22Q11.21) WILD-TYPE   7 255
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q11.21) MUTATED      1   54
  DEL PEAK 48(22Q11.21) WILD-TYPE    7  255
                        clus
vv                       DEL PEAK 48(22Q11.21) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            54
                        clus
vv                       DEL PEAK 48(22Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             255
[1] 2 2
[1] FALSE

Clustering(79) Variable = DEL PEAK 49(22Q13.32) MUTATION ANALYSIS
D79V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 49(22Q13.32) MUTATED    71  49
  DEL PEAK 49(22Q13.32) WILD-TYPE 210 147
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                            120                             357 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                             49                             147 
$`DEL PEAK 49(22Q13.32) MUTATED`
TCGA-18-3407 TCGA-18-3417 TCGA-18-4083 TCGA-21-1070 TCGA-21-1071 TCGA-21-1080 
        7.46        36.07         6.18       119.54        46.88       122.43 
TCGA-21-5783 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0940 TCGA-22-1005 TCGA-22-1016 
       88.11        10.82        32.19        21.99        64.21        27.02 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5483 TCGA-22-5492 TCGA-33-4532 TCGA-33-4566 
       19.30        11.77        18.84        16.64         7.63       174.08 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-6737 TCGA-33-AAS8 TCGA-34-5928 
      103.53       151.27        54.44        19.76        36.62        18.15 
TCGA-34-8454 TCGA-34-8456 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       27.19        26.43         0.39         6.58         8.12         7.46 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5016 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 
        0.39        47.80        74.07        15.58        17.06        40.21 
TCGA-43-2578 TCGA-43-2581 TCGA-43-5668 TCGA-43-6143 TCGA-43-6771 TCGA-43-7658 
       22.49        38.66        18.38        12.36         5.46        66.51 
TCGA-52-7809 TCGA-52-7812 TCGA-56-6546 TCGA-56-7222 TCGA-56-8304 TCGA-56-8307 
        5.46        27.45         0.62         0.43         3.48        26.89 
TCGA-56-8309 TCGA-56-A5DR TCGA-56-A62T TCGA-60-2695 TCGA-63-A5MJ TCGA-63-A5MM 
       14.07         0.13         2.76        21.11        59.97        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       11.34        25.28        16.37        53.88        34.59        16.96 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2771 
        1.02         2.01        43.99        25.05         0.99        19.00 
TCGA-66-2778 TCGA-66-2782 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 
       19.00        12.00         4.04        22.98         5.03        10.06 
TCGA-66-2800 TCGA-68-8250 TCGA-68-A59I TCGA-77-7138 TCGA-77-7142 TCGA-77-7337 
       49.05         8.02        16.18        11.18        42.28       106.95 
TCGA-77-7465 TCGA-77-8128 TCGA-77-8139 TCGA-77-8144 TCGA-77-8150 TCGA-77-8153 
       15.75        37.81       104.09        27.39        54.41        65.49 
TCGA-77-A5G6 TCGA-85-6560 TCGA-85-7697 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 
       22.29        11.97        34.95         1.15        25.15        19.04 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
       32.71         2.01         0.72        13.94        12.59         0.10 
TCGA-85-8666 TCGA-85-A510 TCGA-85-A53L TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       15.62        15.85        12.39        20.22        22.62        10.59 
TCGA-92-8063 TCGA-92-8065 TCGA-94-8491 TCGA-98-7454 TCGA-98-A53B TCGA-MF-A522 
        4.01         2.30        26.63         8.42         2.01        11.84 
TCGA-NC-A5HE TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HO TCGA-NC-A5HQ 
       64.08        13.74         2.89        39.85        30.58        14.73 
TCGA-NK-A5CT TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-O2-A52Q TCGA-O2-A52W TCGA-O2-A5IB 
       65.49         3.65        16.80         3.72         8.58        11.18 

$`DEL PEAK 49(22Q13.32) WILD-TYPE`
TCGA-18-3406 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
       12.20        75.75        79.46         4.80       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       23.54        92.15        31.99         1.64        86.96         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
      154.32        49.94        27.19        99.16        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
       34.78        15.58        31.73         9.34       119.80        43.23 
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 
       31.63        41.69        33.93         7.33        14.93         4.31 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
        1.74        14.10        48.82        20.48        35.08        48.33 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       24.13         0.56        38.17        34.75        13.12        32.02 
TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
        9.57        31.73        64.93        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 
        0.79        54.28        71.34        79.20        11.74        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
       62.86        56.32        22.06       133.74        98.01        79.53 
TCGA-33-4586 TCGA-33-4589 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB 
       14.07         1.55        27.02         4.70         0.30         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
      110.99        44.19       118.36        27.16         2.63        61.61 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 
       31.50        28.96        32.88        31.27        65.23        67.79 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       56.38         9.07        23.24        12.00        16.93        30.94 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
        4.96         1.12         4.04        20.91         3.95         0.43 
TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        7.82         6.81         3.39        44.75        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       70.03        60.79         1.71        24.33         1.94        27.39 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-43-3394 TCGA-43-3920 
       36.39        35.64        35.70        17.88        27.02        33.11 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-7657 
       27.91        24.89        21.47         3.81        19.59         7.76 
TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U 
       13.38        11.77         2.93        11.61         9.73        14.20 
TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       12.03         9.99        10.65        13.91         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 
       29.95        28.34        30.35         8.75        28.96         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7221 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       18.25         2.04         0.99         0.99         1.45         1.32 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8308 TCGA-56-8503 
        0.85         6.51         0.10        17.49        17.00         1.35 
TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       16.77         1.81        22.75         1.18        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY 
       20.25        15.81        20.94        19.23        13.32        17.85 
TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       21.04        18.74         0.26         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       29.95        71.24        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 
       56.65        35.24        29.92         3.58        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       96.82        37.94        92.71        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 
       66.54        41.42         9.01        56.91        50.33        35.34 
TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 
       48.49        42.64         3.19        32.32        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH 
       23.57        26.83        11.77       102.67        70.62        66.61 
TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MU TCGA-63-A5MV 
       58.65        45.57        89.29        78.28        25.41        36.16 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 
       43.10         2.01        21.07         0.99         0.92         0.99 
TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       21.01         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 
       23.01         3.02         2.01        12.03         3.98        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2792 TCGA-66-2794 
        1.97        25.97        40.01        22.98        30.02        54.08 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J 
        4.01         2.73         6.64         6.94        13.35        14.73 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 
       29.56        73.12        75.09        23.28        89.98        20.78 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 
        0.49        70.13         0.16        46.78         6.51        86.76 
TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       53.95        82.92        12.59        53.92        39.09        17.72 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-8156 
       11.54        26.40         6.97         9.63        35.90         0.33 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GA 
      126.18       132.36       117.57         5.92        42.41        42.08 
TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 
       30.81        27.62        38.86         9.67        12.99         6.41 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
       36.53        31.30        32.91         1.38        29.95        18.94 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       24.13        31.56        14.07        16.87        34.52        10.09 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 
        0.76        13.22        22.45        16.77         5.29         3.09 
TCGA-85-8481 TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC 
        7.76        14.63        25.68        19.33        17.72        14.96 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
       24.36        18.18        19.73        12.56        16.21        14.96 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
        0.79         3.65        24.92         9.50         2.93        11.77 
TCGA-90-7964 TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 TCGA-94-7557 
       14.07         2.70         3.48         5.26        21.04         0.16 
TCGA-94-7943 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I4 TCGA-94-A5I6 
       11.70         4.01         5.03        14.14        16.14        17.69 
TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL 
       49.87        57.07        18.31        17.46        19.36        16.57 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        2.76        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J 
       18.15        27.02        21.21        20.32        18.58        20.71 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HD 
       19.10        12.89        16.11        13.18        13.41         0.07 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HN 
        4.54        51.78         1.22        45.37         4.21        37.22 
TCGA-NC-A5HP TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A7XE TCGA-O2-A52N 
       24.00        29.75        22.78        83.57         0.43        33.07 
TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       12.72        43.89         0.20 

