[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/22506957/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUSC-TP/22533935/transformed.cor.cli.txt"

nPatients in clinical file=504, in cluster file=501, common to both=501
[1]  83 501
[1] "AMP PEAK  1(1Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                          258                           243 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                          258                           243 
[1] "AMP PEAK  2(2P16.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                          275                           226 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                          275                           226 
[1] "AMP PEAK  3(2Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                          172                           329 
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                          172                           329 
[1] "AMP PEAK  4(3Q26.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           452                             49 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           452                             49 
[1] "AMP PEAK  5(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                        119                         382 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                        119                         382 
[1] "AMP PEAK  6(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           387                            114 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           387                            114 
[1] "AMP PEAK  7(5P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                        354                         147 
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                        354                         147 
[1] "AMP PEAK  8(6P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                          166                           335 
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                          166                           335 
[1] "AMP PEAK  9(6Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                        152                         349 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                        152                         349 
[1] "AMP PEAK 10(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          256                           245 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          256                           245 
[1] "AMP PEAK 11(7Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                          264                           237 
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                          264                           237 
[1] "AMP PEAK 12(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                           238                            263 
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                           238                            263 
[1] "AMP PEAK 13(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           352                            149 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           352                            149 
[1] "AMP PEAK 14(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          136                           365 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          136                           365 
[1] "AMP PEAK 15(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           185                            316 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           185                            316 
[1] "AMP PEAK 16(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                            255                             246 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                            255                             246 
[1] "AMP PEAK 17(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                         178                          323 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                         178                          323 
[1] "AMP PEAK 18(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          91                          410 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          91                          410 
[1] "AMP PEAK 19(14Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                           159                            342 
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                           159                            342 
[1] "AMP PEAK 20(14Q32.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                            158                             343 
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                            158                             343 
[1] "AMP PEAK 21(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                           179                            322 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                           179                            322 
[1] "AMP PEAK 22(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                           236                            265 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                           236                            265 
[1] "AMP PEAK 23(18P11.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                            179                             322 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                            179                             322 
[1] "AMP PEAK 24(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           151                            350 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           151                            350 
[1] "AMP PEAK 25(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         225                          276 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         225                          276 
[1] "AMP PEAK 26(19Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                           234                            267 
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                           234                            267 
[1] "AMP PEAK 27(20P12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           280                            221 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           280                            221 
[1] "AMP PEAK 28(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                            306                             195 
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                            306                             195 
[1] "AMP PEAK 29(22Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                            256                             245 
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                            256                             245 
[1] "AMP PEAK 30(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                        124                         377 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                        124                         377 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           228                            273 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           228                            273 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          221                           280 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          221                           280 
[1] "DEL PEAK  3(2P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           50                           451 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           50                           451 
[1] "DEL PEAK  4(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          131                           370 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          131                           370 
[1] "DEL PEAK  5(2Q37.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          159                           342 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          159                           342 
[1] "DEL PEAK  6(3P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                          398                           103 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                          398                           103 
[1] "DEL PEAK  7(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                        434                          67 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                        434                          67 
[1] "DEL PEAK  8(3P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          427                            74 
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          427                            74 
[1] "DEL PEAK  9(3P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                          421                            80 
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                          421                            80 
[1] "DEL PEAK 10(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                           79                           422 
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                           79                           422 
[1] "DEL PEAK 11(4P15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          316                           185 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          316                           185 
[1] "DEL PEAK 12(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          285                           216 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          285                           216 
[1] "DEL PEAK 13(4Q32.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                          329                           172 
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                          329                           172 
[1] "DEL PEAK 14(4Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          331                           170 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          331                           170 
[1] "DEL PEAK 15(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          369                           132 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          369                           132 
[1] "DEL PEAK 16(5Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                          386                           115 
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                          386                           115 
[1] "DEL PEAK 17(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                          134                           367 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                          134                           367 
[1] "DEL PEAK 18(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE 
                        135                         366 
  DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE 
                        135                         366 
[1] "DEL PEAK 19(7Q11.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE 
                            48                            453 
  DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE 
                            48                            453 
[1] "DEL PEAK 20(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE 
                          104                           397 
  DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE 
                          104                           397 
[1] "DEL PEAK 21(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                          341                           160 
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                          341                           160 
[1] "DEL PEAK 22(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        332                         169 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        332                         169 
[1] "DEL PEAK 23(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          388                           113 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          388                           113 
[1] "DEL PEAK 24(9P21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE 
                          326                           175 
  DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE 
                          326                           175 
[1] "DEL PEAK 25(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                           251                            250 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                           251                            250 
[1] "DEL PEAK 26(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                           228                            273 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                           228                            273 
[1] "DEL PEAK 27(10P15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE 
                           211                            290 
  DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE 
                           211                            290 
[1] "DEL PEAK 28(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            268                             233 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            268                             233 
[1] "DEL PEAK 29(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           245                            256 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           245                            256 
[1] "DEL PEAK 30(11Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                           163                            338 
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                           163                            338 
[1] "DEL PEAK 31(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                         184                          317 
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                         184                          317 
[1] "DEL PEAK 32(12Q24.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                             86                             415 
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                             86                             415 
[1] "DEL PEAK 33(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            331                             170 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            331                             170 
[1] "DEL PEAK 34(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           344                            157 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           344                            157 
[1] "DEL PEAK 35(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                           175                            326 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                           175                            326 
[1] "DEL PEAK 36(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           167                            334 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           167                            334 
[1] "DEL PEAK 37(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                           169                            332 
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                           169                            332 
[1] "DEL PEAK 38(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                           187                            314 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                           187                            314 
[1] "DEL PEAK 39(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           210                            291 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           210                            291 
[1] "DEL PEAK 40(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           272                            229 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           272                            229 
[1] "DEL PEAK 41(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           132                            369 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           132                            369 
[1] "DEL PEAK 42(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                           102                            399 
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                           102                            399 
[1] "DEL PEAK 43(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                         234                          267 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                         234                          267 
[1] "DEL PEAK 44(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           236                            265 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           236                            265 
[1] "DEL PEAK 45(19Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                            149                             352 
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                            149                             352 
[1] "DEL PEAK 46(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           244                            257 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           244                            257 
[1] "DEL PEAK 47(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                           281                            220 
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                           281                            220 
[1] "DEL PEAK 48(22Q11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                             95                             406 
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                             95                             406 
[1] "DEL PEAK 49(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                            127                             374 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                            127                             374 
[1] "DEL PEAK 50(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                          155                           346 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                          155                           346 
[1] "DEL PEAK 51(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                          151                           350 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                          151                           350 
[1] "DEL PEAK 52(XP11.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                          149                           352 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                          149                           352 
[1] "DEL PEAK 53(XQ22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                          114                           387 
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                          114                           387 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RESIDUAL_TUMOR"                      
[19] "RACE"                                
[20] "ETHNICITY"                           

Input Data has 20 rows and 501 columns.

[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=202,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=253,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=105,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 501 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"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "KARNOFSKY_PERFORMANCE_SCORE"  
 [9] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RESIDUAL_TUMOR"               
[13] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=45, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
112 294  71  24 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
112 294  71  24 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
112 294  71  24 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
112 294  71  24 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
317 133  40   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
317 133  40   5 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
317 133  40   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
317 133  40   5 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=10, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=105, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=55, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, 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   141 113
  AMP PEAK  1(1Q21.2) WILD-TYPE 139 101
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                          254                           240 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                          113                           101 
$`AMP PEAK  1(1Q21.2) MUTATED`
TCGA-18-3416 TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4533 TCGA-34-2605 
       31.99        48.82        60.66        22.06       133.74        28.96 
TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-56-8305 TCGA-56-8308 
        7.76        78.18        11.61        12.03         3.45        17.00 
TCGA-56-8504 TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-77-7140 
       16.77        41.42        35.34        32.32        66.61        20.78 
TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 TCGA-94-7557 TCGA-94-7943 TCGA-96-A4JK 
       42.08        30.81        14.07         0.16        18.38        19.36 
TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3408 
       19.10         0.07        76.80        40.90         0.43        75.75 
TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-4721 TCGA-18-5592 
      117.57        23.54        92.15        36.07       154.32        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1081 
      119.54        46.88        99.16        70.16        34.78         9.34 
TCGA-21-1082 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-1011 
      119.80        41.69        33.93        10.82        21.99         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 
       14.10        27.02        20.48        48.33        24.13         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 
       38.17        34.75        19.30        63.55        14.63        86.30 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4538 
       71.34        79.20        18.84        30.12        62.86        97.94 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 
      173.82       103.53       151.27        14.07        54.44        63.35 
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-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 
       61.61        32.88        65.23        60.30        50.66        39.32 
TCGA-34-7107 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 
        1.12         4.04        33.90         4.01         0.39         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
        7.46         7.82         6.81         0.39         3.39        37.58 
TCGA-37-A5EN TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5034 
       21.70       126.58        68.58        55.20        82.52        36.39 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       68.38        55.56        17.06        40.21        38.66        39.12 
TCGA-43-3920 TCGA-43-6143 TCGA-43-A475 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
       33.11        22.98         9.73         9.83         4.44        10.65 
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-52-7812 TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 TCGA-56-7730 TCGA-56-8622 
       27.45        18.25        21.90        14.53         6.51         1.81 
TCGA-56-A4BX TCGA-58-8388 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L 
       13.32        13.55        16.47        34.78        34.36        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 TCGA-60-2706 TCGA-60-2708 
       35.24        29.92        21.11        10.22        92.71        80.45 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-A5MB 
       29.85        35.90        26.83        11.77        52.67       102.67 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS TCGA-66-2727 TCGA-66-2734 
       59.97        45.57        89.29        78.28        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 
        2.01        21.07         0.92         0.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2782 
        0.99        23.01         3.02         2.01         3.98        12.00 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 
        1.97        40.01         5.03        10.06         4.01        49.05 
TCGA-68-7755 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6723 TCGA-77-6843 
        2.73        13.35        16.18        14.73        12.33        73.12 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7337 TCGA-77-7338 
       23.28        11.18       140.09         0.49       106.95         0.16 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8136 
       32.55        86.76        55.73        37.81        53.92        39.09 
TCGA-77-8139 TCGA-77-8145 TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 
      104.09         6.97        66.51        36.36       150.25        22.29 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
       61.94        27.62        38.86        41.39        40.24         6.41 
TCGA-85-7696 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 
       36.53        32.91         1.38        29.95        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 
       24.13        31.56        30.64        10.09        16.77         5.29 
TCGA-85-8353 TCGA-85-8479 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
        3.09        15.39        18.08        22.59        30.28        34.13 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L 
       19.86        30.48        27.16        14.96        15.29        12.39 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 
        3.65         2.93        20.22        22.62        10.59         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 
        4.01         5.26         2.30         5.03        14.14        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       71.01        18.31        30.81        30.67        21.34        27.16 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HH 
       18.58        20.71        16.11        11.84        64.54         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-O2-A52N 
       13.74        49.28        25.32        14.73        83.57        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-18-4083 TCGA-18-5595 
       12.20         4.47       123.19         4.80         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-5472 TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 
       32.19        14.93        64.93       129.01         1.55        19.76 
TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-8118 
       31.50        31.27        17.88        22.49        18.38         2.93 
TCGA-56-7221 TCGA-56-8201 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       19.99        13.05        17.85        21.04         0.13         3.58 
TCGA-60-2712 TCGA-68-8250 TCGA-90-7766 TCGA-94-7033 TCGA-94-A5I4 TCGA-96-7545 
        9.01         8.02         9.50        21.04        16.14        57.07 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 
        2.76         5.69        21.21        39.85        65.65        16.80 
TCGA-O2-A52W TCGA-18-3412 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-21-1076 
        8.58        11.34        92.42        86.96         2.79        60.89 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       15.58        31.73       122.43        43.23        31.63        88.11 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-4593 TCGA-22-4604 TCGA-22-4605 
        7.33         4.31        64.21        35.08        13.12        32.02 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 TCGA-22-5491 
        9.57        11.77        44.25         0.79        11.74        56.32 
TCGA-22-5492 TCGA-33-4547 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASJ TCGA-34-5232 
       16.64        79.53         0.30        36.62       118.36        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 
       74.66         9.07        16.93        44.75         4.96        38.79 
TCGA-34-8456 TCGA-37-3789 TCGA-37-4129 TCGA-39-5011 TCGA-39-5019 TCGA-39-5027 
       26.43         0.43         7.96       133.25       111.35       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-43-5670 
        1.71        24.33         1.94        60.53        71.18        27.91 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       24.89        21.47         5.46         3.81        19.59        13.38 
TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-6026 
       11.77        14.20        13.32        12.16        13.02        13.91 
TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 
       29.95        28.96        12.43        18.48        31.27        30.41 
TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
       19.76         0.10        17.49        33.24        14.96         4.93 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 TCGA-56-8624 
        3.48        26.89        14.07         1.35        22.75        13.81 
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-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 
       18.74         0.26        14.47         0.03        13.25        29.95 
TCGA-58-8391 TCGA-58-A46J TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 
       71.24        85.12        12.23        96.82        37.94        21.93 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       49.48        66.54        56.91        50.33        48.49        42.64 
TCGA-60-2720 TCGA-60-2724 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
        3.19        23.57        70.13        70.42        68.15        55.30 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MT 
       70.62        58.65        14.99        11.34        25.28        16.37 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       36.16        53.88        34.59         0.99         1.02         2.01 
TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       43.99         2.01         1.02         2.01         2.01         7.07 
TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 
       19.00        19.00        12.03        24.95        25.97        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-68-7756 TCGA-68-7757 
        4.04        22.98        30.02        54.08         6.64         6.94 
TCGA-70-6722 TCGA-77-6842 TCGA-77-6844 TCGA-77-7142 TCGA-77-7335 TCGA-77-7463 
       12.07        29.56        75.09        73.22        70.13        46.78 
TCGA-77-8007 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 
        6.51       156.66        12.59        17.72        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        60.53       126.18       132.36 
TCGA-77-A5G7 TCGA-85-6175 TCGA-85-7697 TCGA-85-7698 TCGA-85-7843 TCGA-85-7950 
        5.92         9.67        34.95        31.30         1.15        18.94 
TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8354 
       26.79        34.52         0.76        13.22        22.45        32.71 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB 
        2.01         7.76        36.59        38.14        12.59        30.97 
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        29.92        24.92 
TCGA-90-7769 TCGA-92-7340 TCGA-94-8035 TCGA-94-8491 TCGA-96-8170 TCGA-96-A4JL 
       11.77         2.70         4.01        26.63        17.46        27.68 
TCGA-98-7454 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 
       21.44        18.15         2.01        27.02        20.32        12.89 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL 
       13.18        13.41         4.54        57.30         4.21         2.89 
TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
       43.92        26.43         3.65         3.72        43.89         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 
                       173.82                        156.66 
  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE 
                       24.130                        19.745 
[1] "0.1 - 173.8 (24.1)" "0.0 - 156.7 (19.7)"
[1] "hr=" "1.1"
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1Q21.2) MUTATED         1       35       83        1        29
  AMP PEAK  1(1Q21.2) WILD-TYPE       1       54       69        1        36
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1Q21.2) MUTATED          50         2         37         10
  AMP PEAK  1(1Q21.2) WILD-TYPE        45         1         26          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                            35                            54
  STAGE IB                            83                            69
  STAGE II                             1                             1
  STAGE IIA                           29                            36
  STAGE IIB                           50                            45
  STAGE III                            2                             1
  STAGE IIIA                          37                            26
  STAGE IIIB                          10                             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    45 158  38  17
  AMP PEAK  1(1Q21.2) WILD-TYPE  67 136  33   7
D1V4, multiclass
    clus
vv   AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  T1                          45                            67
  T2                         158                           136
  T3                          38                            33
  T4                          17                             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   159  69  26   1
  AMP PEAK  1(1Q21.2) WILD-TYPE 158  64  14   4
D1V5, multiclass
    clus
vv   AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  N0                         159                           158
  N1                          69                            64
  N2                          26                            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   219   6
  AMP PEAK  1(1Q21.2) WILD-TYPE 192   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED    219    6
  AMP PEAK  1(1Q21.2) WILD-TYPE  192    1
   clus
vv  AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  0                         219                           192
  1                           6                             1
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.2) MUTATED    59 199
  AMP PEAK  1(1Q21.2) WILD-TYPE  71 172
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED     59  199
  AMP PEAK  1(1Q21.2) WILD-TYPE   71  172
        clus
vv       AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  FEMALE                          59                            71
  MALE                           199                           172
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.2) MUTATED   189  34
  AMP PEAK  1(1Q21.2) WILD-TYPE 195  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED    189   34
  AMP PEAK  1(1Q21.2) WILD-TYPE  195   19
     clus
vv    AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  NO                          189                           195
  YES                          34                            19
[1] 2 2
[1] FALSE
D1V9, 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 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                                                           242
  AMP PEAK  1(1Q21.2) WILD-TYPE                                                         237
D1V10, multiclass
                                                             clus
vv                                                            AMP PEAK  1(1Q21.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         242
                                                             clus
vv                                                            AMP PEAK  1(1Q21.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           237
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
D1V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1Q21.2) MUTATED   208   7   1  11
  AMP PEAK  1(1Q21.2) WILD-TYPE 191   5   3  12
D1V13, multiclass
    clus
vv   AMP PEAK  1(1Q21.2) MUTATED AMP PEAK  1(1Q21.2) WILD-TYPE
  R0                         208                           191
  R1                           7                             5
  R2                           1                             3
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q21.2) MUTATED       4                        14   185
  AMP PEAK  1(1Q21.2) WILD-TYPE     5                        17   164
D1V14, multiclass
                           clus
vv                          AMP PEAK  1(1Q21.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          14
  WHITE                                             185
                           clus
vv                          AMP PEAK  1(1Q21.2) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            17
  WHITE                                               164
[1] 3 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     5 163
  AMP PEAK  1(1Q21.2) WILD-TYPE   3 154
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.2) MUTATED      5  163
  AMP PEAK  1(1Q21.2) WILD-TYPE    3  154
                        clus
vv                       AMP PEAK  1(1Q21.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         163
                        clus
vv                       AMP PEAK  1(1Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           154
[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   158 113
  AMP PEAK  2(2P16.1) WILD-TYPE 122 101
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                          271                           223 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                          113                           101 
$`AMP PEAK  2(2P16.1) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-21-A5DI TCGA-22-5471 TCGA-22-A5C4 
        4.47       123.19        31.99        32.19        60.66        22.06 
TCGA-33-4532 TCGA-34-2604 TCGA-34-2605 TCGA-43-5668 TCGA-43-7658 TCGA-43-8118 
      129.01        31.50        28.96        18.38        78.18         2.93 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-60-2711 
       13.05         3.45        17.00        16.77        17.85        41.42 
TCGA-60-2712 TCGA-60-2715 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
        9.01        35.34        66.61         8.02        20.78        42.08 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-J1-A4AH 
        0.16        18.38        16.14        57.07        19.36        19.10 
TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 
        0.07        39.85        40.90         0.43         8.58       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        92.42        86.96 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1081 
       46.88        99.16        60.89        34.78        31.73         9.34 
TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-22-4591 TCGA-22-4595 TCGA-22-4599 
       43.23        88.11        33.93        20.48        24.13        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       34.75        13.12        32.02        11.77        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        86.30        71.34        18.84        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4566 TCGA-33-4582 TCGA-33-6738 TCGA-33-A4WN 
       56.32        16.64       173.82       103.53        63.35         4.70 
TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-5231 TCGA-34-5236 
      110.99       118.36         2.63        61.61        65.23         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       50.66        16.93        39.32         1.12        38.79         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 
       26.43        33.90         4.01         0.39         8.12         7.82 
TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        0.39        37.58        21.70       133.25       126.58       111.35 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
      102.18         1.71        60.53        68.38        71.18        55.56 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       17.06        40.21        38.66        39.12        33.11        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-8115 TCGA-46-3765 TCGA-46-3767 TCGA-46-3768 
       22.98        24.89        13.38        13.32        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7809 
        4.44        10.65         0.39         0.39        29.95         5.46 
TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 
       30.35         8.75        28.96        18.25        21.90        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-8083 TCGA-56-8304 
       14.53        31.27        19.76         6.51         4.93         3.48 
TCGA-56-8503 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS 
        1.35        20.25        15.81        19.23        13.32         0.26 
TCGA-58-8387 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       13.25        71.24        16.47        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 TCGA-60-2719 TCGA-60-2722 
       29.92        10.22        96.82        80.45        42.64        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7023 TCGA-63-A5MB 
       35.90        23.57        11.77        52.67        55.30       102.67 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       58.65        59.97        45.57        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2737 TCGA-66-2755 
       16.37        36.16        53.88        34.59         2.01         0.92 
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-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2787 TCGA-66-2789 
       19.00         3.02         2.01         3.98        40.01         4.04 
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-A59I TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 
        2.73         6.64        16.18        12.07        12.33        29.56 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       23.28        11.18       140.09         0.49        73.22        70.13 
TCGA-77-7337 TCGA-77-7465 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
      106.95        32.55        55.73       156.66        53.92        39.09 
TCGA-77-8139 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 
      104.09        26.40         6.97        66.51        54.41        36.36 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
      132.36       150.25        61.94        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7843 TCGA-85-7844 TCGA-85-8052 
       41.39         6.41        36.53         1.15        29.95        24.13 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 
       31.56        30.64        34.52        10.09         0.76        22.45 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
        5.29        32.71        18.08        22.59        34.13        30.97 
TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 
       19.86        19.73        27.16        15.85        14.96         3.65 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-8490 
        2.93        11.77        22.62         3.48         5.26         5.03 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-98-7454 TCGA-98-8021 
       26.63        14.14        17.69        18.31        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 
       30.67        21.34        27.16        18.58        20.71        16.11 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HL 
       13.18        11.84        64.54         1.22         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52V 
       49.28        25.32        14.73        83.57        33.07        43.89 
TCGA-XC-AA0X 
        0.20 