  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                           0.10                            0.03 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                         174.08                          154.32 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                          17.01                           20.32 
[1] "0.1 - 174.1 (17.0)" "0.0 - 154.3 (20.3)"
[1] "hr=" "1"  
D79V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 49(22Q13.32) MUTATED         1       22       33        0        21
  DEL PEAK 49(22Q13.32) WILD-TYPE       1       65      118        2        42
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 49(22Q13.32) MUTATED          20         2         18          5
  DEL PEAK 49(22Q13.32) WILD-TYPE        72         1         44         16
                                 vv
clus                              STAGE IV
  DEL PEAK 49(22Q13.32) MUTATED          2
  DEL PEAK 49(22Q13.32) WILD-TYPE        5
D79V3, multiclass
            clus
vv           DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  STAGE I                                1                               1
  STAGE IA                              22                              65
  STAGE IB                              33                             118
  STAGE II                               0                               2
  STAGE IIA                             21                              42
  STAGE IIB                             20                              72
  STAGE III                              2                               1
  STAGE IIIA                            18                              44
  STAGE IIIB                             5                              16
  STAGE IV                               2                               5
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 49(22Q13.32) MUTATED    29  74  19   3
  DEL PEAK 49(22Q13.32) WILD-TYPE  82 216  50  20
D79V4, multiclass
    clus
vv   DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  T1                            29                              82
  T2                            74                             216
  T3                            19                              50
  T4                             3                              20
[1] 4 2
[1] TRUE
[1] "dimension of 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 49(22Q13.32) MUTATED    76  34  12   3
  DEL PEAK 49(22Q13.32) WILD-TYPE 236  97  27   2
D79V5, multiclass
    clus
vv   DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  N0                            76                             236
  N1                            34                              97
  N2                            12                              27
  N3                             3                               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"
D79V6, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.32) MUTATED   102   2
  DEL PEAK 49(22Q13.32) WILD-TYPE 302   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED    102    2
  DEL PEAK 49(22Q13.32) WILD-TYPE  302    5
   clus
vv  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  0                           102                             302
  1                             2                               5
[1] 2 2
[1] FALSE
D79V7, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.32) MUTATED    36  89
  DEL PEAK 49(22Q13.32) WILD-TYPE  91 277
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED     36   89
  DEL PEAK 49(22Q13.32) WILD-TYPE   91  277
        clus
vv       DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  FEMALE                            36                              91
  MALE                              89                             277
[1] 2 2
[1] FALSE
D79V8, continuous
                                 vv
clus                              LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                                       5
  DEL PEAK 49(22Q13.32) WILD-TYPE                                    10
                                 vv
clus                              LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                                         0
  DEL PEAK 49(22Q13.32) WILD-TYPE                                       1
                                 vv
clus                              LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 49(22Q13.32) MUTATED                                        3
  DEL PEAK 49(22Q13.32) WILD-TYPE                                      3
                                 vv
clus                              LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 49(22Q13.32) MUTATED                                         1
  DEL PEAK 49(22Q13.32) WILD-TYPE                                       0
                                 vv
clus                              LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 49(22Q13.32) MUTATED                                                           116
  DEL PEAK 49(22Q13.32) WILD-TYPE                                                         354
D79V9, multiclass
                                                             clus
vv                                                            DEL PEAK 49(22Q13.32) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   5
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           116
                                                             clus
vv                                                            DEL PEAK 49(22Q13.32) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    10
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             354
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V10, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.32) MUTATED     4 121
  DEL PEAK 49(22Q13.32) WILD-TYPE   9 359
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED      4  121
  DEL PEAK 49(22Q13.32) WILD-TYPE    9  359
     clus
vv    DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  NO                              4                               9
  YES                           121                             359
[1] 2 2
[1] FALSE
D79V11, continuous
D79V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 49(22Q13.32) MUTATED    95   4   1   6
  DEL PEAK 49(22Q13.32) WILD-TYPE 299   8   3  16
D79V13, multiclass
    clus
vv   DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  R0                            95                             299
  R1                             4                               8
  R2                             1                               3
  RX                             6                              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 49(22Q13.32) MUTATED       3                         8    82
  DEL PEAK 49(22Q13.32) WILD-TYPE     6                        23   258
D79V14, multiclass
                           clus
vv                          DEL PEAK 49(22Q13.32) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                82
                           clus
vv                          DEL PEAK 49(22Q13.32) WILD-TYPE
  ASIAN                                                   6
  BLACK OR AFRICAN AMERICAN                              23
  WHITE                                                 258
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V15, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.32) MUTATED     1  73
  DEL PEAK 49(22Q13.32) WILD-TYPE   7 236
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED      1   73
  DEL PEAK 49(22Q13.32) WILD-TYPE    7  236
                        clus
vv                       DEL PEAK 49(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            73
                        clus
vv                       DEL PEAK 49(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             236
[1] 2 2
[1] FALSE

Clustering(80) Variable = DEL PEAK 50(XP22.2) MUTATION ANALYSIS
D80V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 50(XP22.2) MUTATED    81  65
  DEL PEAK 50(XP22.2) WILD-TYPE 200 131
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                          146                           331 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                           65                           131 
$`DEL PEAK 50(XP22.2) MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3412 TCGA-18-3416 TCGA-18-3417 TCGA-18-4086 
        7.46        75.75        11.34        31.99        36.07         2.79 
TCGA-18-5592 TCGA-18-5595 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-22-0940 
       49.94        27.19       122.43       119.80        43.23        21.99 
TCGA-22-0944 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4607 TCGA-22-5473 
        7.33        48.82        20.48        35.08        19.30        63.55 
TCGA-22-5477 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-A5C4 TCGA-33-4532 
       44.25        71.34        18.84        30.12        22.06         7.63 
TCGA-33-4566 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASJ TCGA-34-2600 TCGA-34-2605 
      174.08         0.30        36.62       118.36        61.61        28.96 
TCGA-34-2609 TCGA-34-5236 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       31.27         9.07        30.94         4.96         1.12        27.19 
TCGA-34-8456 TCGA-37-3792 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5021 
       26.43         0.39         6.81         0.39         3.39        68.58 
TCGA-39-5027 TCGA-39-5028 TCGA-43-5668 TCGA-43-5670 TCGA-43-6770 TCGA-43-7656 
       60.79         1.71        18.38        27.91        21.47        19.59 
TCGA-43-8118 TCGA-43-A474 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        2.93        11.61        13.91         0.39         0.39        29.95 
TCGA-56-7221 TCGA-56-7730 TCGA-56-8624 TCGA-56-8629 TCGA-56-A5DR TCGA-56-A62T 
        0.99         6.51         1.18        15.81         0.13         2.76 
TCGA-58-8390 TCGA-58-8392 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2707 
       29.95        16.47         3.58        10.22        96.82        21.93 
TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MP 
       66.54        41.42        56.91        70.62        58.65        25.28 
TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2753 TCGA-66-2757 
       16.37        25.41        36.16        34.59         1.02        43.99 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2769 TCGA-66-2773 TCGA-66-2781 TCGA-66-2782 
       21.01         0.99         7.07         3.02         3.98        12.00 
TCGA-66-2786 TCGA-66-2790 TCGA-66-2792 TCGA-66-2800 TCGA-68-7756 TCGA-77-6842 
       25.97        22.98        30.02        49.05         6.64        29.56 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
       23.28        11.18        20.78         0.49        42.28         0.16 
TCGA-77-8009 TCGA-77-8130 TCGA-77-8140 TCGA-77-8144 TCGA-77-8150 TCGA-77-8154 
       53.95        82.92        11.54        27.39        54.41        35.90 
TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-7698 
      117.57        42.08        27.62         9.67        12.99        31.30 
TCGA-85-7699 TCGA-85-8070 TCGA-85-8071 TCGA-85-8288 TCGA-85-8352 TCGA-85-8354 
       32.91        31.56        14.07        13.22         5.29        32.71 
TCGA-85-8580 TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50M TCGA-90-7766 TCGA-90-7964 
       14.63        19.33        19.73        12.56         9.50        14.07 
TCGA-92-8063 TCGA-94-7557 TCGA-94-8035 TCGA-94-8491 TCGA-94-A5I4 TCGA-94-A5I6 
        4.01         0.16         4.01        26.63        16.14        17.69 
TCGA-96-7544 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-8020 TCGA-98-A53A TCGA-98-A53B 
       49.87        19.36        16.57         2.76        18.15         2.01 
TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HG 
       20.71        19.10        12.89        13.18         4.54        51.78 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NK-A5CT TCGA-NK-A5D1 
       45.37         2.89        37.22        30.58        65.49        16.80 
TCGA-O2-A52S TCGA-O2-A5IB 
       12.72        11.18 