$`AMP PEAK  2(2P16.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 
       12.20         4.80         6.18        27.19        14.93        48.82 
TCGA-22-5472 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2609 TCGA-39-5039 
       64.93       133.74         1.55        19.76        31.27        17.88 
TCGA-43-2578 TCGA-43-7657 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-A4ZJ 
       22.49         7.76        11.61        12.03        19.99        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2721 TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 
        0.13         3.58        32.32        30.81         9.50        14.07 
TCGA-94-7033 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HE TCGA-NK-A5CT 
       21.04         2.76         5.69        21.21        76.80        65.65 
TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       16.80        75.75         2.79       154.32        49.94       119.54 
TCGA-21-1075 TCGA-21-1078 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 
       70.16        15.58       122.43       119.80        31.63        41.69 
TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       10.82        21.99         7.33         4.31        64.21         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4607 
       14.10        27.02        35.08        48.33         0.56        19.30 
TCGA-22-4609 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-33-4538 TCGA-33-4547 
        9.57        79.20        11.74        30.12        97.94        79.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
      151.27        14.07        54.44         0.30        36.62         6.94 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
       44.19        27.16        32.88        81.24        74.66        60.30 
TCGA-34-5927 TCGA-34-5929 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 
       44.75         4.96         0.43         7.96         7.46         6.81 
TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 
        3.39        68.58        55.20        82.52        24.33         1.94 
TCGA-39-5034 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8116 
       36.39        21.47         5.46         3.81        19.59        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3766 TCGA-46-6026 TCGA-52-7622 TCGA-52-7812 
        9.73        14.20        12.16        13.91        28.34        27.45 
TCGA-56-5897 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       12.43        30.41         0.10        17.49        33.24        14.96 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       26.89        14.07         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 
        9.93        20.94        18.74        14.47         0.03        13.55 
TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-60-2695 TCGA-60-2697 TCGA-60-2704 
       29.95        34.78        85.12        21.11        12.23        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       92.71        21.93        49.48        66.54        56.91        50.33 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
       48.49         3.19        26.83        70.13        70.42        68.15 
TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
       70.62        14.99        11.34        16.96        43.10        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 
        0.99         1.02         2.01         0.99        43.99        25.05 
TCGA-66-2765 TCGA-66-2768 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
        2.01         2.01        19.00        12.03        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2790 TCGA-68-7757 TCGA-68-8251 
        1.97        25.97        22.98        22.98         6.94        13.35 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6844 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 
       14.73        73.12        75.09         0.16        46.78         6.51 
TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 
       86.76        37.81        12.59        17.72        11.54        27.39 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5G7 TCGA-85-6561 
       65.49        60.53       126.18        22.29         5.92        40.24 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 
       34.95        31.30        32.91         1.38        18.94        25.15 
TCGA-85-8049 TCGA-85-8071 TCGA-85-8288 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 
       19.04        26.79        13.22        16.77         3.09         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL 
       15.39         7.76        36.59        38.14        12.59        30.28 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       24.36        30.48        16.21        15.29        29.92        12.39 
TCGA-90-6837 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 
       24.92        20.22        10.59         2.70         4.01         2.30 
TCGA-94-8035 TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-A53A TCGA-98-A53B 
        4.01        71.01        17.46        27.68        18.15         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HI 
       27.02        20.32        12.89        13.41         4.54        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S 
       13.74        43.92        26.43         3.65         3.72        12.72 
TCGA-O2-A5IB 
       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 
                       173.82                        154.32 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                        24.13                         19.76 
[1] "0.1 - 173.8 (24.1)" "0.0 - 154.3 (19.8)"
[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       43       75        2        38
  AMP PEAK  2(2P16.1) WILD-TYPE       0       46       77        0        27
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(2P16.1) MUTATED          58         0         36         14
  AMP PEAK  2(2P16.1) WILD-TYPE        37         3         27          5
                               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                            43                            46
  STAGE IB                            75                            77
  STAGE II                             2                             0
  STAGE IIA                           38                            27
  STAGE IIB                           58                            37
  STAGE III                            0                             3
  STAGE IIIA                          36                            27
  STAGE IIIB                          14                             5
  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    54 160  43  18
  AMP PEAK  2(2P16.1) WILD-TYPE  58 134  28   6
D2V4, multiclass
    clus
vv   AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  T1                          54                            58
  T2                         160                           134
  T3                          43                            28
  T4                          18                             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   165  86  20   3
  AMP PEAK  2(2P16.1) WILD-TYPE 152  47  20   2
D2V5, multiclass
    clus
vv   AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  N0                         165                           152
  N1                          86                            47
  N2                          20                            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   233   4
  AMP PEAK  2(2P16.1) WILD-TYPE 178   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED    233    4
  AMP PEAK  2(2P16.1) WILD-TYPE  178    3
   clus
vv  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  0                         233                           178
  1                           4                             3
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(2P16.1) MUTATED    57 218
  AMP PEAK  2(2P16.1) WILD-TYPE  73 153
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED     57  218
  AMP PEAK  2(2P16.1) WILD-TYPE   73  153
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  FEMALE                          57                            73
  MALE                           218                           153
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(2P16.1) MUTATED   203  33
  AMP PEAK  2(2P16.1) WILD-TYPE 181  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED    203   33
  AMP PEAK  2(2P16.1) WILD-TYPE  181   20
     clus
vv    AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  NO                          203                           181
  YES                          33                            20
[1] 2 2
[1] FALSE
D2V9, 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 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                                                           262
  AMP PEAK  2(2P16.1) WILD-TYPE                                                         217
D2V10, multiclass
                                                             clus
vv                                                            AMP PEAK  2(2P16.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         262
                                                             clus
vv                                                            AMP PEAK  2(2P16.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           217
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
D2V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(2P16.1) MUTATED   224   6   1  11
  AMP PEAK  2(2P16.1) WILD-TYPE 175   6   3  12
D2V13, multiclass
    clus
vv   AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  R0                         224                           175
  R1                           6                             6
  R2                           1                             3
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(2P16.1) MUTATED       5                        12   194
  AMP PEAK  2(2P16.1) WILD-TYPE     4                        19   155
D2V14, multiclass
                           clus
vv                          AMP PEAK  2(2P16.1) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             194
                           clus
vv                          AMP PEAK  2(2P16.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            19
  WHITE                                               155
[1] 3 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     1 170
  AMP PEAK  2(2P16.1) WILD-TYPE   7 147
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED      1  170
  AMP PEAK  2(2P16.1) WILD-TYPE    7  147
                        clus
vv                       AMP PEAK  2(2P16.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         170
                        clus
vv                       AMP PEAK  2(2P16.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           147
[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    91  78
  AMP PEAK  3(2Q31.2) WILD-TYPE 189 136
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                          169                           325 
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                           78                           136 
$`AMP PEAK  3(2Q31.2) MUTATED`
TCGA-18-3409 TCGA-18-3416 TCGA-21-A5DI TCGA-22-1017 TCGA-33-4532 TCGA-33-6737 
      123.19        31.99        32.19        48.82       129.01        19.76 
TCGA-34-2605 TCGA-43-5668 TCGA-43-A474 TCGA-56-8305 TCGA-56-8504 TCGA-60-2712 
       28.96        18.38        11.61         3.45        16.77         9.01 
TCGA-77-7140 TCGA-77-A5GA TCGA-90-7964 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-7545 
       20.78        42.08        14.07         0.16        16.14        57.07 
TCGA-96-A4JK TCGA-98-8020 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NK-A7XE TCGA-O2-A52W 
       19.36         2.76         0.07        76.80         0.43         8.58 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 
      117.57        11.34        92.15        36.07        86.96       154.32 
TCGA-21-1072 TCGA-21-1081 TCGA-21-1083 TCGA-22-0944 TCGA-22-1012 TCGA-22-4594 
       99.16         9.34        43.23         7.33        14.10        48.33 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4613 TCGA-22-5474 TCGA-22-5483 TCGA-22-5489 
       34.75        32.02        11.77        14.63        18.84        62.86 
TCGA-22-5491 TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 
       56.32        97.94       173.82       103.53       151.27        54.44 
TCGA-33-6738 TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-5236 
       63.35       110.99       118.36         2.63        61.61         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-7107 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3792 
       50.66        16.93         1.12         4.04        33.90         0.39 
TCGA-37-4130 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
        8.12        37.58       133.25       126.58       111.35        68.58 
TCGA-39-5029 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 
       24.33        68.38        71.18        55.56        17.06        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-46-3765 TCGA-46-3768 
       39.12        33.11        27.91        22.98        13.32         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 
        4.44        10.65        30.35         8.75        28.96        12.43 
TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-8629 
       18.25        18.48        14.53        31.27        19.76        15.81 
TCGA-56-A5DS TCGA-58-8391 TCGA-58-A46K TCGA-58-A46N TCGA-60-2703 TCGA-60-2708 
        0.26        71.24        34.36        29.92        96.82        80.45 
TCGA-60-2719 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MS 
       42.64        11.77       102.67        58.65        59.97        78.28 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2754 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 
       53.88        16.96         2.01        21.01        25.05         1.02 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2785 TCGA-66-2791 TCGA-66-2792 TCGA-68-7755 
       23.01         3.02         1.97         5.03        30.02         2.73 
TCGA-68-7756 TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7142 
        6.64        14.73        12.33        29.56        23.28        73.22 
TCGA-77-7338 TCGA-77-8009 TCGA-77-8130 TCGA-77-8139 TCGA-77-8145 TCGA-77-8150 
        0.16        55.73       156.66       104.09         6.97        54.41 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5GH TCGA-85-6175 
       65.49        36.36       132.36       150.25        38.86         9.67 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7698 TCGA-85-7844 TCGA-85-8070 TCGA-85-8072 
       41.39         6.41        31.30        29.95        31.56        30.64 
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        22.59 
TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 
       34.13        19.73        27.16        15.85        14.96         3.65 
TCGA-90-7769 TCGA-92-7341 TCGA-94-8490 TCGA-94-8491 TCGA-98-A538 TCGA-98-A53A 
       11.77         3.48         5.03        26.63        27.16        18.15 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HG 
       18.58        20.71        16.11        13.18        11.84        64.54 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NK-A5CR TCGA-O2-A52N 
        4.21         2.89        49.28        43.92        83.57        33.07 
TCGA-O2-A52S 
       12.72 

$`AMP PEAK  3(2Q31.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 
       12.20         4.47         4.80         6.18        27.19        14.93 
TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-34-2604 
       60.66        64.93        22.06       133.74         1.55        31.50 
TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       31.27        17.88        22.49         7.76        78.18         2.93 
TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A4ZJ 
       12.03        19.99        13.05        17.00        17.85        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
        0.13         3.58        41.42        35.34        32.32        66.61 
TCGA-68-8250 TCGA-77-A5GB TCGA-90-7766 TCGA-94-7033 TCGA-94-7943 TCGA-98-A539 
        8.02        30.81         9.50        21.04        18.38         5.69 
TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 
       21.21        19.10        39.85        40.90        65.65        16.80 
TCGA-18-3408 TCGA-18-3414 TCGA-18-3419 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 
       75.75        23.54        92.42         2.79        49.94       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-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 
      122.43       119.80        31.63        88.11        41.69        33.93 
TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
       10.82        21.99         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-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       19.30         9.57        63.55        44.25         0.79        86.30 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 TCGA-33-4547 
       71.34        79.20        11.74        30.12        16.64        79.53 
TCGA-33-4586 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI 
       14.07         4.70         0.30        36.62         6.94        44.19 
TCGA-33-AASL TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
       27.16        32.88        65.23        81.24        74.66        60.30 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 
       44.75        39.32         4.96        38.79        26.43         4.01 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        0.43         7.96         7.46         7.82         6.81         0.39 
TCGA-37-5819 TCGA-37-A5EN TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
        3.39        21.70        55.20        82.52       102.18         1.71 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-43-2576 TCGA-43-6647 TCGA-43-6770 
        1.94        60.53        36.39        40.21        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
        5.46         3.81        19.59        13.38        11.77         9.73 
TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       14.20        12.16        13.02        13.91         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-6545 TCGA-56-7580 
       29.95        28.34         5.46        27.45        21.90        30.41 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
        6.51         0.10        17.49        33.24        14.96         4.93 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
        3.48        26.89        14.07         1.35         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW 
       13.81        10.36         9.93        20.25        20.94        19.23 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       13.32        18.74        14.47         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-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       21.11        12.23        10.22        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-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 
       29.85        35.90        23.57        26.83        52.67        70.13 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5ML TCGA-63-A5MM 
       70.42        68.15        55.30        70.62        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-68-8251 TCGA-68-A59I TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 
       13.35        16.18        12.07        73.12        75.09        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 
      140.09         0.49        70.13       106.95        46.78        32.55 
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        66.51        60.53 
TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6561 
      126.18        22.29         5.92        61.94        27.62        40.24 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 
       36.53        34.95        32.91         1.38         1.15        18.94 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8288 TCGA-85-8350 
       25.15        19.04        24.13        26.79        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        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC 
       38.14        12.59        18.08        30.28        30.97        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       24.36        30.48        16.21        15.29        29.92        12.39 
TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       24.92         2.93        20.22        22.62        10.59         2.70 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-A4VJ TCGA-94-A5I6 
        4.01         5.26         2.30         4.01        14.14        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       71.01        18.31        17.46        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 
       30.67        21.34         2.01        27.02        20.32        12.89 
TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HP 
       13.41         4.54         1.22        57.30        13.74        25.32 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB 
       14.73        26.43         3.65         3.72        43.89        11.18 
TCGA-XC-AA0X 
        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 
                       173.82                        140.09 
  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE 
                        27.16                         21.04 
[1] "0.1 - 173.8 (27.2)" "0.0 - 140.1 (21.0)"
[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       24       57        1        20
  AMP PEAK  3(2Q31.2) WILD-TYPE       0       65       95        1        45
                               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        62         2         36         15
                               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                            24                            65
  STAGE IB                            57                            95
  STAGE II                             1                             1
  STAGE IIA                           20                            45
  STAGE IIB                           33                            62
  STAGE III                            1                             2
  STAGE IIIA                          27                            36
  STAGE IIIB                           4                            15
  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    33 107  24   8
  AMP PEAK  3(2Q31.2) WILD-TYPE  79 187  47  16
D3V4, multiclass
    clus
vv   AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  T1                          33                            79
  T2                         107                           187
  T3                          24                            47
  T4                           8                            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  3(2Q31.2) MUTATED   106  48  17   1
  AMP PEAK  3(2Q31.2) WILD-TYPE 211  85  23   4
D3V5, multiclass
    clus
vv   AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  N0                         106                           211
  N1                          48                            85
  N2                          17                            23
  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   146   2
  AMP PEAK  3(2Q31.2) WILD-TYPE 265   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q31.2) MUTATED    146    2
  AMP PEAK  3(2Q31.2) WILD-TYPE  265    5
   clus
vv  AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  0                         146                           265
  1                           2                             5
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(2Q31.2) MUTATED    34 138
  AMP PEAK  3(2Q31.2) WILD-TYPE  96 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q31.2) MUTATED     34  138
  AMP PEAK  3(2Q31.2) WILD-TYPE   96  233
        clus
vv       AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  FEMALE                          34                            96
  MALE                           138                           233
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(2Q31.2) MUTATED   134  20
  AMP PEAK  3(2Q31.2) WILD-TYPE 250  33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q31.2) MUTATED    134   20
  AMP PEAK  3(2Q31.2) WILD-TYPE  250   33
     clus
vv    AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  NO                          134                           250
  YES                          20                            33
[1] 2 2
[1] FALSE
D3V9, 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 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                                                           163
  AMP PEAK  3(2Q31.2) WILD-TYPE                                                         316
D3V10, multiclass
                                                             clus
vv                                                            AMP PEAK  3(2Q31.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         163
                                                             clus
vv                                                            AMP PEAK  3(2Q31.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           316
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
D3V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(2Q31.2) MUTATED   137   4   0   5
  AMP PEAK  3(2Q31.2) WILD-TYPE 262   8   4  18
D3V13, multiclass
    clus
vv   AMP PEAK  3(2Q31.2) MUTATED AMP PEAK  3(2Q31.2) WILD-TYPE
  R0                         137                           262
  R1                           4                             8
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(2Q31.2) MUTATED       2                         9   127
  AMP PEAK  3(2Q31.2) WILD-TYPE     7                        22   222
D3V14, multiclass
                           clus
vv                          AMP PEAK  3(2Q31.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                             127
                           clus
vv                          AMP PEAK  3(2Q31.2) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            22
  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"
D3V15, binary
                               cls
clus                              0   1
  AMP PEAK  3(2Q31.2) MUTATED     3 112
  AMP PEAK  3(2Q31.2) WILD-TYPE   5 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(2Q31.2) MUTATED      3  112
  AMP PEAK  3(2Q31.2) WILD-TYPE    5  205
                        clus
vv                       AMP PEAK  3(2Q31.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         112
                        clus
vv                       AMP PEAK  3(2Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           205
[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   260 187
  AMP PEAK  4(3Q26.33) WILD-TYPE  20  27
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           447                             47 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                           187                             27 
$`AMP PEAK  4(3Q26.33) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 
       27.19        32.19        14.93        60.66        64.93       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 
      133.74         1.55        31.50        28.96        31.27        22.49 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
        7.76        78.18         2.93        11.61        12.03        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ 
       13.05         3.45        17.00        16.77        17.85        21.04 
TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
        0.13        41.42         9.01        35.34        32.32        66.61 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 
        8.02        20.78        42.08        30.81         9.50        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       21.04         0.16        18.38        16.14        57.07        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        2.76         5.69        19.10         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       40.90        16.80         0.43         8.58        75.75       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        92.42        86.96 
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-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       70.16        60.89        34.78        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-22-1002 TCGA-22-1012 TCGA-22-1016 
       10.82        21.99         7.33         4.31        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-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       32.02        19.30         9.57        11.77        63.55        14.63 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       44.25        86.30        71.34        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       62.86        56.32        16.64        97.94        79.53       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
      103.53       151.27        14.07        54.44        63.35         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-34-2608 TCGA-34-5231 TCGA-34-5232 
       27.16         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
        9.07        50.66        16.93        44.75        39.32         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        1.12        38.79         4.04        26.43        33.90         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         0.39         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 
        0.39         3.39        37.58        21.70       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
       68.58        55.20        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
        1.94        60.53        68.38        71.18        55.56        17.06 
TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       40.21        39.12        33.11        27.91        22.98        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
       21.47         5.46        19.59        13.38        11.77         9.73 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
       14.20        13.32        12.16        13.02         9.83         4.44 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       10.65        13.91         0.39         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
        5.46        30.35         8.75        28.96        12.43        18.25 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
       21.90        18.48        14.53        31.27        30.41        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
        6.51         0.10        17.49        33.24        14.96         4.93 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 
        3.48        26.89        14.07         1.35         1.81        13.81 
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-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       13.32        18.74         0.26        14.47         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-58-A46N TCGA-60-2695 TCGA-60-2698 
       34.36        56.65        35.24        29.92        21.11        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-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 
       66.54        56.91        50.33        42.64        29.85        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
       23.57        26.83        11.77        70.13        70.42        68.15 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP 
       55.30       102.67        58.65        59.97        45.57        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-66-2744 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-68-8251 
        4.01        49.05         2.73         6.64         6.94        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 
       16.18        14.73        12.07        12.33        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       75.09        23.28        11.18       140.09         0.49        73.22 
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        32.55        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       55.73        37.81       156.66        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        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 
       54.41        65.49        60.53        36.36       132.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       22.29         5.92        61.94        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       41.39        40.24         6.41        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-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       19.04        24.13        31.56        26.79        30.64        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-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
        3.09        32.71         2.01        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
       38.14        18.08        22.59        30.28        34.13        30.97 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       19.86        30.48        19.73        16.21        15.85        14.96 
TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE 
       15.29        12.39         3.65         2.93        11.77        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       10.59         2.70         3.48         4.01         5.26         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        4.01         5.03        26.63        14.14        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       18.31        17.46        21.44        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       27.16        18.15         2.01        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG 
       16.11        13.18        13.41        11.84         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
        1.22        57.30        13.74         4.21         2.89        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N 
       43.92        25.32        14.73        83.57         3.65        33.07 
TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       12.72        43.89         0.20 