$`DEL PEAK 50(XP22.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
       12.20        79.46         4.80       117.57        23.54        92.15 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 
        1.64        86.96         6.18       154.32       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       99.16        70.16        60.89        34.78        15.58        31.73 
TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
        9.34        31.63        88.11        41.69        33.93        10.82 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       32.19        14.93         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 
       27.02        48.33        24.13         0.56        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 
       13.12        32.02         9.57        11.77        31.73        64.93 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5489 
       14.63         0.79        54.28        79.20        11.74        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
       56.32        16.64       133.74        98.01        79.53       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
      151.27        14.07        54.44         1.55        19.76        27.02 
TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 
        4.70         6.94       110.99        44.19        27.16         2.63 
TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
       31.50        32.88        65.23        67.79        56.38        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 
       12.00        16.93        18.15         4.04        20.91         3.95 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-39-5011 
        0.43         6.58         8.12         7.46         7.82        47.80 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 
       74.07        44.75        55.20        70.03        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 
       27.39        36.39        15.58        35.64        35.70        17.88 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       17.06        40.21        22.49        38.66        27.02        33.11 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 
       12.36        24.89         5.46         3.81         7.76        66.51 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
       13.38        11.77         9.73        14.20        12.03         9.99 
TCGA-46-6025 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
       10.65        28.34         5.46        30.35         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7222 
       28.96         0.10        18.25         2.04         0.62         0.43 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 
        0.99         1.45         1.32         0.85         0.10        17.49 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
        3.48        26.89        17.00        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D 
        1.81        22.75        10.36         9.93        20.25        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DS 
       19.23        13.32        17.85        21.04        18.74         0.26 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
        0.03        13.25        13.55        71.24        34.78        85.12 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 
       34.36        56.65        35.24        29.92        21.11        12.23 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2712 TCGA-60-2714 
       37.94        92.71        80.45        49.48         9.01        50.33 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 
       35.34        48.49        42.64         3.19        32.32        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MH 
       35.90        23.57        26.83        11.77       102.67        66.61 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS 
       59.97        45.57        14.99        11.34        89.29        78.28 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       53.88        16.96        43.10         2.01        21.07         0.99 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
        2.01         0.92         0.99        25.05         2.01         1.02 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 
        2.01         2.01        23.01        19.00         2.01        19.00 
TCGA-66-2780 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
       12.03        24.95         1.97        40.01        22.98         4.04 
TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 
        5.03        10.06        54.08         4.01         2.73         6.94 
TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 
        8.02        13.35        16.18        14.73        73.12        75.09 
TCGA-77-7139 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       89.98        70.13       106.95        46.78        15.75         6.51 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       86.76        37.81        12.59        53.92        39.09        17.72 
TCGA-77-8139 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8156 
      104.09        26.40         6.97         9.63        65.49         0.33 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB 
      126.18       132.36        22.29         5.92        42.41        30.81 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 
       38.86        11.97         6.41        36.53        34.95         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 
        1.15        29.95        18.94        25.15        19.04        24.13 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 
       16.87        34.52        10.09         0.76        22.45        16.77 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 
        3.09         2.01         0.72         7.76        13.94        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA 
        0.10        15.62        25.68        17.72        14.96        24.36 
TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       18.18        16.21        15.85        14.96         0.79        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
        3.65        24.92         2.93        11.77        20.22        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 
       10.59         2.70         3.48         5.26         2.30        21.04 
TCGA-94-7943 TCGA-94-8490 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
       11.70         5.03        14.14        57.07        18.31        17.46 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 
        8.42        30.81        30.67        21.34        27.16         3.88 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-L3-A524 TCGA-LA-A7SW 
       27.02        21.21        20.32        18.58        16.11        13.41 
TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK 
       11.84         0.07        64.08         1.22        13.74         4.21 
TCGA-NC-A5HM TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
       39.85        24.00        14.73        29.75        22.78        83.57 
TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W 
        3.65         0.43        33.07         3.72        43.89         8.58 
TCGA-XC-AA0X 
        0.20 

  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                       174.08                        154.32 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                       20.105                        18.580 
[1] "0.1 - 174.1 (20.1)" "0.0 - 154.3 (18.6)"
[1] "hr=" "1.1"
D80V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 50(XP22.2) MUTATED         0       21       47        1        30
  DEL PEAK 50(XP22.2) WILD-TYPE       2       66      104        1        33
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 50(XP22.2) MUTATED          28         2         14          6
  DEL PEAK 50(XP22.2) WILD-TYPE        64         1         48         15
                               vv
clus                            STAGE IV
  DEL PEAK 50(XP22.2) MUTATED          1
  DEL PEAK 50(XP22.2) WILD-TYPE        6
D80V3, multiclass
            clus
vv           DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                            21                            66
  STAGE IB                            47                           104
  STAGE II                             1                             1
  STAGE IIA                           30                            33
  STAGE IIB                           28                            64
  STAGE III                            2                             1
  STAGE IIIA                          14                            48
  STAGE IIIB                           6                            15
  STAGE IV                             1                             6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 50(XP22.2) MUTATED    29  94  18  10
  DEL PEAK 50(XP22.2) WILD-TYPE  82 196  51  13
D80V4, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  T1                          29                            82
  T2                          94                           196
  T3                          18                            51
  T4                          10                            13
[1] 4 2
[1] TRUE
[1] "dimension of 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 50(XP22.2) MUTATED    97  46   7   0
  DEL PEAK 50(XP22.2) WILD-TYPE 215  85  32   5
D80V5, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  N0                          97                           215
  N1                          46                            85
  N2                           7                            32
  N3                           0                             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"
D80V6, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED   126   1
  DEL PEAK 50(XP22.2) WILD-TYPE 278   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED    126    1
  DEL PEAK 50(XP22.2) WILD-TYPE  278    6
   clus
vv  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  0                         126                           278
  1                           1                             6
[1] 2 2
[1] FALSE
D80V7, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED    32 119
  DEL PEAK 50(XP22.2) WILD-TYPE  95 247
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED     32  119
  DEL PEAK 50(XP22.2) WILD-TYPE   95  247
        clus
vv       DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  FEMALE                          32                            95
  MALE                           119                           247
[1] 2 2
[1] FALSE
D80V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                                       3
  DEL PEAK 50(XP22.2) WILD-TYPE                                    12
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                                         1
  DEL PEAK 50(XP22.2) WILD-TYPE                                       0
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 50(XP22.2) MUTATED                                        1
  DEL PEAK 50(XP22.2) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 50(XP22.2) MUTATED                                         0
  DEL PEAK 50(XP22.2) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 50(XP22.2) MUTATED                                                           146
  DEL PEAK 50(XP22.2) WILD-TYPE                                                         324
D80V9, multiclass
                                                             clus
vv                                                            DEL PEAK 50(XP22.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         146
                                                             clus
vv                                                            DEL PEAK 50(XP22.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           324
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V10, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED     5 146
  DEL PEAK 50(XP22.2) WILD-TYPE   8 334
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED      5  146
  DEL PEAK 50(XP22.2) WILD-TYPE    8  334
     clus
vv    DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  NO                            5                             8
  YES                         146                           334
[1] 2 2
[1] FALSE
D80V11, continuous
D80V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 50(XP22.2) MUTATED   118   5   1   8
  DEL PEAK 50(XP22.2) WILD-TYPE 276   7   3  14
D80V13, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  R0                         118                           276
  R1                           5                             7
  R2                           1                             3
  RX                           8                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 50(XP22.2) MUTATED       4                        11    99
  DEL PEAK 50(XP22.2) WILD-TYPE     5                        20   241
D80V14, multiclass
                           clus
vv                          DEL PEAK 50(XP22.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                              99
                           clus
vv                          DEL PEAK 50(XP22.2) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               241
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V15, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED     1  92
  DEL PEAK 50(XP22.2) WILD-TYPE   7 217
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED      1   92
  DEL PEAK 50(XP22.2) WILD-TYPE    7  217
                        clus
vv                       DEL PEAK 50(XP22.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          92
                        clus
vv                       DEL PEAK 50(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           217
[1] 2 2
[1] FALSE