$`AMP PEAK  4(3Q26.33) WILD-TYPE`
TCGA-22-1017 TCGA-22-A5C4 TCGA-33-6737 TCGA-39-5039 TCGA-43-5668 TCGA-60-2696 
       48.82        22.06        19.76        17.88        18.38         3.58 
TCGA-98-A53D TCGA-NK-A5CT TCGA-21-1078 TCGA-22-1005 TCGA-22-1011 TCGA-22-4594 
       21.21        65.65        15.58        64.21         1.74        48.33 
TCGA-22-4596 TCGA-22-5478 TCGA-22-5481 TCGA-34-5234 TCGA-34-5239 TCGA-37-4129 
        0.56         0.79        79.20        74.66        60.30         7.96 
TCGA-39-5011 TCGA-39-5034 TCGA-43-2581 TCGA-43-6773 TCGA-52-7812 TCGA-56-8623 
      133.25        36.39        38.66         3.81        27.45        22.75 
TCGA-60-2697 TCGA-60-2716 TCGA-60-2720 TCGA-63-6202 TCGA-63-A5MG TCGA-63-A5MM 
       12.23        48.49         3.19        52.67        70.62        14.99 
TCGA-63-A5MN TCGA-66-2785 TCGA-77-8007 TCGA-77-8131 TCGA-77-A5FZ TCGA-85-8584 
       11.34         1.97         6.51        12.59       126.18        12.59 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED TCGA-96-A4JL 
       24.36        27.16        29.92        24.92        20.22        27.68 
TCGA-98-A53C TCGA-98-A53H TCGA-NC-A5HT TCGA-O2-A52Q TCGA-O2-A5IB 
       27.02        20.32        26.43         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 
                        173.82                         133.25 
  AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE 
                         21.70                          22.06 
[1] "0.0 - 173.8 (21.7)" "0.6 - 133.2 (22.1)"
[1] "hr=" "1.4"
D4V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(3Q26.33) MUTATED         2       80      140        2        55
  AMP PEAK  4(3Q26.33) WILD-TYPE       0        9       12        0        10
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(3Q26.33) MUTATED          86         1         58         18
  AMP PEAK  4(3Q26.33) WILD-TYPE         9         2          5          1
                                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                             80                              9
  STAGE IB                            140                             12
  STAGE II                              2                              0
  STAGE IIA                            55                             10
  STAGE IIB                            86                              9
  STAGE III                             1                              2
  STAGE IIIA                           58                              5
  STAGE IIIB                           18                              1
  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   101 267  62  22
  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                          101                             11
  T2                          267                             27
  T3                           62                              9
  T4                           22                              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   286 121  36   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                          286                             31
  N1                          121                             12
  N2                           36                              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   370   7
  AMP PEAK  4(3Q26.33) WILD-TYPE  41   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED    370    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                          370                             41
  1                            7                              0
[1] 2 2
[1] FALSE
D4V7, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED   111 341
  AMP PEAK  4(3Q26.33) WILD-TYPE  19  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED    111  341
  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                          111                             19
  MALE                            341                             30
[1] 2 2
[1] FALSE
D4V8, binary
                                cls
clus                               0   1
  AMP PEAK  4(3Q26.33) MUTATED   343  51
  AMP PEAK  4(3Q26.33) WILD-TYPE  41   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED    343   51
  AMP PEAK  4(3Q26.33) WILD-TYPE   41    2
     clus
vv    AMP PEAK  4(3Q26.33) MUTATED AMP PEAK  4(3Q26.33) WILD-TYPE
  NO                           343                             41
  YES                           51                              2
[1] 2 2
[1] FALSE
D4V9, 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 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                                                           433
  AMP PEAK  4(3Q26.33) WILD-TYPE                                                          46
D4V10, multiclass
                                                             clus
vv                                                            AMP PEAK  4(3Q26.33) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 15
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          433
                                                             clus
vv                                                            AMP PEAK  4(3Q26.33) WILD-TYPE
  LUNG BASALOID 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] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
D4V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  4(3Q26.33) MUTATED   363  11   4  20
  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                          363                             36
  R1                           11                              1
  R2                            4                              0
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3Q26.33) MUTATED       6                        29   316
  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                                              316
                           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     7 286
  AMP PEAK  4(3Q26.33) WILD-TYPE   1  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(3Q26.33) MUTATED      7  286
  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                          286
                        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    66  50
  AMP PEAK  5(4Q12) WILD-TYPE 214 164
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                        116                         378 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                         50                         164 
$`AMP PEAK  5(4Q12) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-22-1017 TCGA-22-A5C4 
        4.47       123.19         4.80        31.99        48.82        22.06 
TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       28.96        31.27        22.49         7.76        78.18         2.93 
TCGA-43-A56V TCGA-56-A4ZJ TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
       12.03        21.04        41.42        35.34        32.32        66.61 
TCGA-77-7140 TCGA-96-7545 TCGA-98-8020 TCGA-J1-A4AH TCGA-18-3411 TCGA-18-3412 
       20.78        57.07         2.76        19.10       117.57        11.34 
TCGA-21-1075 TCGA-21-1082 TCGA-21-5782 TCGA-21-5786 TCGA-22-4591 TCGA-22-4593 
       70.16       119.80        31.63        33.93        20.48        35.08 
TCGA-22-4595 TCGA-22-4601 TCGA-22-4604 TCGA-22-5478 TCGA-22-5481 TCGA-33-4566 
       24.13        34.75        13.12         0.79        79.20       173.82 
TCGA-33-4582 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI 
      103.53        63.35         4.70         6.94       110.99        44.19 
TCGA-33-AASJ TCGA-34-2596 TCGA-34-5236 TCGA-34-5241 TCGA-34-5928 TCGA-34-8456 
      118.36         2.63         9.07        16.93        39.32        26.43 
TCGA-37-3789 TCGA-37-4130 TCGA-37-4135 TCGA-37-A5EL TCGA-39-5016 TCGA-39-5019 
        0.43         8.12         6.81        37.58       126.58       111.35 
TCGA-39-5031 TCGA-43-2576 TCGA-43-3920 TCGA-43-6647 TCGA-43-A56U TCGA-46-3765 
       60.53        40.21        33.11        24.89        14.20        13.32 
TCGA-46-3769 TCGA-46-6025 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-7579 
        4.44        10.65         5.46        30.35        28.96        31.27 
TCGA-56-8629 TCGA-56-A49D TCGA-58-8387 TCGA-58-8392 TCGA-58-A46L TCGA-58-A46M 
       15.81        20.94        13.25        16.47        56.65        35.24 
TCGA-60-2703 TCGA-60-2722 TCGA-60-2726 TCGA-63-A5MP TCGA-63-A5MV TCGA-66-2737 
       96.82        29.85        11.77        25.28        36.16         2.01 
TCGA-66-2744 TCGA-66-2758 TCGA-66-2763 TCGA-66-2769 TCGA-66-2778 TCGA-66-2781 
        0.99        21.01         0.99         7.07        19.00         3.98 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2793 TCGA-66-2800 TCGA-68-A59I TCGA-77-7465 
       25.97        40.01        10.06        49.05        16.18        32.55 
TCGA-77-8007 TCGA-77-8009 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-85-6561 
        6.51        55.73       150.25        22.29         5.92        40.24 
TCGA-85-7843 TCGA-85-8072 TCGA-85-8287 TCGA-85-8351 TCGA-85-8354 TCGA-85-8580 
        1.15        30.64         0.76        16.77        32.71        36.59 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
       30.97        19.86        12.39         3.65         2.93        11.77 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-8035 TCGA-94-A4VJ TCGA-98-A538 
        2.70         3.48         5.26         4.01        14.14        27.16 
TCGA-NC-A5HH TCGA-O2-A52V 
        1.22        43.89 

$`AMP PEAK  5(4Q12) WILD-TYPE`
TCGA-18-3406 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 
       12.20         6.18        27.19        32.19        14.93        60.66 
TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 
       64.93       129.01       133.74         1.55        19.76        31.50 
TCGA-39-5039 TCGA-43-5668 TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 
       17.88        18.38        11.61        19.99        13.05         3.45 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A5DR TCGA-60-2696 TCGA-60-2712 
       17.00        16.77        17.85         0.13         3.58         9.01 
TCGA-68-8250 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
        8.02        42.08        30.81         9.50        14.07        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D 
        0.16        18.38        16.14        19.36         5.69        21.21 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 
        0.07        76.80        39.85        40.90        65.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
        0.43         8.58        75.75        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       92.42        86.96         2.79       154.32        49.94       119.54 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
       46.88        99.16        60.89        34.78        15.58        31.73 
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-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       21.99         7.33         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4605 TCGA-22-4607 
       27.02        48.33         0.56        38.17        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
        9.57        11.77        63.55        14.63        44.25        86.30 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       71.34        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       16.64        97.94        79.53       151.27        14.07        54.44 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
        0.30        36.62        27.16        61.61        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5929 
       81.24        74.66        60.30        50.66        44.75         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 
        1.12        38.79         4.04        33.90         4.01         0.39 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EN 
        7.96         7.46         7.82         0.39         3.39        21.70 
TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      133.25        68.58        55.20        82.52       102.18         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        68.38        71.18        55.56 
TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 
       17.06        38.66        39.12        27.91        22.98        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
        5.46         3.81        19.59        13.38        11.77         9.73 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       12.16        13.02         9.83        13.91         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 
       29.95        28.34         8.75        27.45        12.43        18.25 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
       21.90        18.48        14.53        30.41        19.76         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 
        0.10        17.49        33.24        14.96         4.93         3.48 
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        13.81 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK 
       10.36         9.93        20.25        19.23        13.32        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        0.26        14.47         0.03        13.55        29.95        71.24 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 
       34.78        85.12        34.36        29.92        21.11        12.23 
TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 
       10.22        37.94        92.71        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       66.54        56.91        50.33        48.49        42.64         3.19 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
       35.90        23.57        26.83        52.67        70.13        70.42 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
       68.15        55.30       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-A5MT 
       45.57        14.99        11.34        89.29        78.28        16.37 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2753 
       53.88        34.59        16.96        43.10        21.07         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-66-2770 TCGA-66-2771 TCGA-66-2773 
        1.02         2.01         2.01        23.01        19.00         3.02 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 
        2.01        12.03        12.00        24.95         1.97        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
        4.04        22.98         5.03        30.02        54.08         4.01 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-70-6722 
        2.73         6.64         6.94        13.35        14.73        12.07 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       12.33        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
      140.09         0.49        73.22        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
       46.78        86.76        37.81       156.66        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-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        6.97        66.51        54.41        65.49        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
      126.18       132.36        61.94        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       41.39         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        26.79        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        15.39         7.76        38.14 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4PA 
       12.59        18.08        22.59        30.28        34.13        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       30.48        19.73        27.16        16.21        15.85        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       15.29        29.92        24.92        20.22        22.62        10.59 
TCGA-92-8063 TCGA-92-8065 TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 
        4.01         2.30         5.03        26.63        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       18.31        17.46        27.68        21.44        30.81        30.67 
TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       21.34        18.15         2.01        27.02        20.32        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.71        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54        64.54        57.30        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
       49.28        43.92        25.32        14.73        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB TCGA-XC-AA0X 
        3.65        33.07         3.72        12.72        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 
                     173.82                      156.66 
  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE 
                     22.390                      21.455 
[1] "0.4 - 173.8 (22.4)" "0.0 - 156.7 (21.5)"
[1] "hr=" "1"  
D5V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(4Q12) MUTATED         0       24       28        1        16
  AMP PEAK  5(4Q12) WILD-TYPE       2       65      124        1        49
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(4Q12) MUTATED          30         0         13          5
  AMP PEAK  5(4Q12) WILD-TYPE        65         3         50         14
                             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                          24                          65
  STAGE IB                          28                         124
  STAGE II                           1                           1
  STAGE IIA                         16                          49
  STAGE IIB                         30                          65
  STAGE III                          0                           3
  STAGE IIIA                        13                          50
  STAGE IIIB                         5                          14
  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  76  12   6
  AMP PEAK  5(4Q12) WILD-TYPE  87 218  59  18
D5V4, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  T1                        25                          87
  T2                        76                         218
  T3                        12                          59
  T4                         6                          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  5(4Q12) MUTATED    72  35  10   1
  AMP PEAK  5(4Q12) WILD-TYPE 245  98  30   4
D5V5, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  N0                        72                         245
  N1                        35                          98
  N2                        10                          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"
D5V6, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    96   0
  AMP PEAK  5(4Q12) WILD-TYPE 315   7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     96    0
  AMP PEAK  5(4Q12) WILD-TYPE  315    7
   clus
vv  AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  0                        96                         315
  1                         0                           7
[1] 2 2
[1] FALSE
D5V7, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    31  88
  AMP PEAK  5(4Q12) WILD-TYPE  99 283
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     31   88
  AMP PEAK  5(4Q12) WILD-TYPE   99  283
        clus
vv       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  FEMALE                        31                          99
  MALE                          88                         283
[1] 2 2
[1] FALSE
D5V8, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED    86  15
  AMP PEAK  5(4Q12) WILD-TYPE 298  38
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED     86   15
  AMP PEAK  5(4Q12) WILD-TYPE  298   38
     clus
vv    AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  NO                         86                         298
  YES                        15                          38
[1] 2 2
[1] FALSE
D5V9, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  5(4Q12) MUTATED                                       5
  AMP PEAK  5(4Q12) WILD-TYPE                                    10
                             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                                                           114
  AMP PEAK  5(4Q12) WILD-TYPE                                                         365
D5V10, multiclass
                                                             clus
vv                                                            AMP PEAK  5(4Q12) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       114
                                                             clus
vv                                                            AMP PEAK  5(4Q12) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         365
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
D5V12, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  5(4Q12) MUTATED    95   3   1   6
  AMP PEAK  5(4Q12) WILD-TYPE 304   9   3  17
D5V13, multiclass
    clus
vv   AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  R0                        95                         304
  R1                         3                           9
  R2                         1                           3
  RX                         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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(4Q12) MUTATED       2                        10    81
  AMP PEAK  5(4Q12) WILD-TYPE     7                        21   268
D5V14, multiclass
                           clus
vv                          AMP PEAK  5(4Q12) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                        10
  WHITE                                            81
                           clus
vv                          AMP PEAK  5(4Q12) WILD-TYPE
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          21
  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"
D5V15, binary
                             cls
clus                            0   1
  AMP PEAK  5(4Q12) MUTATED     0  80
  AMP PEAK  5(4Q12) WILD-TYPE   8 237
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  5(4Q12) MUTATED      0   80
  AMP PEAK  5(4Q12) WILD-TYPE    8  237
                        clus
vv                       AMP PEAK  5(4Q12) MUTATED AMP PEAK  5(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             0                           8
  NOT HISPANIC OR LATINO                        80                         237
[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   214 167
  AMP PEAK  6(5P15.33) WILD-TYPE  66  47
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           381                            113 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                           167                             47 
$`AMP PEAK  6(5P15.33) MUTATED`
TCGA-18-3410 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 
        4.80         6.18        32.19        48.82        60.66        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
       22.06       129.01        19.76        31.50        28.96        31.27 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       17.88        22.49        18.38         7.76        78.18         2.93 
TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 
       11.61        12.03        19.99        13.05         3.45        17.00 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 
       16.77        17.85        21.04         0.13        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA TCGA-90-7766 
       35.34        32.32        66.61         8.02        42.08         9.50 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-96-7545 TCGA-96-A4JK 
       14.07        21.04         0.16        18.38        57.07        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NK-A5CT 
        2.76         5.69        19.10         0.07        39.85        65.65 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
        0.43         8.58       117.57        11.34        23.54        92.15 
TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       36.07        86.96         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-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-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       34.75        32.02         9.57        11.77        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        86.30        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       18.84        30.12        16.64        97.94        79.53       173.82 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 
      103.53        14.07        54.44        63.35         4.70        36.62 
TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
        6.94        44.19       118.36         2.63        61.61        32.88 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-5929 
        9.07        60.30        50.66        16.93        39.32         4.96 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 
        1.12         4.04        26.43        33.90         4.01         0.39 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
        8.12         7.82         6.81         0.39         3.39        37.58 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      133.25       126.58        68.58        55.20        82.52       102.18 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       24.33         1.94        60.53        36.39        68.38        71.18 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       40.21        38.66        39.12        33.11        27.91        22.98 
TCGA-43-6647 TCGA-43-7656 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       24.89        19.59        11.77        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       13.02         9.83         4.44        10.65        13.91         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-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7580 TCGA-56-7582 
       28.96        18.25        21.90        18.48        30.41        19.76 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 TCGA-56-8503 
        0.10        17.49         4.93         3.48        14.07         1.35 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
        1.81        13.81        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       20.94        19.23        13.32        18.74         0.26        14.47 
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-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-60-2707 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       96.82        37.94        21.93        66.54        56.91        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       42.64         3.19        35.90        23.57        26.83        11.77 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ 
       52.67        70.13        68.15       102.67        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW 
       45.57        11.34        25.28        78.28        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-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
       25.05         0.99         1.02         2.01         7.07        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
       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-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-7756 TCGA-68-7757 
       22.98        30.02        54.08        49.05         6.64         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 
       13.35        16.18        14.73        12.07        12.33        29.56 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       75.09        23.28        11.18       140.09         0.49        73.22 
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        32.55         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
       86.76        55.73        37.81       156.66        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 
       17.72       104.09        11.54        26.40         6.97        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G6 
       54.41        65.49        60.53        36.36       132.36        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
        5.92        61.94        27.62        38.86         9.67        41.39 
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-85-8070 TCGA-85-8071 TCGA-85-8072 
       29.95        18.94        25.15        31.56        26.79        30.64 
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-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        5.29        15.39         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ 
       18.08        22.59        34.13        30.97        19.86        30.48 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-90-7767 
       19.73        27.16        16.21        15.85        14.96         2.93 
TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
       11.77        22.62        10.59         2.70         3.48         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        2.30         4.01        26.63        14.14        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53B 
       18.31        17.46        30.67        21.34        27.16         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-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
       11.84         4.54        64.54         1.22        57.30        13.74 
TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
        4.21        49.28        14.73        26.43        83.57         3.65 
TCGA-O2-A52N TCGA-O2-A52V TCGA-XC-AA0X 
       33.07        43.89         0.20 