Clustering(81) Variable = DEL PEAK 51(XP21.1) MUTATION ANALYSIS
D81V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 51(XP21.1) MUTATED    81  61
  DEL PEAK 51(XP21.1) WILD-TYPE 200 135
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                          142                           335 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           61                           135 
$`DEL PEAK 51(XP21.1) MUTATED`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3412 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 
        7.46        75.75        11.34        31.99        36.07        86.96 
TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1080 TCGA-21-1082 
        2.79        49.94        27.19        99.16       122.43       119.80 
TCGA-21-1083 TCGA-22-0940 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4607 
       43.23        21.99        20.48        35.08        48.33        19.30 
TCGA-22-5473 TCGA-22-5477 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-33-4532 
       63.55        44.25        71.34        18.84        30.12         7.63 
TCGA-33-4566 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASJ TCGA-33-AASL TCGA-34-2605 
      174.08         0.30        36.62       118.36        27.16        28.96 
TCGA-34-2609 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 
       31.27        30.94         4.96         1.12        27.19        26.43 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5021 TCGA-39-5027 TCGA-39-5028 
        6.81         0.39         3.39        68.58        60.79         1.71 
TCGA-43-6770 TCGA-43-7656 TCGA-43-8116 TCGA-43-8118 TCGA-51-4079 TCGA-51-4080 
       21.47        19.59        11.77         2.93         0.39         0.39 
TCGA-51-4081 TCGA-52-7810 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7730 
       29.95        30.35         0.99         0.43         0.99         6.51 
TCGA-56-8624 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A5DR TCGA-58-8390 TCGA-58-8391 
        1.18        15.81        19.23         0.13        29.95        71.24 
TCGA-58-8392 TCGA-60-2696 TCGA-60-2698 TCGA-60-2707 TCGA-60-2710 TCGA-60-2711 
       16.47         3.58        10.22        21.93        66.54        41.42 
TCGA-60-2712 TCGA-60-2713 TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MY 
        9.01        56.91        58.65        25.28        16.37        34.59 
TCGA-66-2753 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2773 TCGA-66-2780 
        1.02        43.99        21.01         0.99         3.02        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-66-2792 TCGA-66-2795 TCGA-66-2800 
        3.98        12.00        25.97        30.02         4.01        49.05 
TCGA-68-7756 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7140 TCGA-77-7141 
        6.64        29.56        23.28        11.18        20.78         0.49 
TCGA-77-7142 TCGA-77-7338 TCGA-77-8009 TCGA-77-8130 TCGA-77-8140 TCGA-77-8144 
       42.28         0.16        53.95        82.92        11.54        27.39 
TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GA TCGA-77-A5GF 
       54.41        35.90         0.33       117.57        42.08        27.62 
TCGA-85-6175 TCGA-85-6561 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-8070 
        9.67        12.99        31.30        32.91         1.15        31.56 
TCGA-85-8071 TCGA-85-8288 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8580 
       14.07        13.22         5.29        32.71         2.01        14.63 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50M TCGA-90-7766 TCGA-92-8063 
       25.68        19.33        19.73        12.56         9.50         4.01 
TCGA-94-7557 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I4 TCGA-94-A5I6 
        0.16         4.01         5.03        26.63        16.14        17.69 
TCGA-96-7544 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J 
       49.87        19.36         2.76        18.15         2.01        20.71 
TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN 
       13.18         4.54        51.78        45.37         2.89        37.22 
TCGA-NC-A5HO TCGA-NK-A5CT TCGA-O2-A52S TCGA-O2-A5IB 
       30.58        65.49        12.72        11.18 

$`DEL PEAK 51(XP21.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
       12.20        79.46         4.80       117.57        23.54        92.15 
TCGA-18-3419 TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 
        1.64         6.18       154.32       119.54        46.88        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-5782 
       60.89        34.78        15.58        31.73         9.34        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 
       88.11        41.69        33.93        10.82        32.19         7.33 
TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       14.93         4.31        64.21         1.74        14.10        27.02 
TCGA-22-1017 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       48.82        24.13         0.56        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 
       32.02         9.57        11.77        31.73        64.93        14.63 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5489 TCGA-22-5491 
        0.79        54.28        79.20        11.74        62.86        56.32 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
       16.64        22.06       133.74        98.01        79.53       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
      151.27        14.07        54.44         1.55        19.76        27.02 
TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 
        4.70         6.94       110.99        44.19         2.63        61.61 
TCGA-34-2604 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       31.50        32.88        65.23        67.79        56.38         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-8455 TCGA-34-A5IX 
       23.24        12.00        16.93        18.15         4.04        20.91 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        3.95         0.43         0.39         6.58         8.12         7.46 
TCGA-37-4133 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 
        7.82        47.80        74.07        44.75        55.20        70.03 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       24.33         1.94        27.39        36.39        15.58        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
       35.70        17.88        17.06        40.21        22.49        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       27.02        33.11        18.38        27.91        12.36        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-A474 
        5.46         3.81         7.76        66.51        13.38        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
        9.73        14.20        12.03         9.99        10.65        13.91 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
       28.34         5.46         8.75        27.45        28.96         0.10 
TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
       18.25         2.04         0.62         1.45         1.32         0.85 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.10        17.49         3.48        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 
        1.35        16.77         1.81        22.75        10.36         9.93 
TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       20.25        20.94        13.32        17.85        21.04        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8393 
        0.26         2.76         0.03        13.25        13.55        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       85.12        34.36        56.65        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 
       12.23        96.82        37.94        92.71        80.45        49.48 
TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 
       50.33        35.34        48.49        42.64         3.19        32.32 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB 
       29.85        35.90        23.57        26.83        11.77       102.67 
TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
       70.62        66.61        59.97        45.57        14.99        11.34 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 
       89.29        78.28        25.41        36.16        53.88        16.96 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 
       43.10         2.01        21.07         0.99         2.01         0.92 
TCGA-66-2756 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
        0.99        25.05         2.01         1.02         2.01         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2783 
        7.07        23.01        19.00         2.01        19.00        24.95 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
        1.97        40.01        22.98         4.04        22.98         5.03 
TCGA-66-2793 TCGA-66-2794 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 
       10.06        54.08         2.73         6.94         8.02        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7335 
       16.18        14.73        73.12        75.09        89.98        70.13 
TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 
      106.95        46.78        15.75         6.51        86.76        37.81 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 
       12.59        53.92        39.09        17.72       104.09        26.40 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
        6.97         9.63        65.49       126.18       132.36        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
        5.92        42.41        30.81        38.86        11.97         6.41 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       36.53        34.95         1.38        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       19.04        24.13        16.87        34.52        10.09         0.76 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 
       22.45        16.77         3.09         0.72         7.76        13.94 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA 
       12.59         0.10        15.62        17.72        14.96        24.36 
TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       18.18        16.21        15.85        14.96         0.79        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 TCGA-90-A4ED 
        3.65        24.92         2.93        11.77        14.07        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 
       22.62        10.59         2.70         3.48         5.26         2.30 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A4VJ TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 
       21.04        11.70        14.14        57.07        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       16.57         8.42        30.81        30.67        21.34        27.16 
TCGA-98-A539 TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH 
        3.88        27.02        21.21        20.32        18.58        19.10 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       12.89        16.11        13.41        11.84         0.07        64.08 
TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HM TCGA-NC-A5HP TCGA-NC-A5HQ 
        1.22        13.74         4.21        39.85        24.00        14.73 
TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE 
       29.75        22.78        83.57         3.65        16.80         0.43 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       33.07         3.72        43.89         8.58         0.20 