$`AMP PEAK  6(5P15.33) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-5595 TCGA-22-1000 
       12.20         4.47       123.19        31.99        27.19        14.93 
TCGA-33-4533 TCGA-33-4589 TCGA-60-2696 TCGA-77-7140 TCGA-77-A5GB TCGA-94-A5I4 
      133.74         1.55         3.58        20.78        30.81        16.14 
TCGA-98-A53D TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3419 
       21.21        76.80        40.90        16.80        75.75        92.42 
TCGA-18-4721 TCGA-21-1076 TCGA-21-1078 TCGA-21-1083 TCGA-22-1005 TCGA-22-4604 
      154.32        60.89        15.58        43.23        64.21        13.12 
TCGA-22-4607 TCGA-22-5489 TCGA-22-5491 TCGA-33-4583 TCGA-33-A5GW TCGA-33-AASD 
       19.30        62.86        56.32       151.27         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        81.24        74.66        44.75        38.79 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-A5EN TCGA-39-5019 TCGA-39-5028 
        0.43         7.96         7.46        21.70       111.35         1.71 
TCGA-39-5037 TCGA-39-5040 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 
       55.56        17.06        21.47         5.46         3.81        13.38 
TCGA-43-A475 TCGA-51-4080 TCGA-56-5897 TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 
        9.73         0.39        12.43        14.53        31.27         6.51 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8307 TCGA-56-8623 TCGA-58-8393 TCGA-58-A46L 
       33.24        14.96        26.89        22.75        34.78        56.65 
TCGA-60-2698 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2716 TCGA-60-2722 
       10.22        92.71        80.45        49.48        48.49        29.85 
TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MT 
       70.42        55.30        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-77-8131 TCGA-77-8144 TCGA-77-A5FZ TCGA-77-A5G3 
        2.73        73.12        12.59        27.39       126.18       150.25 
TCGA-85-6561 TCGA-85-7697 TCGA-85-8049 TCGA-85-8052 TCGA-85-8353 TCGA-85-8354 
       40.24        34.95        19.04        24.13         3.09        32.71 
TCGA-85-8355 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
        2.01        30.28        24.36        15.29        29.92        12.39 
TCGA-85-A5B5 TCGA-90-6837 TCGA-90-A4ED TCGA-92-8063 TCGA-94-8490 TCGA-96-A4JL 
        3.65        24.92        20.22         4.01         5.03        27.68 
TCGA-98-7454 TCGA-98-8021 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-NC-A5HL 
       21.44        30.81        18.15        27.02        20.32         2.89 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB 
       43.92        25.32         3.72        12.72        11.18 

  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                          0.03                           0.30 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                        173.82                         154.32 
  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE 
                         21.11                          24.13 
[1] "0.0 - 173.8 (21.1)" "0.3 - 154.3 (24.1)"
[1] "hr=" "1.2"
D6V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(5P15.33) MUTATED         2       65      124        2        46
  AMP PEAK  6(5P15.33) WILD-TYPE       0       24       28        0        19
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(5P15.33) MUTATED          75         0         53         11
  AMP PEAK  6(5P15.33) WILD-TYPE        20         3         10          8
                                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                             24
  STAGE IB                            124                             28
  STAGE II                              2                              0
  STAGE IIA                            46                             19
  STAGE IIB                            75                             20
  STAGE III                             0                              3
  STAGE IIIA                           53                             10
  STAGE IIIB                           11                              8
  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    80 235  55  17
  AMP PEAK  6(5P15.33) WILD-TYPE  32  59  16   7
D6V4, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  T1                           80                             32
  T2                          235                             59
  T3                           55                             16
  T4                           17                              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  6(5P15.33) MUTATED   253  95  35   2
  AMP PEAK  6(5P15.33) WILD-TYPE  64  38   5   3
D6V5, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  N0                          253                             64
  N1                           95                             38
  N2                           35                              5
  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   320   5
  AMP PEAK  6(5P15.33) WILD-TYPE  91   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED    320    5
  AMP PEAK  6(5P15.33) WILD-TYPE   91    2
   clus
vv  AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  0                          320                             91
  1                            5                              2
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED    96 291
  AMP PEAK  6(5P15.33) WILD-TYPE  34  80
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED     96  291
  AMP PEAK  6(5P15.33) WILD-TYPE   34   80
        clus
vv       AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  FEMALE                           96                             34
  MALE                            291                             80
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED   291  43
  AMP PEAK  6(5P15.33) WILD-TYPE  93  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED    291   43
  AMP PEAK  6(5P15.33) WILD-TYPE   93   10
     clus
vv    AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  NO                           291                             93
  YES                           43                             10
[1] 2 2
[1] FALSE
D6V9, 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 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                                                           372
  AMP PEAK  6(5P15.33) WILD-TYPE                                                         107
D6V10, multiclass
                                                             clus
vv                                                            AMP PEAK  6(5P15.33) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          372
                                                             clus
vv                                                            AMP PEAK  6(5P15.33) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
D6V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  6(5P15.33) MUTATED   311   9   3  17
  AMP PEAK  6(5P15.33) WILD-TYPE  88   3   1   6
D6V13, multiclass
    clus
vv   AMP PEAK  6(5P15.33) MUTATED AMP PEAK  6(5P15.33) WILD-TYPE
  R0                          311                             88
  R1                            9                              3
  R2                            3                              1
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(5P15.33) MUTATED       5                        22   270
  AMP PEAK  6(5P15.33) WILD-TYPE     4                         9    79
D6V14, multiclass
                           clus
vv                          AMP PEAK  6(5P15.33) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           22
  WHITE                                              270
                           clus
vv                          AMP PEAK  6(5P15.33) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              9
  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"
D6V15, binary
                                cls
clus                               0   1
  AMP PEAK  6(5P15.33) MUTATED     7 240
  AMP PEAK  6(5P15.33) WILD-TYPE   1  77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(5P15.33) MUTATED      7  240
  AMP PEAK  6(5P15.33) WILD-TYPE    1   77
                        clus
vv                       AMP PEAK  6(5P15.33) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          240
                        clus
vv                       AMP PEAK  6(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             77
[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   195 153
  AMP PEAK  7(5P12) WILD-TYPE  85  61
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                        348                         146 
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                        153                          61 
$`AMP PEAK  7(5P12) MUTATED`
TCGA-18-3410 TCGA-18-4083 TCGA-21-A5DI TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
        4.80         6.18        32.19        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
      129.01       133.74        19.76        31.50        28.96        31.27 
TCGA-39-5039 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
       17.88         7.76        78.18         2.93        11.61        12.03 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY 
       19.99        13.05         3.45        17.00        16.77        17.85 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH 
       21.04         0.13        41.42         9.01        32.32        66.61 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7557 
        8.02        20.78        42.08         9.50        14.07         0.16 
TCGA-94-7943 TCGA-96-7545 TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD 
       18.38        57.07         2.76         5.69        19.10         0.07 
TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 
       39.85        65.65         0.43         8.58       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-5592 TCGA-21-1070 
       23.54        92.15        36.07        86.96        49.94       119.54 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       46.88        70.16        34.78        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-22-1002 TCGA-22-1011 TCGA-22-1012 
       10.82        21.99         7.33         4.31         1.74        14.10 
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-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 
       38.17        34.75        13.12        32.02         9.57        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5481 TCGA-22-5482 
       63.55        14.63        44.25         0.79        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       18.84        30.12        16.64        97.94        79.53       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 
      103.53       151.27        14.07        63.35         4.70        36.62 
TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
        6.94        44.19       118.36         2.63        61.61        32.88 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-5929 
        9.07        60.30        50.66        16.93        39.32         4.96 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 
        1.12         4.04        26.43        33.90         4.01         0.39 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
        8.12         7.82         6.81         0.39         3.39        37.58 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 
      133.25       126.58        68.58        55.20        82.52        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-43-2576 TCGA-43-2581 
        1.94        60.53        68.38        71.18        40.21        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6773 
       39.12        33.11        27.91        22.98        24.89         3.81 
TCGA-43-7656 TCGA-43-8116 TCGA-46-3765 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
       19.59        11.77        13.32        13.02         9.83         4.44 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
       10.65        13.91        29.95        28.34         5.46        30.35 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7580 
        8.75        28.96        18.25        21.90        18.48        30.41 
TCGA-56-7582 TCGA-56-7822 TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 TCGA-56-8503 
       19.76        17.49         4.93         3.48        14.07         1.35 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.81        13.81         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       19.23        13.32         0.26         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M 
       29.95        71.24        16.47        85.12        34.36        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
       29.92        21.11        12.23        96.82        37.94        92.71 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
       21.93        49.48        66.54        56.91        50.33        42.64 
TCGA-60-2720 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 
        3.19        35.90        26.83        11.77        52.67        70.13 
TCGA-63-7022 TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP 
       68.15        58.65        59.97        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-66-2737 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-68-8251 TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 
       13.35        14.73        12.33        29.56        75.09        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
      140.09         0.49        73.22       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       32.55         6.51        86.76        55.73        37.81       156.66 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       53.92        39.09        17.72       104.09        11.54        26.40 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        6.97        66.51        54.41        65.49        60.53        36.36 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      132.36       150.25        22.29         5.92        61.94        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
       38.86         9.67        41.39         6.41        36.53        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-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
       26.79        30.64        34.52        10.09         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       22.45        16.77         5.29         7.76        36.59        38.14 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR 
       18.08        22.59        34.13        19.86        30.48        19.73 
TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
       27.16        15.85        14.96         3.65         2.93        11.77 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-8035 TCGA-94-8491 TCGA-94-A5I6 
        2.70         3.48         5.26         4.01        26.63        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       71.01        18.31        17.46        30.81        30.67        21.34 
TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
        2.01        18.58        20.71        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ 
       13.41        11.84         4.54        64.54         1.22        13.74 
TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-XC-AA0X 
       49.28        14.73        26.43        83.57         3.65         0.20 

$`AMP PEAK  7(5P12) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-5595 TCGA-22-1000 
       12.20         4.47       123.19        31.99        27.19        14.93 
TCGA-22-1017 TCGA-33-4589 TCGA-43-2578 TCGA-43-5668 TCGA-60-2696 TCGA-60-2715 
       48.82         1.55        22.49        18.38         3.58        35.34 
TCGA-77-A5GB TCGA-94-7033 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-A53D TCGA-NC-A5HE 
       30.81        21.04        16.14        19.36        21.21        76.80 
TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 
       40.90        16.80        75.75        92.42         2.79       154.32 
TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 TCGA-22-1005 TCGA-22-4607 TCGA-22-5479 
       99.16        60.89        15.58        64.21        19.30        86.30 
TCGA-22-5480 TCGA-22-5489 TCGA-22-5491 TCGA-33-4587 TCGA-33-A5GW TCGA-33-AASD 
       71.34        62.86        56.32        54.44         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        81.24        74.66        44.75        38.79 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-A5EN TCGA-39-5019 TCGA-39-5027 
        0.43         7.96         7.46        21.70       111.35       102.18 
TCGA-39-5028 TCGA-39-5034 TCGA-39-5037 TCGA-39-5040 TCGA-43-6770 TCGA-43-6771 
        1.71        36.39        55.56        17.06        21.47         5.46 
TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U TCGA-46-3766 TCGA-51-4079 TCGA-51-4080 
       13.38         9.73        14.20        12.16         0.39         0.39 
TCGA-52-7812 TCGA-56-5897 TCGA-56-7223 TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 
       27.45        12.43        14.53        31.27         6.51         0.10 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8307 TCGA-56-8623 TCGA-56-8625 TCGA-56-A4ZK 
       33.24        14.96        26.89        22.75        10.36        18.74 
TCGA-56-A62T TCGA-58-8393 TCGA-58-A46L TCGA-60-2698 TCGA-60-2708 TCGA-60-2716 
       14.47        34.78        56.65        10.22        80.45        48.49 
TCGA-60-2722 TCGA-60-2724 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG 
       29.85        23.57        70.42        55.30       102.67        70.62 
TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MT TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 
       14.99        89.29        16.37        21.01         0.99         2.01 
TCGA-66-2767 TCGA-66-2773 TCGA-66-2781 TCGA-66-2783 TCGA-66-2790 TCGA-66-2793 
        2.01         3.02         3.98        24.95        22.98        10.06 
TCGA-68-7755 TCGA-68-A59I TCGA-70-6722 TCGA-77-6843 TCGA-77-6845 TCGA-77-7335 
        2.73        16.18        12.07        73.12        23.28        70.13 
TCGA-77-8131 TCGA-77-8144 TCGA-77-A5FZ TCGA-85-6561 TCGA-85-7697 TCGA-85-8049 
       12.59        27.39       126.18        40.24        34.95        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       24.13        31.56         3.09        32.71         2.01        15.39 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A512 
       12.59        30.28        30.97        24.36        16.21        15.29 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       29.92        12.39        24.92        20.22        22.62        10.59 
TCGA-92-8063 TCGA-92-8065 TCGA-94-8490 TCGA-94-A4VJ TCGA-96-A4JL TCGA-98-7454 
        4.01         2.30         5.03        14.14        27.68        21.44 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-NC-A5HI TCGA-NC-A5HK 
       27.16        18.15        27.02        20.32        57.30         4.21 
TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
        2.89        43.92        25.32        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A5IB 
       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 
                     173.82                      154.32 
  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE 
                     21.620                      22.095 
[1] "0.0 - 173.8 (21.6)" "0.1 - 154.3 (22.1)"
[1] "hr=" "1"  
D7V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(5P12) MUTATED         1       62      110        1        40
  AMP PEAK  7(5P12) WILD-TYPE       1       27       42        1        25
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(5P12) MUTATED          71         0         49         12
  AMP PEAK  7(5P12) WILD-TYPE        24         3         14          7
                             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                          27
  STAGE IB                         110                          42
  STAGE II                           1                           1
  STAGE IIA                         40                          25
  STAGE IIB                         71                          24
  STAGE III                          0                           3
  STAGE IIIA                        49                          14
  STAGE IIIB                        12                           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  7(5P12) MUTATED    76 217  44  17
  AMP PEAK  7(5P12) WILD-TYPE  36  77  27   7
D7V4, multiclass
    clus
vv   AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  T1                        76                          36
  T2                       217                          77
  T3                        44                          27
  T4                        17                           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  7(5P12) MUTATED   226  90  33   3
  AMP PEAK  7(5P12) WILD-TYPE  91  43   7   2
D7V5, multiclass
    clus
vv   AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  N0                       226                          91
  N1                        90                          43
  N2                        33                           7
  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   297   5
  AMP PEAK  7(5P12) WILD-TYPE 114   2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(5P12) MUTATED    297    5
  AMP PEAK  7(5P12) WILD-TYPE  114    2
   clus
vv  AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  0                       297                         114
  1                         5                           2
[1] 2 2
[1] FALSE
D7V7, binary
                             cls
clus                            0   1
  AMP PEAK  7(5P12) MUTATED    80 274
  AMP PEAK  7(5P12) WILD-TYPE  50  97
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(5P12) MUTATED     80  274
  AMP PEAK  7(5P12) WILD-TYPE   50   97
        clus
vv       AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  FEMALE                        80                          50
  MALE                         274                          97
[1] 2 2
[1] FALSE
D7V8, binary
                             cls
clus                            0   1
  AMP PEAK  7(5P12) MUTATED   269  36
  AMP PEAK  7(5P12) WILD-TYPE 115  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(5P12) MUTATED    269   36
  AMP PEAK  7(5P12) WILD-TYPE  115   17
     clus
vv    AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  NO                        269                         115
  YES                        36                          17
[1] 2 2
[1] FALSE
D7V9, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  7(5P12) MUTATED                                      10
  AMP PEAK  7(5P12) WILD-TYPE                                     5
                             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                                                           342
  AMP PEAK  7(5P12) WILD-TYPE                                                         137
D7V10, multiclass
                                                             clus
vv                                                            AMP PEAK  7(5P12) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                              10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       342
                                                             clus
vv                                                            AMP PEAK  7(5P12) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         137
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
D7V12, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  7(5P12) MUTATED   288   8   3  13
  AMP PEAK  7(5P12) WILD-TYPE 111   4   1  10
D7V13, multiclass
    clus
vv   AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  R0                       288                         111
  R1                         8                           4
  R2                         3                           1
  RX                        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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(5P12) MUTATED       4                        20   244
  AMP PEAK  7(5P12) WILD-TYPE     5                        11   105
D7V14, multiclass
                           clus
vv                          AMP PEAK  7(5P12) MUTATED
  ASIAN                                             4
  BLACK OR AFRICAN AMERICAN                        20
  WHITE                                           244
                           clus
vv                          AMP PEAK  7(5P12) WILD-TYPE
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                          11
  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"
D7V15, binary
                             cls
clus                            0   1
  AMP PEAK  7(5P12) MUTATED     6 214
  AMP PEAK  7(5P12) WILD-TYPE   2 103
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  7(5P12) MUTATED      6  214
  AMP PEAK  7(5P12) WILD-TYPE    2  103
                        clus
vv                       AMP PEAK  7(5P12) MUTATED AMP PEAK  7(5P12) WILD-TYPE
  HISPANIC OR LATINO                             6                           2
  NOT HISPANIC OR LATINO                       214                         103
[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    98  66
  AMP PEAK  8(6P12.1) WILD-TYPE 182 148
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                          164                           330 
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                           66                           148 
$`AMP PEAK  8(6P12.1) MUTATED`
TCGA-18-3409 TCGA-22-1017 TCGA-22-5471 TCGA-33-4533 TCGA-34-2605 TCGA-34-2609 
      123.19        48.82        60.66       133.74        28.96        31.27 
TCGA-43-2578 TCGA-56-8308 TCGA-60-2711 TCGA-60-2715 TCGA-63-A5MH TCGA-94-7943 
       22.49        17.00        41.42        35.34        66.61        18.38 
TCGA-98-8020 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR 
        2.76        19.10         0.07        76.80        39.85        40.90 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3421 TCGA-21-1070 
        0.43         8.58       117.57        11.34        86.96       119.54 
TCGA-21-1072 TCGA-21-1076 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 
       99.16        60.89        31.73       119.80        43.23        33.93 
TCGA-21-5787 TCGA-22-1002 TCGA-22-1012 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
       10.82         4.31        14.10        20.48        48.33        24.13 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5482 TCGA-22-5483 
       34.75        13.12        32.02        19.30        11.74        18.84 
TCGA-33-4587 TCGA-33-AAS8 TCGA-33-AASI TCGA-34-5928 TCGA-34-7107 TCGA-34-8456 
       54.44        36.62        44.19        39.32         1.12        26.43 
TCGA-37-4133 TCGA-37-4141 TCGA-37-A5EL TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        7.82         0.39        37.58       111.35        68.58        55.20 
TCGA-39-5027 TCGA-39-5037 TCGA-43-3394 TCGA-43-5670 TCGA-43-6770 TCGA-46-3768 
      102.18        55.56        39.12        27.91        21.47         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
        4.44        10.65        13.91         5.46        30.35         8.75 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7582 TCGA-56-7730 TCGA-56-8082 
       28.96        18.25        21.90        19.76         6.51        14.96 
TCGA-56-8503 TCGA-56-8629 TCGA-56-A49D TCGA-58-8386 TCGA-58-8387 TCGA-58-8391 
        1.35        15.81        20.94         0.03        13.25        71.24 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 
       34.78        85.12        34.36        29.92        21.11        10.22 
TCGA-60-2703 TCGA-60-2706 TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 TCGA-60-2726 
       96.82        92.71        50.33        42.64        29.85        11.77 
TCGA-63-6202 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW 
       52.67       102.67        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-70-6723 TCGA-77-7138 
        4.01        49.05        13.35        14.73        12.33        11.18 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7465 TCGA-77-8007 TCGA-77-8130 TCGA-77-8143 
        0.49        73.22        32.55         6.51       156.66        26.40 
TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6798 TCGA-85-7699 
       36.36       150.25        27.62         9.67         6.41        32.91 
TCGA-85-7843 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 
        1.15        24.13        31.56        30.64        34.52         0.76 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8582 TCGA-85-8584 
        5.29         3.09        32.71         2.01        38.14        12.59 
TCGA-85-8664 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-7769 
       18.08        34.13        30.97        19.73         3.65        11.77 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8064 TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 
       22.62        10.59         5.26        21.44        30.67        21.34 
TCGA-98-A538 TCGA-98-A53B TCGA-98-A53I TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
       27.16         2.01        18.58        16.11        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HT 
       11.84        64.54         4.21         2.89        49.28        26.43 
TCGA-NK-A5CR TCGA-O2-A5IB 
       83.57        11.18 