  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                       174.08                        154.32 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                       20.105                        18.580 
[1] "0.1 - 174.1 (20.1)" "0.0 - 154.3 (18.6)"
[1] "hr=" "1.1"
D81V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 51(XP21.1) MUTATED         0       23       46        1        23
  DEL PEAK 51(XP21.1) WILD-TYPE       2       64      105        1        40
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 51(XP21.1) MUTATED          27         2         17          6
  DEL PEAK 51(XP21.1) WILD-TYPE        65         1         45         15
                               vv
clus                            STAGE IV
  DEL PEAK 51(XP21.1) MUTATED          1
  DEL PEAK 51(XP21.1) WILD-TYPE        6
D81V3, multiclass
            clus
vv           DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                            23                            64
  STAGE IB                            46                           105
  STAGE II                             1                             1
  STAGE IIA                           23                            40
  STAGE IIB                           27                            65
  STAGE III                            2                             1
  STAGE IIIA                          17                            45
  STAGE IIIB                           6                            15
  STAGE IV                             1                             6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 51(XP21.1) MUTATED    30  87  21  10
  DEL PEAK 51(XP21.1) WILD-TYPE  81 203  48  13
D81V4, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  T1                          30                            81
  T2                          87                           203
  T3                          21                            48
  T4                          10                            13
[1] 4 2
[1] TRUE
[1] "dimension of 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 51(XP21.1) MUTATED    93  45   9   0
  DEL PEAK 51(XP21.1) WILD-TYPE 219  86  30   5
D81V5, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  N0                          93                           219
  N1                          45                            86
  N2                           9                            30
  N3                           0                             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"
D81V6, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED   123   1
  DEL PEAK 51(XP21.1) WILD-TYPE 281   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED    123    1
  DEL PEAK 51(XP21.1) WILD-TYPE  281    6
   clus
vv  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  0                         123                           281
  1                           1                             6
[1] 2 2
[1] FALSE
D81V7, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED    35 113
  DEL PEAK 51(XP21.1) WILD-TYPE  92 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED     35  113
  DEL PEAK 51(XP21.1) WILD-TYPE   92  253
        clus
vv       DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  FEMALE                          35                            92
  MALE                           113                           253
[1] 2 2
[1] FALSE
D81V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 51(XP21.1) MUTATED                                       2
  DEL PEAK 51(XP21.1) WILD-TYPE                                    13
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 51(XP21.1) MUTATED                                         0
  DEL PEAK 51(XP21.1) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 51(XP21.1) MUTATED                                        1
  DEL PEAK 51(XP21.1) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 51(XP21.1) MUTATED                                         0
  DEL PEAK 51(XP21.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 51(XP21.1) MUTATED                                                           145
  DEL PEAK 51(XP21.1) WILD-TYPE                                                         325
D81V9, multiclass
                                                             clus
vv                                                            DEL PEAK 51(XP21.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 2
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         145
                                                             clus
vv                                                            DEL PEAK 51(XP21.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  13
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           325
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V10, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED     4 144
  DEL PEAK 51(XP21.1) WILD-TYPE   9 336
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED      4  144
  DEL PEAK 51(XP21.1) WILD-TYPE    9  336
     clus
vv    DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  NO                            4                             9
  YES                         144                           336
[1] 2 2
[1] FALSE
D81V11, continuous
D81V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 51(XP21.1) MUTATED   119   3   0   8
  DEL PEAK 51(XP21.1) WILD-TYPE 275   9   4  14
D81V13, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  R0                         119                           275
  R1                           3                             9
  R2                           0                             4
  RX                           8                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 51(XP21.1) MUTATED       3                        11    97
  DEL PEAK 51(XP21.1) WILD-TYPE     6                        20   243
D81V14, multiclass
                           clus
vv                          DEL PEAK 51(XP21.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                              97
                           clus
vv                          DEL PEAK 51(XP21.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               243
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V15, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED     1  89
  DEL PEAK 51(XP21.1) WILD-TYPE   7 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED      1   89
  DEL PEAK 51(XP21.1) WILD-TYPE    7  220
                        clus
vv                       DEL PEAK 51(XP21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          89
                        clus
vv                       DEL PEAK 51(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           220
[1] 2 2
[1] FALSE

Clustering(82) Variable = DEL PEAK 52(XP11.3) MUTATION ANALYSIS
D82V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 52(XP11.3) MUTATED    76  63
  DEL PEAK 52(XP11.3) WILD-TYPE 205 133
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                          139                           338 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                           63                           133 
$`DEL PEAK 52(XP11.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
       12.20         7.46        75.75        11.34        92.15        31.99 
TCGA-18-3417 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 TCGA-21-1080 
       36.07         2.79        49.94        27.19        99.16       122.43 
TCGA-21-1082 TCGA-21-1083 TCGA-22-0940 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
      119.80        43.23        21.99        20.48        35.08        48.33 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 
       19.30        11.77        63.55        44.25        71.34        79.20 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4566 
       18.84        30.12        56.32        22.06         7.63       174.08 
TCGA-33-4582 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL 
      103.53         0.30        36.62       110.99       118.36        27.16 
TCGA-34-2600 TCGA-34-2605 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       61.61        28.96        30.94         4.96         1.12        27.19 
TCGA-34-8456 TCGA-37-4135 TCGA-37-4141 TCGA-39-5016 TCGA-39-5027 TCGA-39-5028 
       26.43         6.81         0.39        74.07        60.79         1.71 
TCGA-43-6770 TCGA-43-7656 TCGA-43-8116 TCGA-43-8118 TCGA-46-6025 TCGA-51-4079 
       21.47        19.59        11.77         2.93        10.65         0.39 
TCGA-51-4080 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 
        0.39         0.99         0.43         0.99         0.85         6.51 
TCGA-56-8624 TCGA-56-A4BW TCGA-56-A5DR TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        1.18        19.23         0.13        29.95        71.24        16.47 
TCGA-58-A46M TCGA-60-2696 TCGA-60-2707 TCGA-60-2710 TCGA-60-2711 TCGA-60-2712 
       35.24         3.58        21.93        66.54        41.42         9.01 
TCGA-60-2713 TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2753 
       56.91        58.65        25.28        16.37        34.59         1.02 
TCGA-66-2757 TCGA-66-2770 TCGA-66-2773 TCGA-66-2780 TCGA-66-2782 TCGA-66-2786 
       43.99        23.01         3.02        12.03        12.00        25.97 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-7756 
       22.98        30.02        10.06        54.08        49.05         6.64 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-8009 
       29.56        23.28        11.18         0.49        42.28        53.95 
TCGA-77-8133 TCGA-77-8140 TCGA-77-8144 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 
       53.92        11.54        27.39        35.90         0.33       117.57 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-7698 TCGA-85-7699 
       42.08        27.62         9.67        12.99        31.30        32.91 
TCGA-85-8071 TCGA-85-8288 TCGA-85-8352 TCGA-85-8354 TCGA-85-8580 TCGA-85-A4CN 
       14.07        13.22         5.29        32.71        14.63        19.33 
TCGA-85-A4QR TCGA-85-A50M TCGA-90-7766 TCGA-92-8063 TCGA-94-8035 TCGA-94-8490 
       19.73        12.56         9.50         4.01         4.01         5.03 
TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A53A 
       26.63        17.69        49.87        19.36         2.76        18.15 
TCGA-98-A53J TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK 
       20.71        13.18         4.54        51.78        45.37         4.21 
TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NK-A5CT TCGA-O2-A52S 
        2.89        39.85        37.22        30.58        65.49        12.72 
TCGA-O2-A5IB 
       11.18 