$`AMP PEAK  8(6P12.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 
       32.19        14.93        64.93        22.06       129.01         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       19.76        31.50        17.88        18.38         7.76        78.18 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 
        2.93        11.61        12.03        19.99        13.05         3.45 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2712 
       16.77        17.85        21.04         0.13         3.58         9.01 
TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 
       32.32         8.02        20.78        42.08        30.81         9.50 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       14.07        21.04         0.16        16.14        57.07        19.36 
TCGA-98-A539 TCGA-98-A53D TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3414 
        5.69        21.21        65.65        16.80        75.75        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       92.15        36.07        92.42         2.79       154.32        49.94 
TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
       46.88        70.16        34.78        15.58       122.43         9.34 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 
       31.63        88.11        41.69        21.99         7.33        64.21 
TCGA-22-1011 TCGA-22-1016 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4609 
        1.74        27.02        35.08         0.56        38.17         9.57 
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        86.30 
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-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       97.94        79.53       173.82       103.53       151.27        14.07 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ 
       63.35         4.70         0.30         6.94       110.99       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       27.16         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
        4.96        38.79         4.04        33.90         4.01         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-5819 
        0.39         7.96         8.12         7.46         6.81         3.39 
TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
       21.70       133.25       126.58        82.52         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 
        1.94        60.53        36.39        68.38        71.18        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 
       40.21        38.66        33.11        22.98        24.89         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
        3.81        19.59        13.38        11.77         9.73        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
       13.32        12.16        13.02         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       28.34        27.45        12.43        18.48        14.53        31.27 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 
       30.41         0.10        17.49        33.24         4.93         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       26.89        14.07         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
        9.93        20.25        19.23        13.32        18.74         0.26 
TCGA-56-A62T TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 TCGA-58-A46L TCGA-58-A46M 
       14.47        13.55        29.95        16.47        56.65        35.24 
TCGA-60-2697 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       12.23        37.94        21.93        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2716 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       56.91        48.49         3.19        35.90        23.57        26.83 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MJ 
       70.13        70.42        68.15        55.30        70.62        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MV 
       45.57        14.99        11.34        25.28        89.29        36.16 
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-66-2759 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 
        0.99        21.01        25.05         0.99         2.01         2.01 
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-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
       12.00        24.95        40.01        22.98         4.04        22.98 
TCGA-66-2792 TCGA-66-2794 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I 
       30.02        54.08         2.73         6.64         6.94        16.18 
TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 
       12.07        29.56        73.12        75.09        23.28       140.09 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 TCGA-77-8009 
       70.13       106.95         0.16        46.78        86.76        55.73 
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-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       11.54        27.39         6.97        66.51        54.41        65.49 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
       60.53       126.18       132.36        22.29         5.92        61.94 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       38.86        41.39        40.24        36.53        34.95        31.30 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 
        1.38        29.95        18.94        25.15        19.04        26.79 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8479 TCGA-85-8481 
       10.09        13.22        22.45        16.77        15.39         7.76 
TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       36.59        22.59        30.28        19.86        24.36        30.48 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
       27.16        16.21        15.85        14.96        15.29        29.92 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 
       12.39        24.92         2.93        20.22         2.70         3.48 
TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        4.01         2.30         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 
       17.69        71.01        18.31        17.46        27.68        30.81 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 TCGA-NC-A5HF 
       18.15        27.02        20.32        20.71        12.89         4.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
        1.22        57.30        13.74        43.92        25.32        14.73 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
        3.65        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 
                       156.66                        173.82 
  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE 
                       22.555                        21.140 
[1] "0.0 - 156.7 (22.6)" "0.1 - 173.8 (21.1)"
[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       21       50        1        25
  AMP PEAK  8(6P12.1) WILD-TYPE       1       68      102        1        40
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(6P12.1) MUTATED          31         1         26          7
  AMP PEAK  8(6P12.1) WILD-TYPE        64         2         37         12
                               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                            21                            68
  STAGE IB                            50                           102
  STAGE II                             1                             1
  STAGE IIA                           25                            40
  STAGE IIB                           31                            64
  STAGE III                            1                             2
  STAGE IIIA                          26                            37
  STAGE IIIB                           7                            12
  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    25 104  27  10
  AMP PEAK  8(6P12.1) WILD-TYPE  87 190  44  14
D8V4, multiclass
    clus
vv   AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  T1                          25                            87
  T2                         104                           190
  T3                          27                            44
  T4                          10                            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  8(6P12.1) MUTATED   103  45  15   1
  AMP PEAK  8(6P12.1) WILD-TYPE 214  88  25   4
D8V5, multiclass
    clus
vv   AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  N0                         103                           214
  N1                          45                            88
  N2                          15                            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"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P12.1) MUTATED   142   1
  AMP PEAK  8(6P12.1) WILD-TYPE 269   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P12.1) MUTATED    142    1
  AMP PEAK  8(6P12.1) WILD-TYPE  269    6
   clus
vv  AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  0                         142                           269
  1                           1                             6
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P12.1) MUTATED    40 126
  AMP PEAK  8(6P12.1) WILD-TYPE  90 245
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P12.1) MUTATED     40  126
  AMP PEAK  8(6P12.1) WILD-TYPE   90  245
        clus
vv       AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  FEMALE                          40                            90
  MALE                           126                           245
[1] 2 2
[1] FALSE
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P12.1) MUTATED   119  24
  AMP PEAK  8(6P12.1) WILD-TYPE 265  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P12.1) MUTATED    119   24
  AMP PEAK  8(6P12.1) WILD-TYPE  265   29
     clus
vv    AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  NO                          119                           265
  YES                          24                            29
[1] 2 2
[1] FALSE
D8V9, 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 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                                                           156
  AMP PEAK  8(6P12.1) WILD-TYPE                                                         323
D8V10, multiclass
                                                             clus
vv                                                            AMP PEAK  8(6P12.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         156
                                                             clus
vv                                                            AMP PEAK  8(6P12.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
D8V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(6P12.1) MUTATED   138   5   2   7
  AMP PEAK  8(6P12.1) WILD-TYPE 261   7   2  16
D8V13, multiclass
    clus
vv   AMP PEAK  8(6P12.1) MUTATED AMP PEAK  8(6P12.1) WILD-TYPE
  R0                         138                           261
  R1                           5                             7
  R2                           2                             2
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(6P12.1) MUTATED       1                        12   119
  AMP PEAK  8(6P12.1) WILD-TYPE     8                        19   230
D8V14, multiclass
                           clus
vv                          AMP PEAK  8(6P12.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                          12
  WHITE                                             119
                           clus
vv                          AMP PEAK  8(6P12.1) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            19
  WHITE                                               230
[1] 3 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     2 107
  AMP PEAK  8(6P12.1) WILD-TYPE   6 210
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P12.1) MUTATED      2  107
  AMP PEAK  8(6P12.1) WILD-TYPE    6  210
                        clus
vv                       AMP PEAK  8(6P12.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         107
                        clus
vv                       AMP PEAK  8(6P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           210
[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    89  60
  AMP PEAK  9(6Q12) WILD-TYPE 191 154
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                        149                         345 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                         60                         154 
$`AMP PEAK  9(6Q12) MUTATED`
TCGA-18-3409 TCGA-22-1017 TCGA-22-5471 TCGA-33-4533 TCGA-34-2605 TCGA-34-2609 
      123.19        48.82        60.66       133.74        28.96        31.27 
TCGA-43-2578 TCGA-56-8308 TCGA-60-2711 TCGA-63-A5MH TCGA-94-7557 TCGA-94-7943 
       22.49        17.00        41.42        66.61         0.16        18.38 
TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8020 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE 
       16.14        19.36         2.76        19.10         0.07        76.80 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3412 TCGA-18-3421 
       39.85        40.90         0.43         8.58        11.34        86.96 
TCGA-18-4721 TCGA-21-1076 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 
      154.32        60.89        31.73       119.80        43.23        33.93 
TCGA-21-5787 TCGA-22-1002 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4601 
       10.82         4.31        14.10        48.33        24.13        34.75 
TCGA-22-4605 TCGA-22-5477 TCGA-22-5482 TCGA-22-5483 TCGA-33-4547 TCGA-33-4582 
       32.02        44.25        11.74        18.84        79.53       103.53 
TCGA-33-4587 TCGA-33-AAS8 TCGA-34-7107 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
       54.44        36.62         1.12         7.82         6.81         0.39 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 
      111.35        68.58        55.20        55.56        39.12        33.11 
TCGA-43-6770 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-52-7810 TCGA-52-7811 
       21.47         9.83        10.65        13.91        30.35         8.75 
TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 
       28.96        18.25        21.90        19.76         6.51        17.49 
TCGA-56-8082 TCGA-56-8629 TCGA-58-8386 TCGA-58-8387 TCGA-58-8393 TCGA-58-A46J 
       14.96        15.81         0.03        13.25        34.78        85.12 
TCGA-58-A46K TCGA-58-A46N TCGA-60-2703 TCGA-60-2714 TCGA-60-2719 TCGA-60-2723 
       34.36        29.92        96.82        50.33        42.64        35.90 
TCGA-63-6202 TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MS TCGA-63-A5MT TCGA-66-2734 
       52.67        58.65        45.57        78.28        16.37        43.10 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
        0.99         2.01        43.99        25.05         2.01         1.02 
TCGA-66-2769 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-66-2791 
        7.07         3.98         1.97        25.97         4.04         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-8251 TCGA-68-A59J 
       30.02        10.06         4.01        49.05        13.35        14.73 
TCGA-70-6723 TCGA-77-7142 TCGA-77-7465 TCGA-77-8009 TCGA-77-8130 TCGA-77-A5G3 
       12.33        73.22        32.55        55.73       156.66       150.25 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-6798 TCGA-85-7699 TCGA-85-7843 
       27.62         9.67        41.39         6.41        32.91         1.15 
TCGA-85-7950 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8352 
       18.94        24.13        30.64        34.52         0.76         5.29 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 
        3.09        32.71         2.01        38.14        18.08        22.59 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q 
       34.13        30.97         3.65        11.77        22.62        10.59 
TCGA-92-7341 TCGA-92-8064 TCGA-94-A4VJ TCGA-98-7454 TCGA-98-8022 TCGA-98-A53B 
        3.48         5.26        14.14        21.44        30.67         2.01 
TCGA-98-A53I TCGA-98-A53J TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HH 
       18.58        20.71        13.18        13.41        11.84         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A5IB 
       13.74         2.89        26.43        83.57        11.18 

$`AMP PEAK  9(6Q12) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 
       32.19        14.93        64.93        22.06       129.01         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       19.76        31.50        17.88        18.38         7.76        78.18 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 
        2.93        11.61        12.03        19.99        13.05         3.45 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2712 
       16.77        17.85        21.04         0.13         3.58         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       35.34        32.32         8.02        20.78        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-96-7545 TCGA-98-A539 TCGA-98-A53D 
        9.50        14.07        21.04        57.07         5.69        21.21 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
       65.65        16.80        75.75       117.57        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       36.07        92.42         2.79        49.94       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
       99.16        70.16        34.78        15.58       122.43         9.34 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 
       31.63        88.11        41.69        21.99         7.33        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-22-5473 TCGA-22-5474 
       13.12        19.30         9.57        11.77        63.55        14.63 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 
        0.79        86.30        71.34        79.20        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 
       56.32        16.64        97.94       173.82       151.27        14.07 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI 
       63.35         4.70         0.30         6.94       110.99        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
      118.36        27.16         2.63        61.61        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       81.24        74.66         9.07        60.30        50.66        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       44.75        39.32         4.96        38.79         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       33.90         4.01         0.43         0.39         7.96         8.12 
TCGA-37-4132 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 
        7.46         3.39        37.58        21.70       133.25       126.58 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
       36.39        68.38        71.18        17.06        40.21        38.66 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.91        22.98        24.89         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       13.38        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3769 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       13.02         4.44         0.39         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7812 TCGA-56-5897 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
        5.46        27.45        12.43        18.48        14.53        31.27 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
       30.41         0.10        33.24         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK 
        9.93        20.25        20.94        19.23        13.32        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
        0.26        14.47        13.55        29.95        71.24        16.47 
TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 
       56.65        35.24        21.11        12.23        10.22        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       92.71        21.93        80.45        49.48        66.54        56.91 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       48.49         3.19        29.85        23.57        26.83        11.77 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG 
       70.13        70.42        68.15        55.30       102.67        70.62 
TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MV 
       59.97        14.99        11.34        25.28        89.29        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 
       53.88        34.59        16.96         2.01        21.07         1.02 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 
        0.92         0.99        21.01         0.99         2.01         2.01 
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-66-2787 TCGA-66-2788 TCGA-66-2790 TCGA-66-2794 
       12.00        24.95        40.01        22.98        22.98        54.08 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I TCGA-70-6722 TCGA-77-6842 
        2.73         6.64         6.94        16.18        12.07        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       140.09         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        66.51        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
       65.49        60.53        36.36       126.18       132.36        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 
        5.92        61.94        38.86        40.24        36.53        34.95 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8070 
       31.30         1.38        29.95        25.15        19.04        31.56 
TCGA-85-8071 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8479 
       26.79        10.09        13.22        22.45        16.77        15.39 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA 
        7.76        36.59        12.59        30.28        19.86        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       30.48        19.73        27.16        16.21        15.85        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED 
       15.29        29.92        12.39        24.92         2.93        20.22 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        2.70         4.01         2.30         4.01         5.03        26.63 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 
       17.69        71.01        18.31        17.46        27.68        30.81 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 
       21.34        27.16        18.15        27.02        20.32        12.89 
TCGA-L3-A524 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HN 
       16.11         4.54        64.54        57.30         4.21        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q 
       43.92        25.32        14.73         3.65        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       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 
                     156.66                      173.82 
  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE 
                       21.9                        21.7 
[1] "0.0 - 156.7 (21.9)" "0.1 - 173.8 (21.7)"
[1] "hr=" "1.1"
D9V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(6Q12) MUTATED         1       24       49        1        22
  AMP PEAK  9(6Q12) WILD-TYPE       1       65      103        1        43
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(6Q12) MUTATED          25         1         19          8
  AMP PEAK  9(6Q12) WILD-TYPE        70         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                          24                          65
  STAGE IB                          49                         103
  STAGE II                           1                           1
  STAGE IIA                         22                          43
  STAGE IIB                         25                          70
  STAGE III                          1                           2
  STAGE IIIA                        19                          44
  STAGE IIIB                         8                          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  93  20   9
  AMP PEAK  9(6Q12) WILD-TYPE  82 201  51  15
D9V4, multiclass
    clus
vv   AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  T1                        30                          82
  T2                        93                         201
  T3                        20                          51
  T4                         9                          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  9(6Q12) MUTATED    98  40  10   2
  AMP PEAK  9(6Q12) WILD-TYPE 219  93  30   3
D9V5, multiclass
    clus
vv   AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  N0                        98                         219
  N1                        40                          93
  N2                        10                          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"
D9V6, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED   127   1
  AMP PEAK  9(6Q12) WILD-TYPE 284   6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED    127    1
  AMP PEAK  9(6Q12) WILD-TYPE  284    6
   clus
vv  AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  0                       127                         284
  1                         1                           6
[1] 2 2
[1] FALSE
D9V7, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED    33 119
  AMP PEAK  9(6Q12) WILD-TYPE  97 252
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED     33  119
  AMP PEAK  9(6Q12) WILD-TYPE   97  252
        clus
vv       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  FEMALE                        33                          97
  MALE                         119                         252
[1] 2 2
[1] FALSE
D9V8, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED   112  18
  AMP PEAK  9(6Q12) WILD-TYPE 272  35
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED    112   18
  AMP PEAK  9(6Q12) WILD-TYPE  272   35
     clus
vv    AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  NO                        112                         272
  YES                        18                          35
[1] 2 2
[1] FALSE
D9V9, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK  9(6Q12) MUTATED                                       5
  AMP PEAK  9(6Q12) WILD-TYPE                                    10
                             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                                                           145
  AMP PEAK  9(6Q12) WILD-TYPE                                                         334
D9V10, multiclass
                                                             clus
vv                                                            AMP PEAK  9(6Q12) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       145
                                                             clus
vv                                                            AMP PEAK  9(6Q12) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
D9V12, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  9(6Q12) MUTATED   127   4   2   7
  AMP PEAK  9(6Q12) WILD-TYPE 272   8   2  16
D9V13, multiclass
    clus
vv   AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  R0                       127                         272
  R1                         4                           8
  R2                         2                           2
  RX                         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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6Q12) MUTATED       1                        13   106
  AMP PEAK  9(6Q12) WILD-TYPE     8                        18   243
D9V14, multiclass
                           clus
vv                          AMP PEAK  9(6Q12) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                        13
  WHITE                                           106
                           clus
vv                          AMP PEAK  9(6Q12) WILD-TYPE
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          18
  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"
D9V15, binary
                             cls
clus                            0   1
  AMP PEAK  9(6Q12) MUTATED     2 101
  AMP PEAK  9(6Q12) WILD-TYPE   6 216
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  9(6Q12) MUTATED      2  101
  AMP PEAK  9(6Q12) WILD-TYPE    6  216
                        clus
vv                       AMP PEAK  9(6Q12) MUTATED AMP PEAK  9(6Q12) WILD-TYPE
  HISPANIC OR LATINO                             2                           6
  NOT HISPANIC OR LATINO                       101                         216
[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   153  98
  AMP PEAK 10(7P11.2) WILD-TYPE 127 116
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          251                           243 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                           98                           116 
$`AMP PEAK 10(7P11.2) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1017 TCGA-22-5471 
        4.47       123.19         6.18        32.19        48.82        60.66 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-34-2605 TCGA-34-2609 
       64.93        22.06       133.74         1.55        28.96        31.27 
TCGA-43-5668 TCGA-43-7657 TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 TCGA-56-8504 
       18.38         7.76        12.03        19.99         3.45        16.77 
TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 
        0.13        41.42         9.01        66.61         8.02        20.78 
TCGA-77-A5GA TCGA-77-A5GB TCGA-94-7557 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
       42.08        30.81         0.16        57.07        19.36         2.76 
TCGA-98-A539 TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W 
        5.69        76.80        39.85        40.90         0.43         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
       75.75       117.57        11.34        23.54        36.07        86.96 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
      154.32        49.94       119.54        99.16        70.16        60.89 
TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-5783 TCGA-21-5784 TCGA-22-0944 
       31.73         9.34       119.80        88.11        41.69         7.33 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
        1.74        14.10        35.08        24.13         0.56        38.17 
TCGA-22-4604 TCGA-22-4605 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       13.12        32.02        63.55        44.25         0.79        86.30 
TCGA-22-5482 TCGA-22-5491 TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
       11.74        56.32        97.94       173.82       103.53        14.07 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 
       63.35         4.70       110.99        44.19        27.16         2.63 
TCGA-34-5231 TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 TCGA-34-5928 TCGA-34-8456 
       65.23        74.66         9.07        50.66        39.32        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4141 TCGA-37-5819 
       33.90         4.01         0.43         8.12         0.39         3.39 
TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5031 
       37.58        21.70       126.58       111.35       102.18        60.53 
TCGA-39-5035 TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 
       68.38        55.56        40.21        38.66        39.12        27.91 
TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-A475 TCGA-46-3765 TCGA-46-3767 
       24.89         5.46         3.81         9.73        13.32        13.02 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        9.83         4.44        10.65         0.39         0.39        29.95 
TCGA-52-7809 TCGA-52-7810 TCGA-56-6545 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
        5.46        30.35        21.90        14.53        31.27        19.76 
TCGA-56-8304 TCGA-56-8624 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A62T 
        3.48        13.81        20.94        19.23        13.32        14.47 
TCGA-58-8386 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46N 
        0.03        71.24        16.47        34.78        56.65        29.92 
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-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 
       56.91        50.33        42.64        29.85        35.90        11.77 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       52.67        70.13        70.42       102.67        70.62        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW 
       59.97        45.57        89.29        78.28        16.37        53.88 
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-66-2763 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2782 
        0.99         2.01        23.01        19.00         2.01        12.00 
TCGA-66-2785 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 
        1.97         5.03        30.02        10.06         4.01        49.05 
TCGA-68-7755 TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6845 TCGA-77-7138 
        2.73        14.73        12.07        12.33        23.28        11.18 
TCGA-77-7141 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
        0.49         0.16        46.78        32.55         6.51        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 
       55.73        37.81       156.66        53.92        39.09       104.09 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 
       26.40        27.39        66.51        54.41        65.49        36.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 
      150.25        22.29         5.92        61.94        27.62         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7844 TCGA-85-7950 
       40.24         6.41        36.53        34.95        29.95        18.94 
TCGA-85-8049 TCGA-85-8052 TCGA-85-8276 TCGA-85-8287 TCGA-85-8351 TCGA-85-8354 
       19.04        24.13        34.52         0.76        16.77        32.71 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR 
       18.08        22.59        34.13        30.97        30.48        19.73 
TCGA-85-A50M TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-90-7769 TCGA-90-A4ED 
       27.16        15.85        29.92        12.39        11.77        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-A4VJ 
       22.62        10.59         3.48         4.01         5.26        14.14 
TCGA-94-A5I6 TCGA-96-A4JL TCGA-98-8023 TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       17.69        27.68        21.34        18.58        20.71        12.89 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN 
       13.41        11.84        64.54        57.30         2.89        49.28 
TCGA-NC-A5HP TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       25.32        83.57        33.07         3.72        12.72 