$`DEL PEAK 52(XP11.3) WILD-TYPE`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 
       79.46         4.80       117.57        23.54         1.64        86.96 
TCGA-18-4083 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 
        6.18       154.32       119.54        46.88        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 
       34.78        15.58        31.73         9.34        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 
       41.69        33.93        10.82        32.19         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
        4.31        64.21         1.74        14.10        27.02        48.82 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       24.13         0.56        38.17        34.75        13.12        32.02 
TCGA-22-4609 TCGA-22-5471 TCGA-22-5472 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 
        9.57        31.73        64.93        14.63         0.79        54.28 
TCGA-22-5482 TCGA-22-5489 TCGA-22-5492 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
       11.74        62.86        16.64       133.74        98.01        79.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
      151.27        14.07        54.44         1.55        19.76        27.02 
TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASI TCGA-34-2596 TCGA-34-2604 TCGA-34-2608 
        4.70         6.94        44.19         2.63        31.50        32.88 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       31.27        65.23        67.79        56.38         9.07        23.24 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 
       12.00        16.93        18.15         4.04        20.91         3.95 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        0.43         0.39         6.58         8.12         7.46         7.82 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        3.39        47.80        44.75        68.58        55.20        70.03 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       24.33         1.94        27.39        36.39        15.58        35.64 
TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 
       35.70        17.88        17.06        40.21        22.49        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       27.02        33.11        18.38        27.91        12.36        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-A474 
        5.46         3.81         7.76        66.51        13.38        11.61 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 TCGA-46-6026 TCGA-51-4081 
        9.73        14.20        12.03         9.99        13.91        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
       28.34         5.46        30.35         8.75        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 TCGA-56-7579 TCGA-56-7580 
        0.10        18.25         2.04         0.62         1.45         1.32 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8308 TCGA-56-8309 
        0.10        17.49         3.48        26.89        17.00        14.07 
TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 
        1.35        16.77         1.81        22.75        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ 
       20.25        15.81        20.94        13.32        17.85        21.04 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       18.74         0.26         2.76         0.03        13.25        13.55 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 
       34.78        85.12        34.36        56.65        29.92        21.11 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 
       12.23        10.22        96.82        37.94        92.71        80.45 
TCGA-60-2709 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       49.48        50.33        35.34        48.49        42.64         3.19 
TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       32.32        29.85        35.90        23.57        26.83        11.77 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
      102.67        70.62        66.61        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MU TCGA-63-A5MV TCGA-63-A5MW 
       11.34        89.29        78.28        25.41        36.16        53.88 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2754 
       16.96        43.10         2.01        21.07         0.99         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        0.92         0.99        21.01        25.05         0.99         2.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2777 
        1.02         2.01         2.01         7.07        19.00         2.01 
TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 
       19.00         3.98        24.95         1.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-8250 
        4.04         5.03         4.01         2.73         6.94         8.02 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 
       13.35        16.18        14.73        73.12        75.09        89.98 
TCGA-77-7140 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       20.78        70.13       106.95         0.16        46.78        15.75 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 
        6.51        86.76        37.81        82.92        12.59        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       17.72       104.09        26.40         6.97         9.63        54.41 
TCGA-77-8153 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
       65.49       126.18       132.36        22.29         5.92        42.41 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       30.81        38.86        11.97         6.41        36.53        34.95 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
        1.38         1.15        29.95        18.94        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       24.13        31.56        16.87        34.52        10.09         0.76 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       22.45        16.77         3.09         2.01         0.72         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB 
       13.94        12.59         0.10        15.62        25.68        17.72 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       14.96        24.36        18.18        16.21        15.85        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 
        0.79        12.39         3.65        24.92         2.93        11.77 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
       14.07        20.22        22.62        10.59         2.70         3.48 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A4VJ 
        5.26         2.30        21.04         0.16        11.70        14.14 
TCGA-94-A5I4 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       16.14        57.07        18.31        17.46        16.57         8.42 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A539 TCGA-98-A53B 
       30.81        30.67        21.34        27.16         3.88         2.01 
TCGA-98-A53C TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-J1-A4AH TCGA-L3-A4E7 
       27.02        21.21        20.32        18.58        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HH 
       16.11        13.41        11.84         0.07        64.08         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HR TCGA-NC-A5HT TCGA-NK-A5CR 
       13.74        24.00        14.73        29.75        22.78        83.57 
TCGA-NK-A5CX TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V 
        3.65        16.80         0.43        33.07         3.72        43.89 
TCGA-O2-A52W TCGA-XC-AA0X 
        8.58         0.20 