$`AMP PEAK 10(7P11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-22-1000 TCGA-33-4532 
       12.20         4.80        31.99        27.19        14.93       129.01 
TCGA-33-6737 TCGA-34-2604 TCGA-39-5039 TCGA-43-2578 TCGA-43-7658 TCGA-43-8118 
       19.76        31.50        17.88        22.49        78.18         2.93 
TCGA-43-A474 TCGA-56-8201 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 
       11.61        13.05        17.00        17.85        21.04         3.58 
TCGA-60-2715 TCGA-60-2721 TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 
       35.34        32.32         9.50        14.07        21.04        18.38 
TCGA-94-A5I4 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NK-A5CT TCGA-NK-A5D1 
       16.14        21.21        19.10         0.07        65.65        16.80 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 
       92.15        92.42         2.79        46.88        34.78        15.58 
TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
      122.43        43.23        31.63        33.93        10.82        21.99 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4601 
        4.31        64.21        27.02        20.48        48.33        34.75 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 
       19.30         9.57        11.77        14.63        71.34        79.20 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4547 TCGA-33-4583 
       18.84        30.12        62.86        16.64        79.53       151.27 
TCGA-33-4587 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-34-2600 
       54.44         0.30        36.62         6.94       118.36        61.61 
TCGA-34-2608 TCGA-34-5232 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 
       32.88        81.24        60.30        16.93        44.75         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
        1.12        38.79         4.04         0.39         7.96         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        7.82         6.81       133.25        68.58        55.20        82.52 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5036 TCGA-39-5040 
        1.71        24.33         1.94        36.39        71.18        17.06 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       33.11        22.98        21.47        19.59        13.38        11.77 
TCGA-43-A56U TCGA-46-3766 TCGA-46-6026 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 
       14.20        12.16        13.91        28.34         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7222 TCGA-56-7580 TCGA-56-7730 
       28.96        12.43        18.25        18.48        30.41         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 
        0.10        17.49        33.24        14.96         4.93        26.89 
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-56-8629 TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 
       20.25        15.81        18.74         0.26        13.25        13.55 
TCGA-58-8390 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 TCGA-60-2697 
       29.95        85.12        34.36        35.24        21.11        12.23 
TCGA-60-2707 TCGA-60-2710 TCGA-60-2716 TCGA-60-2720 TCGA-60-2724 TCGA-60-2725 
       21.93        66.54        48.49         3.19        23.57        26.83 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MV 
       68.15        55.30        14.99        11.34        25.28        36.16 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2753 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
       34.59        16.96         1.02         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2773 
       25.05         2.01         1.02         2.01         7.07         3.02 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 
       19.00        12.03         3.98        24.95        25.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 TCGA-68-7756 TCGA-68-7757 
       22.98         4.04        22.98        54.08         6.64         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 
       13.35        16.18        29.56        73.12        75.09       140.09 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8131 TCGA-77-8138 TCGA-77-8140 
       73.22        70.13       106.95        12.59        17.72        11.54 
TCGA-77-8145 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5GH TCGA-85-6560 
        6.97        60.53       126.18       132.36        38.86        41.39 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8070 
       31.30        32.91         1.38         1.15        25.15        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 
       26.79        30.64        10.09        13.22        22.45         5.29 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
        3.09         2.01        15.39         7.76        36.59        38.14 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A511 
       12.59        30.28        19.86        24.36        16.21        14.96 
TCGA-85-A512 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-92-7340 TCGA-92-8065 
       15.29         3.65        24.92         2.93         2.70         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
        4.01         5.03        26.63        71.01        18.31        17.46 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B 
       21.44        30.81        30.67        27.16        18.15         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HH 
       27.02        20.32        16.11        13.18         4.54         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX 
       13.74         4.21        43.92        14.73        26.43         3.65 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        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 
                       173.82                        151.27 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                        26.43                         19.30 
[1] "0.0 - 173.8 (26.4)" "0.1 - 151.3 (19.3)"
[1] "hr=" "1.5"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(7P11.2) MUTATED         2       31       85        0        30
  AMP PEAK 10(7P11.2) WILD-TYPE       0       58       67        2        35
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(7P11.2) MUTATED          57         2         32          9
  AMP PEAK 10(7P11.2) WILD-TYPE        38         1         31         10
                               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                            31                            58
  STAGE IB                            85                            67
  STAGE II                             0                             2
  STAGE IIA                           30                            35
  STAGE IIB                           57                            38
  STAGE III                            2                             1
  STAGE IIIA                          32                            31
  STAGE IIIB                           9                            10
  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    39 171  36  10
  AMP PEAK 10(7P11.2) WILD-TYPE  73 123  35  14
D10V4, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  T1                          39                            73
  T2                         171                           123
  T3                          36                            35
  T4                          10                            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   150  77  23   2
  AMP PEAK 10(7P11.2) WILD-TYPE 167  56  17   3
D10V5, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  N0                         150                           167
  N1                          77                            56
  N2                          23                            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   211   5
  AMP PEAK 10(7P11.2) WILD-TYPE 200   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED    211    5
  AMP PEAK 10(7P11.2) WILD-TYPE  200    2
   clus
vv  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  0                         211                           200
  1                           5                             2
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED    60 196
  AMP PEAK 10(7P11.2) WILD-TYPE  70 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED     60  196
  AMP PEAK 10(7P11.2) WILD-TYPE   70  175
        clus
vv       AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  FEMALE                          60                            70
  MALE                           196                           175
[1] 2 2
[1] FALSE
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED   196  29
  AMP PEAK 10(7P11.2) WILD-TYPE 188  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED    196   29
  AMP PEAK 10(7P11.2) WILD-TYPE  188   24
     clus
vv    AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  NO                          196                           188
  YES                          29                            24
[1] 2 2
[1] FALSE
D10V9, 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 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                                                           246
  AMP PEAK 10(7P11.2) WILD-TYPE                                                         233
D10V10, multiclass
                                                             clus
vv                                                            AMP PEAK 10(7P11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         246
                                                             clus
vv                                                            AMP PEAK 10(7P11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
D10V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(7P11.2) MUTATED   206   5   1  13
  AMP PEAK 10(7P11.2) WILD-TYPE 193   7   3  10
D10V13, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  R0                         206                           193
  R1                           5                             7
  R2                           1                             3
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7P11.2) MUTATED       8                        19   164
  AMP PEAK 10(7P11.2) WILD-TYPE     1                        12   185
D10V14, multiclass
                           clus
vv                          AMP PEAK 10(7P11.2) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          19
  WHITE                                             164
                           clus
vv                          AMP PEAK 10(7P11.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                            12
  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"
D10V15, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED     2 156
  AMP PEAK 10(7P11.2) WILD-TYPE   6 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED      2  156
  AMP PEAK 10(7P11.2) WILD-TYPE    6  161
                        clus
vv                       AMP PEAK 10(7P11.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         156
                        clus
vv                       AMP PEAK 10(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           161
[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   155 104
  AMP PEAK 11(7Q21.2) WILD-TYPE 125 110
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                          259                           235 
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                          104                           110 
$`AMP PEAK 11(7Q21.2) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI 
       12.20         4.47       123.19        31.99         6.18        32.19 
TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-34-2605 
       60.66        64.93        22.06       133.74         1.55        28.96 
TCGA-34-2609 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
       31.27         7.76        78.18        11.61        12.03        19.99 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 
        3.45        17.00        16.77         0.13        41.42         9.01 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
        8.02        20.78        42.08        16.14        57.07        19.36 
TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-O2-A52W 
       19.10         0.07        76.80        39.85        40.90         8.58 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
      117.57        11.34        23.54        36.07        92.42        86.96 
TCGA-18-4721 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
      154.32       119.54        99.16        70.16        60.89        34.78 
TCGA-21-1081 TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
        9.34        43.23        88.11        33.93        10.82         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-22-5473 TCGA-22-5477 
        0.56        38.17        13.12        32.02        63.55        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-22-5492 
        0.79        86.30        11.74        18.84        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 TCGA-33-6738 TCGA-33-AASD 
       97.94        79.53       173.82        14.07        63.35       110.99 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-5231 TCGA-34-5236 
       44.19        27.16         2.63        61.61        65.23         9.07 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8456 
       50.66        16.93        44.75        39.32         1.12        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
       33.90         4.01         0.43         7.82         6.81         0.39 
TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 
       37.58        21.70       133.25       126.58       111.35       102.18 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 TCGA-43-3394 TCGA-43-3920 
       24.33        60.53        68.38        71.18        39.12        33.11 
TCGA-43-6647 TCGA-43-6773 TCGA-43-A475 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
       24.89         3.81         9.73        13.02         9.83         4.44 
TCGA-46-6025 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 
       10.65         0.39        29.95         5.46        30.35        28.96 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-8083 
       18.25        21.90        14.53        31.27        19.76         4.93 
TCGA-56-8304 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A62T TCGA-58-8386 
        3.48        20.94        19.23        13.32        14.47         0.03 
TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N 
       71.24        16.47        34.78        34.36        35.24        29.92 
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-60-2714 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2726 TCGA-63-6202 
       50.33        42.64        29.85        35.90        11.77        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR 
       70.13        70.42       102.67        59.97        45.57        89.29 
TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       78.28        36.16        53.88        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2755 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 
        0.99         0.92        21.01         0.99         1.02         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        7.07        23.01        19.00        12.03         3.98        12.00 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
        1.97        40.01         5.03        30.02        10.06        54.08 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-70-6722 TCGA-70-6723 TCGA-77-6843 
        4.01        49.05         2.73        12.07        12.33        73.12 
TCGA-77-6845 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       23.28         0.49        73.22         0.16        46.78        32.55 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8143 
        6.51        55.73        37.81       156.66        53.92        26.40 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 
       66.51        54.41        65.49        36.36       150.25        22.29 
TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 
       61.94        38.86        40.24         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        30.64 
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        22.59 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A512 
       34.13        30.97        30.48        19.73        27.16        15.29 
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-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-94-A4VJ TCGA-94-A5I6 
       10.59         2.70         3.48         4.01        14.14        17.69 
TCGA-96-8169 TCGA-96-A4JL TCGA-98-8023 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53I 
       18.31        27.68        21.34        27.16         2.01        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.71        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR 
       64.54        57.30         2.89        25.32        14.73        83.57 
TCGA-O2-A52Q 
        3.72 