  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                       174.08                        154.32 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                       21.990                        18.165 
[1] "0.1 - 174.1 (22.0)" "0.0 - 154.3 (18.2)"
[1] "hr=" "1"  
D82V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 52(XP11.3) MUTATED         0       27       41        1        23
  DEL PEAK 52(XP11.3) WILD-TYPE       2       60      110        1        40
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 52(XP11.3) MUTATED          25         2         15          7
  DEL PEAK 52(XP11.3) WILD-TYPE        67         1         47         14
                               vv
clus                            STAGE IV
  DEL PEAK 52(XP11.3) MUTATED          1
  DEL PEAK 52(XP11.3) WILD-TYPE        6
D82V3, multiclass
            clus
vv           DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                            27                            60
  STAGE IB                            41                           110
  STAGE II                             1                             1
  STAGE IIA                           23                            40
  STAGE IIB                           25                            67
  STAGE III                            2                             1
  STAGE IIIA                          15                            47
  STAGE IIIB                           7                            14
  STAGE IV                             1                             6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 52(XP11.3) MUTATED    35  78  20  11
  DEL PEAK 52(XP11.3) WILD-TYPE  76 212  49  12
D82V4, multiclass
    clus
vv   DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  T1                          35                            76
  T2                          78                           212
  T3                          20                            49
  T4                          11                            12
[1] 4 2
[1] TRUE
[1] "dimension of 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 52(XP11.3) MUTATED    92  42   9   0
  DEL PEAK 52(XP11.3) WILD-TYPE 220  89  30   5
D82V5, multiclass
    clus
vv   DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  N0                          92                           220
  N1                          42                            89
  N2                           9                            30
  N3                           0                             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"
D82V6, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP11.3) MUTATED   120   1
  DEL PEAK 52(XP11.3) WILD-TYPE 284   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED    120    1
  DEL PEAK 52(XP11.3) WILD-TYPE  284    6
   clus
vv  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  0                         120                           284
  1                           1                             6
[1] 2 2
[1] FALSE
D82V7, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP11.3) MUTATED    36 108
  DEL PEAK 52(XP11.3) WILD-TYPE  91 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED     36  108
  DEL PEAK 52(XP11.3) WILD-TYPE   91  258
        clus
vv       DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  FEMALE                          36                            91
  MALE                           108                           258
[1] 2 2
[1] FALSE
D82V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 52(XP11.3) MUTATED                                       3
  DEL PEAK 52(XP11.3) WILD-TYPE                                    12
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 52(XP11.3) MUTATED                                         0
  DEL PEAK 52(XP11.3) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 52(XP11.3) MUTATED                                        1
  DEL PEAK 52(XP11.3) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 52(XP11.3) MUTATED                                         0
  DEL PEAK 52(XP11.3) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 52(XP11.3) MUTATED                                                           140
  DEL PEAK 52(XP11.3) WILD-TYPE                                                         330
D82V9, multiclass
                                                             clus
vv                                                            DEL PEAK 52(XP11.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         140
                                                             clus
vv                                                            DEL PEAK 52(XP11.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  12
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           330
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V10, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP11.3) MUTATED     4 140
  DEL PEAK 52(XP11.3) WILD-TYPE   9 340
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED      4  140
  DEL PEAK 52(XP11.3) WILD-TYPE    9  340
     clus
vv    DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  NO                            4                             9
  YES                         140                           340
[1] 2 2
[1] FALSE
D82V11, continuous
D82V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 52(XP11.3) MUTATED   120   2   0   6
  DEL PEAK 52(XP11.3) WILD-TYPE 274  10   4  16
D82V13, multiclass
    clus
vv   DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  R0                         120                           274
  R1                           2                            10
  R2                           0                             4
  RX                           6                            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 52(XP11.3) MUTATED       3                        10    95
  DEL PEAK 52(XP11.3) WILD-TYPE     6                        21   245
D82V14, multiclass
                           clus
vv                          DEL PEAK 52(XP11.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              95
                           clus
vv                          DEL PEAK 52(XP11.3) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V15, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP11.3) MUTATED     1  83
  DEL PEAK 52(XP11.3) WILD-TYPE   7 226
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED      1   83
  DEL PEAK 52(XP11.3) WILD-TYPE    7  226
                        clus
vv                       DEL PEAK 52(XP11.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          83
                        clus
vv                       DEL PEAK 52(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           226
[1] 2 2
[1] FALSE

Clustering(83) Variable = DEL PEAK 53(XQ22.3) MUTATION ANALYSIS
D83V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 53(XQ22.3) MUTATED    63  45
  DEL PEAK 53(XQ22.3) WILD-TYPE 218 151
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                          108                           369 
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                           45                           151 
$`DEL PEAK 53(XQ22.3) MUTATED`
TCGA-18-3406 TCGA-18-3419 TCGA-18-4086 TCGA-18-5592 TCGA-18-5595 TCGA-21-1072 
       12.20         1.64         2.79        49.94        27.19        99.16 
TCGA-21-1080 TCGA-21-1082 TCGA-22-0940 TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 
      122.43       119.80        21.99        19.30        11.77        31.73 
TCGA-22-5473 TCGA-22-5481 TCGA-22-5485 TCGA-22-5491 TCGA-33-4533 TCGA-33-4582 
       63.55        79.20        30.12        56.32       133.74       103.53 
TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI 
       54.44         4.70         0.30        36.62       110.99        44.19 
TCGA-33-AASL TCGA-34-2600 TCGA-34-2609 TCGA-34-5929 TCGA-37-4135 TCGA-37-4141 
       27.16        61.61        31.27         4.96         6.81         0.39 
TCGA-39-5027 TCGA-43-7656 TCGA-51-4080 TCGA-52-7810 TCGA-56-7221 TCGA-56-7222 
       60.79        19.59         0.39        30.35         0.99         0.43 
TCGA-56-7223 TCGA-56-8307 TCGA-56-A4BW TCGA-56-A5DR TCGA-58-8388 TCGA-58-8390 
        0.99        26.89        19.23         0.13        13.55        29.95 
TCGA-58-8392 TCGA-60-2695 TCGA-60-2696 TCGA-60-2712 TCGA-60-2713 TCGA-60-2719 
       16.47        21.11         3.58         9.01        56.91        42.64 
TCGA-60-2721 TCGA-60-2724 TCGA-60-2726 TCGA-63-A5MI TCGA-63-A5MW TCGA-63-A5MY 
       32.32        23.57        11.77        58.65        53.88        34.59 
TCGA-66-2727 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2763 
       16.96        21.07         1.02         2.01        43.99         0.99 
TCGA-66-2766 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-66-2790 
        1.02        12.03         3.98        12.00        25.97        22.98 
TCGA-66-2795 TCGA-68-7755 TCGA-77-6844 TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 
        4.01         2.73        75.09        11.18        42.28        70.13 
TCGA-77-7337 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8153 
      106.95        39.09       104.09        11.54        27.39        65.49 
TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5GA TCGA-85-7699 TCGA-85-8070 TCGA-85-8071 
       35.90       117.57        42.08        32.91        31.56        14.07 
TCGA-85-8072 TCGA-85-8288 TCGA-85-8479 TCGA-90-7766 TCGA-94-7557 TCGA-94-8035 
       16.87        13.22         0.72         9.50         0.16         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-98-8022 TCGA-98-A538 
        5.03        26.63        14.14        49.87        30.67        27.16 
TCGA-98-A53A TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK 
       18.15         4.54        51.78         1.22        45.37         4.21 
TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52S TCGA-O2-A5IB 
       30.58        22.78        65.49        16.80        12.72        11.18 

$`DEL PEAK 53(XQ22.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
        7.46        75.75        79.46         4.80       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3421 TCGA-18-4083 
       23.54        92.15        31.99        36.07        86.96         6.18 
TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
      154.32       119.54        46.88        70.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       15.58        31.73         9.34        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1000 
       41.69        33.93        10.82        32.19         7.33        14.93 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 
        4.31        64.21         1.74        14.10        27.02        48.82 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
       20.48        35.08        48.33        24.13         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-5472 TCGA-22-5474 
       34.75        13.12        32.02         9.57        64.93        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 
       44.25         0.79        54.28        71.34        11.74        18.84 
TCGA-22-5489 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4538 TCGA-33-4547 
       62.86        16.64        22.06         7.63        98.01        79.53 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-33-6737 TCGA-33-6738 
      174.08       151.27        14.07         1.55        19.76        27.02 
TCGA-33-AASB TCGA-33-AASJ TCGA-34-2596 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
        6.94       118.36         2.63        31.50        28.96        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        67.79        56.38         9.07        23.24        12.00 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       16.93        30.94        18.15         1.12        27.19         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       26.43        20.91         3.95         0.43         0.39         6.58 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 
        8.12         7.46         7.82         3.39        47.80        74.07 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
       44.75        68.58        55.20        70.03         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        27.39        36.39        15.58        35.64        35.70 
TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 
       17.88        17.06        40.21        22.49        38.66        27.02 
TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       33.11        18.38        27.91        12.36        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 
        5.46         3.81         7.76        66.51        13.38        11.77 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3768 
        2.93        11.61         9.73        14.20        12.03         9.99 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 
       10.65        13.91         0.39        29.95        28.34         5.46 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        8.75        27.45        28.96         0.10        18.25         2.04 
TCGA-56-6546 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
        0.62         1.45         1.32         0.85         6.51         0.10 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8308 TCGA-56-8309 TCGA-56-8503 TCGA-56-8504 
       17.49         3.48        17.00        14.07         1.35        16.77 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75         1.18        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK 
       15.81        20.94        13.32        17.85        21.04        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8391 TCGA-58-8393 
        0.26         2.76         0.03        13.25        71.24        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 
       85.12        34.36        56.65        35.24        29.92        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       10.22        96.82        37.94        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
       49.48        66.54        41.42        50.33        35.34        48.49 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5MG 
        3.19        29.85        35.90        26.83       102.67        70.62 
TCGA-63-A5MH TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       66.61        59.97        45.57        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MU TCGA-63-A5MV TCGA-66-2734 
       89.29        78.28        16.37        25.41        36.16        43.10 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 
        2.01         0.99         0.92         0.99        21.01        25.05 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
        2.01         2.01         2.01         7.07        23.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 
        3.02         2.01        19.00        24.95         1.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
       22.98         4.04         5.03        30.02        10.06        54.08 
TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
       49.05         6.64         6.94         8.02        13.35        16.18 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7140 
       14.73        29.56        73.12        23.28        89.98        20.78 
TCGA-77-7141 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
        0.49         0.16        46.78        15.75         6.51        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 
       53.95        37.81        82.92        12.59        53.92        17.72 
TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ 
       26.40         6.97         9.63        54.41         0.33       126.18 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GF 
      132.36        22.29         5.92        42.41        30.81        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       38.86         9.67        11.97        12.99         6.41        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
       34.95        31.30         1.38         1.15        29.95        18.94 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       25.15        19.04        24.13        34.52        10.09         0.76 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       22.45        16.77         5.29         3.09        32.71         2.01 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        7.76        14.63        13.94        12.59         0.10        15.62 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       25.68        19.33        17.72        14.96        24.36        18.18 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       19.73        12.56        16.21        15.85        14.96         0.79 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-7964 
       12.39         3.65        24.92         2.93        11.77        14.07 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 
       20.22        22.62        10.59         2.70         3.48         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-94-A5I4 TCGA-94-A5I6 
        5.26         2.30        21.04        11.70        16.14        17.69 
TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK TCGA-96-A4JL TCGA-98-7454 
       57.07        18.31        17.46        19.36        16.57         8.42 
TCGA-98-8020 TCGA-98-8021 TCGA-98-8023 TCGA-98-A539 TCGA-98-A53B TCGA-98-A53C 
        2.76        30.81        21.34         3.88         2.01        27.02 
TCGA-98-A53D TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-J1-A4AH TCGA-L3-A4E7 
       21.21        20.32        18.58        20.71        19.10        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HD TCGA-NC-A5HE 
       16.11        13.18        13.41        11.84         0.07        64.08 
TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HM TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ 
       13.74         2.89        39.85        37.22        24.00        14.73 
TCGA-NC-A5HR TCGA-NK-A5CR TCGA-NK-A5CX TCGA-NK-A7XE TCGA-O2-A52N TCGA-O2-A52Q 
       29.75        83.57         3.65         0.43        33.07         3.72 
TCGA-O2-A52V TCGA-O2-A52W TCGA-XC-AA0X 
       43.89         8.58         0.20 

  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                       133.74                        174.08 
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                        22.88                         18.58 
[1] "0.1 - 133.7 (22.9)" "0.0 - 174.1 (18.6)"
[1] "hr=" "1.1"
D83V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 53(XQ22.3) MUTATED         0       24       34        0        12
  DEL PEAK 53(XQ22.3) WILD-TYPE       2       63      117        2        51
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 53(XQ22.3) MUTATED          20         2         11          5
  DEL PEAK 53(XQ22.3) WILD-TYPE        72         1         51         16
                               vv
clus                            STAGE IV
  DEL PEAK 53(XQ22.3) MUTATED          1
  DEL PEAK 53(XQ22.3) WILD-TYPE        6
D83V3, multiclass
            clus
vv           DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                            24                            63
  STAGE IB                            34                           117
  STAGE II                             0                             2
  STAGE IIA                           12                            51
  STAGE IIB                           20                            72
  STAGE III                            2                             1
  STAGE IIIA                          11                            51
  STAGE IIIB                           5                            16
  STAGE IV                             1                             6
[1] 10  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 53(XQ22.3) MUTATED    31  57  17   6
  DEL PEAK 53(XQ22.3) WILD-TYPE  80 233  52  17
D83V4, multiclass
    clus
vv   DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  T1                          31                            80
  T2                          57                           233
  T3                          17                            52
  T4                           6                            17
[1] 4 2
[1] TRUE
[1] "dimension of 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 53(XQ22.3) MUTATED    73  32   6   0
  DEL PEAK 53(XQ22.3) WILD-TYPE 239  99  33   5
D83V5, multiclass
    clus
vv   DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  N0                          73                           239
  N1                          32                            99
  N2                           6                            33
  N3                           0                             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"
D83V6, binary
                               cls
clus                              0   1
  DEL PEAK 53(XQ22.3) MUTATED    91   1
  DEL PEAK 53(XQ22.3) WILD-TYPE 313   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ22.3) MUTATED     91    1
  DEL PEAK 53(XQ22.3) WILD-TYPE  313    6
   clus
vv  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  0                          91                           313
  1                           1                             6
[1] 2 2
[1] FALSE
D83V7, binary
                               cls
clus                              0   1
  DEL PEAK 53(XQ22.3) MUTATED    34  77
  DEL PEAK 53(XQ22.3) WILD-TYPE  93 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ22.3) MUTATED     34   77
  DEL PEAK 53(XQ22.3) WILD-TYPE   93  289
        clus
vv       DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  FEMALE                          34                            93
  MALE                            77                           289
[1] 2 2
[1] FALSE
D83V8, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 53(XQ22.3) MUTATED                                       6
  DEL PEAK 53(XQ22.3) WILD-TYPE                                     9
                               vv
clus                            LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 53(XQ22.3) MUTATED                                         0
  DEL PEAK 53(XQ22.3) WILD-TYPE                                       1
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 53(XQ22.3) MUTATED                                        1
  DEL PEAK 53(XQ22.3) WILD-TYPE                                      5
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 53(XQ22.3) MUTATED                                         1
  DEL PEAK 53(XQ22.3) WILD-TYPE                                       0
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 53(XQ22.3) MUTATED                                                           103
  DEL PEAK 53(XQ22.3) WILD-TYPE                                                         367
D83V9, multiclass
                                                             clus
vv                                                            DEL PEAK 53(XQ22.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         103
                                                             clus
vv                                                            DEL PEAK 53(XQ22.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG CLEAR CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           367
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V10, binary
                               cls
clus                              0   1
  DEL PEAK 53(XQ22.3) MUTATED     3 108
  DEL PEAK 53(XQ22.3) WILD-TYPE  10 372
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ22.3) MUTATED      3  108
  DEL PEAK 53(XQ22.3) WILD-TYPE   10  372
     clus
vv    DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  NO                            3                            10
  YES                         108                           372
[1] 2 2
[1] FALSE
D83V11, continuous
D83V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 53(XQ22.3) MUTATED    93   0   1   2
  DEL PEAK 53(XQ22.3) WILD-TYPE 301  12   3  20
D83V13, multiclass
    clus
vv   DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  R0                          93                           301
  R1                           0                            12
  R2                           1                             3
  RX                           2                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 53(XQ22.3) MUTATED       0                        10    70
  DEL PEAK 53(XQ22.3) WILD-TYPE     9                        21   270
D83V14, multiclass
                           clus
vv                          DEL PEAK 53(XQ22.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              70
                           clus
vv                          DEL PEAK 53(XQ22.3) WILD-TYPE
  ASIAN                                                 9
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               270
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V15, binary
                               cls
clus                              0   1
  DEL PEAK 53(XQ22.3) MUTATED     0  61
  DEL PEAK 53(XQ22.3) WILD-TYPE   8 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ22.3) MUTATED      0   61
  DEL PEAK 53(XQ22.3) WILD-TYPE    8  248
                        clus
vv                       DEL PEAK 53(XQ22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          61
                        clus
vv                       DEL PEAK 53(XQ22.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           248
[1] 2 2
[1] FALSE