$`AMP PEAK 11(7Q21.2) WILD-TYPE`
TCGA-18-3410 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-33-4532 TCGA-33-6737 
        4.80        27.19        14.93        48.82       129.01        19.76 
TCGA-34-2604 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-8118 TCGA-56-8201 
       31.50        17.88        22.49        18.38         2.93        13.05 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
       17.85        21.04         3.58        35.34        32.32        66.61 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       30.81         9.50        14.07        21.04         0.16        18.38 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE 
        2.76         5.69        21.21        65.65        16.80         0.43 
TCGA-18-3408 TCGA-18-3415 TCGA-18-4086 TCGA-18-5592 TCGA-21-1071 TCGA-21-1078 
       75.75        92.15         2.79        49.94        46.88        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 TCGA-22-0940 
       31.73       122.43       119.80        31.63        41.69        21.99 
TCGA-22-1002 TCGA-22-1016 TCGA-22-4595 TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 
        4.31        27.02        24.13        34.75        19.30         9.57 
TCGA-22-4613 TCGA-22-5474 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 
       11.77        14.63        71.34        79.20        30.12        62.86 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      103.53       151.27        54.44         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASJ TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
        6.94       118.36        32.88        81.24        74.66        60.30 
TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
        4.96        38.79         4.04         0.39         7.96         8.12 
TCGA-37-4132 TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
        7.46         3.39        68.58        55.20        82.52         1.71 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
        1.94        36.39        55.56        17.06        40.21        38.66 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 
       27.91        22.98        21.47         5.46        19.59        13.38 
TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-6026 TCGA-51-4080 
       11.77        14.20        13.32        12.16        13.91         0.39 
TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-7222 TCGA-56-7580 
       28.34         8.75        27.45        12.43        18.48        30.41 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8307 
        6.51         0.10        17.49        33.24        14.96        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8387 
        9.93        20.25        15.81        18.74         0.26        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J TCGA-58-A46L TCGA-60-2695 TCGA-60-2697 
       13.55        29.95        85.12        56.65        21.11        12.23 
TCGA-60-2707 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2720 TCGA-60-2724 
       21.93        66.54        56.91        48.49         3.19        23.57 
TCGA-60-2725 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM 
       26.83        68.15        55.30        70.62        58.65        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2727 TCGA-66-2753 
       11.34        25.28        16.37        34.59        16.96         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-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 
        3.02         2.01        19.00        24.95        25.97        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
        4.04        22.98         6.64         6.94        13.35        16.18 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7335 
       14.73        29.56        75.09        11.18       140.09        70.13 
TCGA-77-7337 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
      106.95        86.76        12.59        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
       11.54        27.39         6.97        60.53       126.18       132.36 
TCGA-77-A5G7 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 
        5.92        27.62         9.67        41.39        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        26.79        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        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A4PA 
       38.14        12.59        18.08        30.28        19.86        24.36 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-92-8064 
       16.21        15.85        14.96        29.92        24.92         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-8170 
        2.30         4.01         5.03        26.63        71.01        17.46 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H 
       21.44        30.81        30.67        18.15        27.02        20.32 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO 
        4.54         1.22        13.74         4.21        49.28        43.92 
TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       26.43         3.65        33.07        12.72        43.89        11.18 
TCGA-XC-AA0X 
        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 
                       173.82                        151.27 
  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE 
                        24.13                         19.86 
[1] "0.0 - 173.8 (24.1)" "0.1 - 151.3 (19.9)"
[1] "hr=" "1.4"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(7Q21.2) MUTATED         1       36       85        1        34
  AMP PEAK 11(7Q21.2) WILD-TYPE       1       53       67        1        31
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(7Q21.2) MUTATED          55         1         35          9
  AMP PEAK 11(7Q21.2) WILD-TYPE        40         2         28         10
                               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                            36                            53
  STAGE IB                            85                            67
  STAGE II                             1                             1
  STAGE IIA                           34                            31
  STAGE IIB                           55                            40
  STAGE III                            1                             2
  STAGE IIIA                          35                            28
  STAGE IIIB                           9                            10
  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    46 172  35  11
  AMP PEAK 11(7Q21.2) WILD-TYPE  66 122  36  13
D11V4, multiclass
    clus
vv   AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  T1                          46                            66
  T2                         172                           122
  T3                          35                            36
  T4                          11                            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   158  79  23   2
  AMP PEAK 11(7Q21.2) WILD-TYPE 159  54  17   3
D11V5, multiclass
    clus
vv   AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  N0                         158                           159
  N1                          79                            54
  N2                          23                            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   220   5
  AMP PEAK 11(7Q21.2) WILD-TYPE 191   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q21.2) MUTATED    220    5
  AMP PEAK 11(7Q21.2) WILD-TYPE  191    2
   clus
vv  AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  0                         220                           191
  1                           5                             2
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q21.2) MUTATED    56 208
  AMP PEAK 11(7Q21.2) WILD-TYPE  74 163
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q21.2) MUTATED     56  208
  AMP PEAK 11(7Q21.2) WILD-TYPE   74  163
        clus
vv       AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  FEMALE                          56                            74
  MALE                           208                           163
[1] 2 2
[1] FALSE
D11V8, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q21.2) MUTATED   197  29
  AMP PEAK 11(7Q21.2) WILD-TYPE 187  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q21.2) MUTATED    197   29
  AMP PEAK 11(7Q21.2) WILD-TYPE  187   24
     clus
vv    AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  NO                          197                           187
  YES                          29                            24
[1] 2 2
[1] FALSE
D11V9, 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 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                                                           255
  AMP PEAK 11(7Q21.2) WILD-TYPE                                                         224
D11V10, multiclass
                                                             clus
vv                                                            AMP PEAK 11(7Q21.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 8
  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 11(7Q21.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           224
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
D11V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(7Q21.2) MUTATED   213   8   1  11
  AMP PEAK 11(7Q21.2) WILD-TYPE 186   4   3  12
D11V13, multiclass
    clus
vv   AMP PEAK 11(7Q21.2) MUTATED AMP PEAK 11(7Q21.2) WILD-TYPE
  R0                         213                           186
  R1                           8                             4
  R2                           1                             3
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7Q21.2) MUTATED       7                        16   179
  AMP PEAK 11(7Q21.2) WILD-TYPE     2                        15   170
D11V14, multiclass
                           clus
vv                          AMP PEAK 11(7Q21.2) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          16
  WHITE                                             179
                           clus
vv                          AMP PEAK 11(7Q21.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               170
[1] 3 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     3 160
  AMP PEAK 11(7Q21.2) WILD-TYPE   5 157
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q21.2) MUTATED      3  160
  AMP PEAK 11(7Q21.2) WILD-TYPE    5  157
                        clus
vv                       AMP PEAK 11(7Q21.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         160
                        clus
vv                       AMP PEAK 11(7Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           157
[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   133  99
  AMP PEAK 12(8P11.23) WILD-TYPE 147 115
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                           232                            262 
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                            99                            115 
$`AMP PEAK 12(8P11.23) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
        4.47       123.19         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1017 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-6737 
       32.19        48.82        64.93        22.06       133.74        19.76 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-8118 
       31.50        28.96        31.27        17.88        22.49         2.93 
TCGA-43-A56V TCGA-56-8201 TCGA-56-8308 TCGA-56-A5DR TCGA-60-2721 TCGA-63-A5MH 
       12.03        13.05        17.00         0.13        32.32        66.61 
TCGA-68-8250 TCGA-77-A5GA TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
        8.02        42.08        21.04         0.16        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM 
       57.07        19.36         5.69        19.10         0.07        39.85 
TCGA-NC-A5HR TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
       40.90         8.58       117.57        11.34        23.54        92.15 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 
       92.42        86.96       154.32       119.54        99.16        70.16 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5783 
       34.78        31.73       122.43         9.34       119.80        88.11 
TCGA-21-5784 TCGA-22-1002 TCGA-22-1011 TCGA-22-4591 TCGA-22-4595 TCGA-22-4596 
       41.69         4.31         1.74        20.48        24.13         0.56 
TCGA-22-4601 TCGA-22-4604 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
       34.75        13.12        63.55        14.63        44.25        86.30 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-33-4547 
       71.34        11.74        18.84        62.86        56.32        79.53 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
      103.53       151.27        14.07        54.44        63.35         4.70 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 TCGA-34-5231 TCGA-34-5232 
        6.94       110.99        44.19         2.63        65.23        81.24 
TCGA-34-5239 TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       60.30        16.93        39.32         1.12        38.79         4.04 
TCGA-34-A5IX TCGA-37-3789 TCGA-37-4132 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 
       33.90         0.43         7.46        37.58        21.70       126.58 
TCGA-39-5019 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5035 TCGA-39-5037 
      111.35        82.52         1.71        24.33        68.38        55.56 
TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 
       17.06        40.21        39.12        33.11        27.91        24.89 
TCGA-43-6770 TCGA-43-8116 TCGA-46-3765 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 
       21.47        11.77        13.32        30.35         8.75        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-7579 TCGA-56-7730 TCGA-56-8304 TCGA-56-8622 
       12.43        18.25        31.27         6.51         3.48         1.81 
TCGA-56-8628 TCGA-56-A49D TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8390 
       20.25        20.94         0.26        14.47        13.25        29.95 
TCGA-58-8392 TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 TCGA-60-2706 TCGA-60-2708 
       16.47        34.36        35.24        21.11        92.71        80.45 
TCGA-60-2709 TCGA-60-2720 TCGA-60-2722 TCGA-60-2724 TCGA-60-2725 TCGA-63-7020 
       49.48         3.19        29.85        23.57        26.83        70.13 
TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MP TCGA-63-A5MR 
       55.30        70.62        58.65        59.97        25.28        89.29 
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-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7335 
        6.64         6.94        73.12        75.09       140.09        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 TCGA-77-8128 TCGA-77-8136 
      106.95         0.16        46.78        86.76        37.81        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 
       17.72       104.09        11.54        26.40        66.51        54.41 
TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 
       60.53       150.25         5.92        61.94        38.86        41.39 
TCGA-85-7696 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 
       36.53        32.91         1.15        25.15        24.13        31.56 
TCGA-85-8276 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4JB 
       34.52        36.59        38.14        12.59        18.08        30.97 
TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       19.86        19.73        16.21        15.85        14.96        29.92 
TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7340 TCGA-96-7544 
       12.39         2.93        11.77        22.62         2.70        71.01 
TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-L3-A4E7 
       30.81        21.34        27.16        18.15         2.01        12.89 
TCGA-LA-A446 TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL 
       13.18        64.54         1.22        57.30         4.21         2.89 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-XC-AA0X 
       26.43        83.57         3.65         0.20 

$`AMP PEAK 12(8P11.23) WILD-TYPE`
TCGA-18-3406 TCGA-22-1000 TCGA-22-5471 TCGA-33-4532 TCGA-33-4589 TCGA-43-5668 
       12.20        14.93        60.66       129.01         1.55        18.38 
TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-56-7221 TCGA-56-8305 TCGA-56-8504 
        7.76        78.18        11.61        19.99         3.45        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       17.85        21.04         3.58        41.42         9.01        35.34 
TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-98-8020 TCGA-98-A53D 
       20.78        30.81         9.50        14.07         2.76        21.21 
TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3417 
       76.80        65.65        16.80         0.43        75.75        36.07 
TCGA-18-4086 TCGA-18-5592 TCGA-21-1071 TCGA-21-1076 TCGA-21-1078 TCGA-21-1083 
        2.79        49.94        46.88        60.89        15.58        43.23 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 
       31.63        33.93        10.82        21.99         7.33        64.21 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4605 
       14.10        27.02        35.08        48.33        38.17        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5478 TCGA-22-5481 TCGA-22-5485 
       19.30         9.57        11.77         0.79        79.20        30.12 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4566 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASJ 
       16.64        97.94       173.82         0.30        36.62       118.36 
TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 
       27.16        61.61        32.88        74.66         9.07        50.66 
TCGA-34-5927 TCGA-34-5929 TCGA-34-8456 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 
       44.75         4.96        26.43         4.01         0.39         7.96 
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       133.25 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       68.58        55.20       102.18         1.94        60.53        36.39 
TCGA-39-5036 TCGA-43-2581 TCGA-43-6143 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       71.18        38.66        22.98         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
       13.38         9.73        14.20        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        4.44        10.65        13.91         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 
       28.34         5.46        27.45        21.90        18.48        14.53 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       30.41        19.76         0.10        17.49        33.24        14.96 
TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 TCGA-56-8624 
        4.93        26.89        14.07         1.35        22.75        13.81 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK 
       10.36         9.93        15.81        19.23        13.32        18.74 
TCGA-58-8386 TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L 
        0.03        13.55        71.24        34.78        85.12        56.65 
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-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2723 
       66.54        56.91        50.33        48.49        42.64        35.90 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5ML 
       11.77        52.67        70.42        68.15       102.67        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2737 
       14.99        11.34        78.28        16.37        53.88         2.01 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 
        0.99         2.01        21.01         2.01         1.02         2.01 
TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
       19.00         2.01        19.00        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-8251 
       40.01        22.98         5.03        54.08         4.01        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 
       16.18        14.73        12.07        12.33        29.56        23.28 
TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 
       11.18         0.49        73.22        32.55         6.51        55.73 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8144 TCGA-77-8145 TCGA-77-8153 
      156.66        12.59        53.92        27.39         6.97        65.49 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5GF TCGA-85-6175 
       36.36       126.18       132.36        22.29        27.62         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 
       40.24         6.41        34.95        31.30         1.38        29.95 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 
       18.94        19.04        26.79        30.64        10.09         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       13.22        22.45        16.77         5.29         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
        2.01        15.39         7.76        22.59        30.28        34.13 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A512 TCGA-85-A5B5 TCGA-90-6837 
       24.36        30.48        27.16        15.29         3.65        24.92 
TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       20.22        10.59         3.48         4.01         5.26         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 
        4.01         5.03        26.63        14.14        17.69        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-A53C TCGA-98-A53H 
       17.46        27.68        21.44        30.67        27.02        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF 
       18.58        20.71        16.11        13.41        11.84         4.54 
TCGA-NC-A5HJ TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-O2-A52N 
       13.74        49.28        43.92        25.32        14.73        33.07 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
        3.72        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                         173.82 
  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE 
                         25.84                          19.02 
[1] "0.1 - 154.3 (25.8)" "0.0 - 173.8 (19.0)"
[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       42       69        1        32
  AMP PEAK 12(8P11.23) WILD-TYPE       1       47       83        1        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(8P11.23) MUTATED          45         0         34          9
  AMP PEAK 12(8P11.23) WILD-TYPE        50         3         29         10
                                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                             42                             47
  STAGE IB                             69                             83
  STAGE II                              1                              1
  STAGE IIA                            32                             33
  STAGE IIB                            45                             50
  STAGE III                             0                              3
  STAGE IIIA                           34                             29
  STAGE IIIB                            9                             10
  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  29  14
  AMP PEAK 12(8P11.23) WILD-TYPE  58 153  42  10
D12V4, multiclass
    clus
vv   AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  T1                           54                             58
  T2                          141                            153
  T3                           29                             42
  T4                           14                             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   152  62  20   2
  AMP PEAK 12(8P11.23) WILD-TYPE 165  71  20   3
D12V5, multiclass
    clus
vv   AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  N0                          152                            165
  N1                           62                             71
  N2                           20                             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   195   4
  AMP PEAK 12(8P11.23) WILD-TYPE 216   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.23) MUTATED    195    4
  AMP PEAK 12(8P11.23) WILD-TYPE  216    3
   clus
vv  AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  0                          195                            216
  1                            4                              3
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.23) MUTATED    47 191
  AMP PEAK 12(8P11.23) WILD-TYPE  83 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.23) MUTATED     47  191
  AMP PEAK 12(8P11.23) WILD-TYPE   83  180
        clus
vv       AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  FEMALE                           47                             83
  MALE                            191                            180
[1] 2 2
[1] FALSE
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.23) MUTATED   186  24
  AMP PEAK 12(8P11.23) WILD-TYPE 198  29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.23) MUTATED    186   24
  AMP PEAK 12(8P11.23) WILD-TYPE  198   29
     clus
vv    AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  NO                           186                            198
  YES                           24                             29
[1] 2 2
[1] FALSE
D12V9, 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 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                                                           229
  AMP PEAK 12(8P11.23) WILD-TYPE                                                         250
D12V10, multiclass
                                                             clus
vv                                                            AMP PEAK 12(8P11.23) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          229
                                                             clus
vv                                                            AMP PEAK 12(8P11.23) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            250
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
D12V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 12(8P11.23) MUTATED   196   6   0   5
  AMP PEAK 12(8P11.23) WILD-TYPE 203   6   4  18
D12V13, multiclass
    clus
vv   AMP PEAK 12(8P11.23) MUTATED AMP PEAK 12(8P11.23) WILD-TYPE
  R0                          196                            203
  R1                            6                              6
  R2                            0                              4
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8P11.23) MUTATED       4                        18   159
  AMP PEAK 12(8P11.23) WILD-TYPE     5                        13   190
D12V14, multiclass
                           clus
vv                          AMP PEAK 12(8P11.23) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           18
  WHITE                                              159
                           clus
vv                          AMP PEAK 12(8P11.23) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                190
[1] 3 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     2 146
  AMP PEAK 12(8P11.23) WILD-TYPE   6 171
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.23) MUTATED      2  146
  AMP PEAK 12(8P11.23) WILD-TYPE    6  171
                        clus
vv                       AMP PEAK 12(8P11.23) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          146
                        clus
vv                       AMP PEAK 12(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            171
[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   188 158
  AMP PEAK 13(8Q24.21) WILD-TYPE  92  56
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           346                            148 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           158                             56 
$`AMP PEAK 13(8Q24.21) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
        4.47       123.19         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 
       32.19        48.82        60.66        64.93        22.06       129.01 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 
        1.55        19.76        31.50        28.96        31.27        22.49 
TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
       18.38         7.76        78.18         2.93        11.61        12.03 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A5DR 
       13.05         3.45        17.00        16.77        17.85         0.13 
TCGA-60-2712 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-94-7033 
        9.01        66.61         8.02        20.78        42.08        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
        0.16        18.38        16.14        57.07        19.36         2.76 
TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE 
        5.69        19.10         0.07        39.85        40.90         0.43 
TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 
        8.58       117.57        11.34        23.54        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 
       86.96         2.79       154.32       119.54        99.16        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       60.89        34.78        31.73       122.43         9.34       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
       43.23        31.63        88.11        41.69        33.93        10.82 
TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 
        1.74        14.10        27.02        20.48        48.33         0.56 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       34.75        13.12        32.02         9.57        11.77        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        86.30        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 
       18.84        30.12        62.86       173.82       151.27        14.07 
TCGA-33-4587 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
       54.44         6.94       110.99        44.19       118.36        27.16 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5239 TCGA-34-5241 TCGA-34-5928 TCGA-34-8454 
       65.23        81.24        60.30        16.93        39.32        38.79 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4132 TCGA-37-4133 
        4.04        33.90         4.01         0.43         7.46         7.82 
TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        6.81         3.39        37.58       133.25       126.58       111.35 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 
       55.20        82.52         1.71        24.33        60.53        36.39 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       68.38        55.56        17.06        40.21        38.66        39.12 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-8116 
       33.11        27.91        22.98        24.89        21.47        11.77 
TCGA-43-A475 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
        9.73        12.16        13.02         9.83         4.44        10.65 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
        0.39        28.34         5.46        30.35         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 
       28.96        12.43        18.25        21.90        18.48        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8503 
       30.41        19.76         0.10        17.49         3.48         1.35 
TCGA-56-8622 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
        1.81         9.93        20.25        20.94        19.23        13.32 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8392 
       18.74         0.26        14.47         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-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
       80.45        66.54        56.91        50.33        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
       29.85        35.90        23.57        26.83        11.77        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
       70.13        70.42        55.30        70.62        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 
       45.57        89.29        16.37        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-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2769 
       43.99        21.01         0.99         1.02         2.01         7.07 
TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2782 TCGA-66-2785 
       23.01         3.02         2.01        12.03        12.00         1.97 
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-66-2800 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-70-6722 
       54.08        49.05         6.64        13.35        16.18        12.07 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       12.33        29.56        75.09        23.28        11.18       140.09 
TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        0.49        70.13       106.95         0.16        46.78        32.55 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
        6.51        55.73        37.81       156.66        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-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G6 
        6.97        66.51        54.41        65.49       150.25        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
        5.92        61.94        27.62        38.86         9.67        41.39 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 
       40.24         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        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
       38.14        12.59        18.08        22.59        34.13        30.97 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       19.86        30.48        19.73        15.85        14.96        29.92 
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-94-8491 TCGA-94-A4VJ 
        2.70         3.48         5.26         2.30        26.63        14.14 
TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       17.69        18.31        17.46        30.67        21.34        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
       18.15         2.01        12.89        16.11        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK 
       11.84         4.54        64.54         1.22        13.74         4.21 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
       49.28        25.32        14.73        26.43        83.57         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-XC-AA0X 
       33.07         3.72        12.72         0.20 

$`AMP PEAK 13(8Q24.21) WILD-TYPE`
TCGA-18-3406 TCGA-22-1000 TCGA-33-4533 TCGA-39-5039 TCGA-56-7221 TCGA-56-A4ZJ 
       12.20        14.93       133.74        17.88        19.99        21.04 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-77-A5GB TCGA-90-7766 
        3.58        41.42        35.34        32.32        30.81         9.50 
TCGA-90-7964 TCGA-98-A53D TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3408 
       14.07        21.21        76.80        65.65        16.80        75.75 
TCGA-18-3415 TCGA-18-5592 TCGA-21-1071 TCGA-21-1078 TCGA-22-0940 TCGA-22-0944 
       92.15        49.94        46.88        15.58        21.99         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4607 
        4.31        64.21        35.08        24.13        38.17        19.30 
TCGA-22-5480 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
       71.34        56.32        16.64        97.94        79.53       103.53 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-34-2596 TCGA-34-2600 
       63.35         4.70         0.30        36.62         2.63        61.61 
TCGA-34-2608 TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 TCGA-34-5927 TCGA-34-5929 
       32.88        74.66         9.07        50.66        44.75         4.96 
TCGA-34-7107 TCGA-34-8456 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4141 
        1.12        26.43         0.39         7.96         8.12         0.39 
TCGA-37-A5EN TCGA-39-5021 TCGA-39-5027 TCGA-39-5030 TCGA-39-5036 TCGA-43-6771 
       21.70        68.58       102.18         1.94        71.18         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-A56U TCGA-46-3765 TCGA-46-6026 
        3.81        19.59        13.38        14.20        13.32        13.91 
TCGA-51-4079 TCGA-51-4081 TCGA-56-7223 TCGA-56-7730 TCGA-56-7823 TCGA-56-8082 
        0.39        29.95        14.53         6.51        33.24        14.96 
TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
        4.93        26.89        14.07        22.75        13.81        10.36 
TCGA-56-8629 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-60-2697 TCGA-60-2709 
       15.81        13.55        29.95        71.24        12.23        49.48 
TCGA-60-2716 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       48.49        68.15       102.67        14.99        11.34        25.28 
TCGA-63-A5MS TCGA-63-A5MV TCGA-66-2727 TCGA-66-2754 TCGA-66-2759 TCGA-66-2765 
       78.28        36.16        16.96         2.01        25.05         2.01 
TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 
        2.01        19.00        19.00         3.98        24.95        25.97 
TCGA-66-2787 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59J TCGA-77-6843 
       40.01         4.01         2.73         6.94        14.73        73.12 
TCGA-77-7142 TCGA-77-8008 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       73.22        86.76        60.53        36.36       126.18       132.36 
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 
       26.79        30.64        32.71         2.01        15.39        30.28 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A512 TCGA-90-6837 TCGA-90-A4ED 
       24.36        27.16        16.21        15.29        24.92        20.22 
TCGA-92-8063 TCGA-94-8035 TCGA-94-8490 TCGA-96-7544 TCGA-96-A4JL TCGA-98-7454 
        4.01         4.01         5.03        71.01        27.68        21.44 
TCGA-98-8021 TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-NC-A5HI 
       30.81        27.02        20.32        18.58        20.71        57.30 
TCGA-NC-A5HL TCGA-NC-A5HO TCGA-O2-A52V TCGA-O2-A5IB 
        2.89        43.92        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 
                        173.82                         133.74 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                        21.685                         21.845 
[1] "0.0 - 173.8 (21.7)" "0.3 - 133.7 (21.8)"
[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       53      107        0        41
  AMP PEAK 13(8Q24.21) WILD-TYPE       0       36       45        2        24
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(8Q24.21) MUTATED          72         2         50         14
  AMP PEAK 13(8Q24.21) WILD-TYPE        23         1         13          5
                                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                             53                             36
  STAGE IB                            107                             45
  STAGE II                              0                              2
  STAGE IIA                            41                             24
  STAGE IIB                            72                             23
  STAGE III                             2                              1
  STAGE IIIA                           50                             13
  STAGE IIIB                           14                              5
  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    68 209  54  21
  AMP PEAK 13(8Q24.21) WILD-TYPE  44  85  17   3
D13V4, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  T1                           68                             44
  T2                          209                             85
  T3                           54                             17
  T4                           21                              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
  AMP PEAK 13(8Q24.21) MUTATED   213 102  29   3
  AMP PEAK 13(8Q24.21) WILD-TYPE 104  31  11   2
D13V5, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  N0                          213                            104
  N1                          102                             31
  N2                           29                             11
  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   293   7
  AMP PEAK 13(8Q24.21) WILD-TYPE 118   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED    293    7
  AMP PEAK 13(8Q24.21) WILD-TYPE  118    0
   clus
vv  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  0                          293                            118
  1                            7                              0
[1] 2 2
[1] FALSE
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED    83 269
  AMP PEAK 13(8Q24.21) WILD-TYPE  47 102
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED     83  269
  AMP PEAK 13(8Q24.21) WILD-TYPE   47  102
        clus
vv       AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  FEMALE                           83                             47
  MALE                            269                            102
[1] 2 2
[1] FALSE
D13V8, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED   269  38
  AMP PEAK 13(8Q24.21) WILD-TYPE 115  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED    269   38
  AMP PEAK 13(8Q24.21) WILD-TYPE  115   15
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  NO                           269                            115
  YES                           38                             15
[1] 2 2
[1] FALSE
D13V9, 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 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                                                           336
  AMP PEAK 13(8Q24.21) WILD-TYPE                                                         143
D13V10, multiclass
                                                             clus
vv                                                            AMP PEAK 13(8Q24.21) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          336
                                                             clus
vv                                                            AMP PEAK 13(8Q24.21) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
D13V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(8Q24.21) MUTATED   283  10   1  15
  AMP PEAK 13(8Q24.21) WILD-TYPE 116   2   3   8
D13V13, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  R0                          283                            116
  R1                           10                              2
  R2                            1                              3
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(8Q24.21) MUTATED       6                        25   239
  AMP PEAK 13(8Q24.21) WILD-TYPE     3                         6   110
D13V14, multiclass
                           clus
vv                          AMP PEAK 13(8Q24.21) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           25
  WHITE                                              239
                           clus
vv                          AMP PEAK 13(8Q24.21) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              6
  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"
D13V15, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED     7 218
  AMP PEAK 13(8Q24.21) WILD-TYPE   1  99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED      7  218
  AMP PEAK 13(8Q24.21) WILD-TYPE    1   99
                        clus
vv                       AMP PEAK 13(8Q24.21) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          218
                        clus
vv                       AMP PEAK 13(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                             99
[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    73  60
  AMP PEAK 14(9P13.3) WILD-TYPE 207 154
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                          133                           361 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                           60                           154 
$`AMP PEAK 14(9P13.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-4083 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 
       12.20         4.47         6.18       129.01       133.74         1.55 
TCGA-43-7658 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8504 TCGA-60-2712 
       78.18        12.03        19.99        13.05        16.77         9.01 
TCGA-68-8250 TCGA-77-A5GA TCGA-96-A4JK TCGA-98-A539 TCGA-NC-A5HM TCGA-NC-A5HR 
        8.02        42.08        19.36         5.69        39.85        40.90 
TCGA-18-3417 TCGA-18-4721 TCGA-21-1070 TCGA-21-1075 TCGA-22-0944 TCGA-22-4591 
       36.07       154.32       119.54        70.16         7.33        20.48 
TCGA-22-4595 TCGA-22-4604 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 TCGA-22-5479 
       24.13        13.12         9.57        11.77        14.63        86.30 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5489 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       79.20        11.74        62.86       173.82       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-AAS8 TCGA-34-2600 TCGA-34-5239 TCGA-34-5240 
       14.07        54.44        36.62        61.61        60.30        50.66 
TCGA-34-7107 TCGA-37-3792 TCGA-37-4133 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5021 
        1.12         0.39         7.82        21.70       133.25        68.58 
TCGA-39-5024 TCGA-39-5031 TCGA-43-6143 TCGA-43-A475 TCGA-46-3765 TCGA-46-3768 
       82.52        60.53        22.98         9.73        13.32         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
        4.44        10.65         0.39        28.34         5.46        30.35 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8626 TCGA-56-A49D TCGA-58-8386 
        4.93         3.48        26.89         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-60-2714 TCGA-60-2719 TCGA-63-6202 TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MT 
       50.33        42.64        52.67        59.97        45.57        16.37 
TCGA-63-A5MV TCGA-66-2744 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
       36.16         0.99         0.99        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J 
        0.99         2.01        54.08        49.05         2.73        14.73 
TCGA-77-6842 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-8007 TCGA-77-8009 
       29.56        11.18       140.09         0.49         6.51        55.73 
TCGA-77-8128 TCGA-77-8136 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF 
       37.81        39.09        54.41        36.36       150.25        27.62 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 
       40.24         6.41        36.53        31.30        32.91         1.15 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8352 TCGA-85-8353 TCGA-85-A4CL 
       30.64        34.52        10.09         5.29         3.09        30.28 
TCGA-85-A4JB TCGA-85-A511 TCGA-90-7767 TCGA-92-8064 TCGA-94-8035 TCGA-94-8490 
       30.97        14.96         2.93         5.26         4.01         5.03 
TCGA-96-7544 TCGA-98-8022 TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       71.01        30.67        18.58        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HT 
       13.41        57.30         2.89        49.28        25.32        26.43 
TCGA-O2-A52S 
       12.72 

$`AMP PEAK 14(9P13.3) WILD-TYPE`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
      123.19         4.80        31.99        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-6737 TCGA-34-2604 
       48.82        60.66        64.93        22.06        19.76        31.50 
TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 
       28.96        31.27        17.88        22.49        18.38         7.76 
TCGA-43-8118 TCGA-43-A474 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A4ZJ 
        2.93        11.61         3.45        17.00        17.85        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
        0.13         3.58        41.42        35.34        32.32        66.61 
TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       20.78        30.81         9.50        14.07        21.04         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH 
       18.38        16.14        57.07         2.76        21.21        19.10 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W 
        0.07        76.80        65.65        16.80         0.43         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 
       75.75       117.57        11.34        23.54        92.15        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 
       86.96         2.79        49.94        46.88        99.16        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-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
       43.23        31.63        88.11        41.69        33.93        10.82 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       21.99         4.31        64.21         1.74        14.10        27.02 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 
       35.08        48.33         0.56        38.17        34.75        32.02 
TCGA-22-4607 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5483 
       19.30        63.55        44.25         0.79        71.34        18.84 
TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-6738 
       30.12        56.32        16.64        97.94        79.53        63.35 
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-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       27.16         2.63        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 
        9.07        16.93        44.75        39.32         4.96        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
        4.04        26.43        33.90         4.01         0.43         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
        8.12         7.46         6.81         0.39         3.39        37.58 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
      126.58       111.35        55.20       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
        1.94        36.39        68.38        71.18        55.56        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 
       40.21        38.66        39.12        33.11        27.91        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-46-3766 TCGA-46-3767 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 
       14.20        12.16        13.02        13.91         0.39        29.95 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
        8.75        27.45        28.96        12.43        18.25        21.90 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
       18.48        14.53        31.27        30.41        19.76         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8309 TCGA-56-8503 
        0.10        17.49        33.24        14.96        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        13.81        10.36        20.25        15.81 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8388 
       19.23        13.32        18.74         0.26        14.47        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46N 
       29.95        71.24        16.47        34.78        34.36        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-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 
       49.48        66.54        56.91        48.49         3.19        29.85 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 
       35.90        23.57        26.83        11.77        70.13        70.42 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM 
       68.15        55.30       102.67        70.62        58.65        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MW TCGA-63-A5MY 
       11.34        25.28        89.29        78.28        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-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
        0.92         1.02         2.01         2.01         7.07        23.01 
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-66-2783 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-66-2790 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-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-70-6722 TCGA-70-6723 
        6.64         6.94        13.35        16.18        12.07        12.33 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       73.12        75.09        23.28        73.22        70.13       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 
        0.16        46.78        32.55        86.76       156.66        12.59 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       53.92        17.72       104.09        11.54        26.40        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
        6.97        66.51        65.49        60.53       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       22.29         5.92        61.94        38.86         9.67        41.39 
TCGA-85-7697 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
       34.95         1.38        29.95        18.94        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       24.13        31.56        26.79         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
       16.77        32.71         2.01        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JC 
       38.14        12.59        18.08        22.59        34.13        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       24.36        30.48        19.73        27.16        16.21        15.85 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 
       15.29        29.92        12.39         3.65        24.92        11.77 
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-92-8065 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 
        2.30        26.63        14.14        17.69        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A 
       27.68        21.44        30.81        21.34        27.16        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-MF-A522 TCGA-NC-A5HF 
        2.01        27.02        20.32        20.71        11.84         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HQ 
       64.54         1.22        13.74         4.21        43.92        14.73 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB 
       83.57         3.65        33.07         3.72        43.89        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 
                       173.82                        156.66 
  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE 
                        22.98                         21.47 
[1] "0.0 - 173.8 (23.0)" "0.1 - 156.7 (21.5)"
[1] "hr=" "1.1"
D14V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(9P13.3) MUTATED         0       24       32        1        13
  AMP PEAK 14(9P13.3) WILD-TYPE       2       65      120        1        52
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(9P13.3) MUTATED          35         1         21          4
  AMP PEAK 14(9P13.3) WILD-TYPE        60         2         42         15
                               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                            65
  STAGE IB                            32                           120
  STAGE II                             1                             1
  STAGE IIA                           13                            52
  STAGE IIB                           35                            60
  STAGE III                            1                             2
  STAGE IIIA                          21                            42
  STAGE IIIB                           4                            15
  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  78  22   9
  AMP PEAK 14(9P13.3) WILD-TYPE  85 216  49  15
D14V4, multiclass
    clus
vv   AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  T1                          27                            85
  T2                          78                           216
  T3                          22                            49
  T4                           9                            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    79  43  12   0
  AMP PEAK 14(9P13.3) WILD-TYPE 238  90  28   5
D14V5, multiclass
    clus
vv   AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  N0                          79                           238
  N1                          43                            90
  N2                          12                            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   114   3
  AMP PEAK 14(9P13.3) WILD-TYPE 297   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED    114    3
  AMP PEAK 14(9P13.3) WILD-TYPE  297    4
   clus
vv  AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  0                         114                           297
  1                           3                             4
[1] 2 2
[1] FALSE
D14V7, binary
                               cls
clus                              0   1
  AMP PEAK 14(9P13.3) MUTATED    34 102
  AMP PEAK 14(9P13.3) WILD-TYPE  96 269
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED     34  102
  AMP PEAK 14(9P13.3) WILD-TYPE   96  269
        clus
vv       AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  FEMALE                          34                            96
  MALE                           102                           269
[1] 2 2
[1] FALSE
D14V8, binary
                               cls
clus                              0   1
  AMP PEAK 14(9P13.3) MUTATED   106  14
  AMP PEAK 14(9P13.3) WILD-TYPE 278  39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED    106   14
  AMP PEAK 14(9P13.3) WILD-TYPE  278   39
     clus
vv    AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  NO                          106                           278
  YES                          14                            39
[1] 2 2
[1] FALSE
D14V9, 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 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                                                           129
  AMP PEAK 14(9P13.3) WILD-TYPE                                                         350
D14V10, multiclass
                                                             clus
vv                                                            AMP PEAK 14(9P13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         129
                                                             clus
vv                                                            AMP PEAK 14(9P13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           350
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
D14V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 14(9P13.3) MUTATED   118   2   0   3
  AMP PEAK 14(9P13.3) WILD-TYPE 281  10   4  20
D14V13, multiclass
    clus
vv   AMP PEAK 14(9P13.3) MUTATED AMP PEAK 14(9P13.3) WILD-TYPE
  R0                         118                           281
  R1                           2                            10
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(9P13.3) MUTATED       1                         7    98
  AMP PEAK 14(9P13.3) WILD-TYPE     8                        24   251
D14V14, multiclass
                           clus
vv                          AMP PEAK 14(9P13.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              98
                           clus
vv                          AMP PEAK 14(9P13.3) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            24
  WHITE                                               251
[1] 3 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  80
  AMP PEAK 14(9P13.3) WILD-TYPE   6 237
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(9P13.3) MUTATED      2   80
  AMP PEAK 14(9P13.3) WILD-TYPE    6  237
                        clus
vv                       AMP PEAK 14(9P13.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          80
                        clus
vv                       AMP PEAK 14(9P13.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           237
[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   110  73
  AMP PEAK 15(11Q13.3) WILD-TYPE 170 141
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           183                            311 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            73                            141 
$`AMP PEAK 15(11Q13.3) MUTATED`
TCGA-18-3410 TCGA-18-3416 TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4589 
        4.80        31.99        48.82        60.66        22.06         1.55 
TCGA-33-6737 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-56-7221 
       19.76        22.49        18.38         7.76        78.18        19.99 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A5DR TCGA-60-2715 TCGA-77-A5GB 
        3.45        17.00        16.77         0.13        35.34        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 TCGA-96-A4JK 
        9.50        14.07        21.04        18.38        57.07        19.36 
TCGA-98-8020 TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-18-3412 
        2.76         0.07        39.85        40.90        16.80        11.34 
TCGA-21-1070 TCGA-21-1072 TCGA-21-1079 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 
      119.54        99.16        31.73        43.23        31.63        33.93 
TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
        4.31         1.74        14.10        20.48        35.08        48.33 
TCGA-22-4595 TCGA-22-5491 TCGA-33-4582 TCGA-33-4583 TCGA-33-AASB TCGA-33-AASD 
       24.13        56.32       103.53       151.27         6.94       110.99 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5239 TCGA-34-8455 TCGA-34-8456 TCGA-37-3789 
       65.23        81.24        60.30         4.04        26.43         0.43 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5029 
        7.46         6.81         0.39         3.39       133.25        24.33 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-43-5670 TCGA-43-6143 
       60.53        36.39        71.18        55.56        27.91        22.98 
TCGA-43-6771 TCGA-43-8116 TCGA-46-3766 TCGA-46-3769 TCGA-46-6025 TCGA-52-7809 
        5.46        11.77        12.16         4.44        10.65         5.46 
TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7579 
       30.35        27.45        28.96        18.25        21.90        31.27 
TCGA-56-7582 TCGA-56-7822 TCGA-56-8083 TCGA-56-8503 TCGA-56-A49D TCGA-56-A4BX 
       19.76        17.49         4.93         1.35        20.94        13.32 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-60-2698 TCGA-60-2714 
        0.03        13.25        29.95        71.24        10.22        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 
       42.64         3.19        29.85        26.83        11.77        70.13 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       58.65        59.97        78.28        16.37        36.16        53.88 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2759 TCGA-66-2763 
       43.10         2.01        21.07         0.99        25.05         0.99 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2777 TCGA-66-2781 TCGA-66-2786 
        2.01         2.01         2.01         2.01         3.98        25.97 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-68-7755 TCGA-68-A59J 
        4.04        22.98         5.03        10.06         2.73        14.73 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 
       12.33        29.56        23.28        11.18         0.49        73.22 
TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8133 
      106.95        46.78        32.55         6.51        55.73        53.92 
TCGA-77-8139 TCGA-77-8143 TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 
      104.09        26.40        27.39        66.51        65.49        60.53 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-85-7697 TCGA-85-7699 TCGA-85-7843 
      132.36       150.25         5.92        34.95        32.91         1.15 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       18.94        25.15        26.79        30.64        34.52        10.09 
TCGA-85-8287 TCGA-85-8352 TCGA-85-8354 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4CN 
        0.76         5.29        32.71        38.14        18.08        34.13 
TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 
       30.97        30.48        19.73        27.16        15.85        14.96 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 
       12.39         3.65         2.93        22.62         3.48         5.26 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53B 
       14.14        71.01        18.31        30.67        27.16         2.01 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HO TCGA-NC-A5HQ 
       13.41        11.84        64.54         1.22        43.92        14.73 
TCGA-NC-A5HT TCGA-O2-A52S TCGA-XC-AA0X 
       26.43        12.72         0.20 

$`AMP PEAK 15(11Q13.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
       12.20         4.47       123.19         6.18        27.19        32.19 
TCGA-22-1000 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-34-2604 TCGA-34-2605 
       14.93        64.93       129.01       133.74        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 
       31.27        17.88         2.93        11.61        12.03        13.05 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 
       17.85        21.04         3.58        41.42         9.01        32.32 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-94-7557 TCGA-94-A5I4 
       66.61         8.02        20.78        42.08         0.16        16.14 
TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A7XE 
        5.69        21.21        19.10        76.80        65.65         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
        8.58        75.75       117.57        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 
       92.42        86.96         2.79       154.32        49.94        46.88 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
       70.16        60.89        34.78        15.58       122.43         9.34 
TCGA-21-1082 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
      119.80        88.11        41.69        10.82        21.99         7.33 
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-22-5473 TCGA-22-5474 
       32.02        19.30         9.57        11.77        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        86.30        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 
       18.84        30.12        62.86        16.64        97.94        79.53 
TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
      173.82        14.07        54.44        63.35         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 
       36.62        44.19       118.36        27.16         2.63        61.61 
TCGA-34-2608 TCGA-34-5234 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       32.88        74.66         9.07        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 
       39.32         4.96         1.12        38.79        33.90         4.01 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 TCGA-37-A5EL TCGA-37-A5EN 
        0.39         7.96         8.12         7.82        37.58        21.70 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5030 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
        1.71         1.94        68.38        17.06        40.21        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 
       39.12        33.11        24.89        21.47         3.81        19.59 
TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3767 TCGA-46-3768 
       13.38         9.73        14.20        13.32        13.02         9.83 
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-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 
       12.43        18.48        14.53        30.41         6.51         0.10 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8622 
       33.24        14.96         3.48        26.89        14.07         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75        13.81        10.36         9.93        20.25        15.81 
TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8388 TCGA-58-8392 
       19.23        18.74         0.26        14.47        13.55        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-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       21.11        12.23        96.82        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2723 
       80.45        49.48        66.54        56.91        48.49        35.90 
TCGA-60-2724 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB 
       23.57        52.67        70.42        68.15        55.30       102.67 
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-A5MY TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
       34.59        16.96         1.02         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
       43.99        21.01         1.02         7.07        23.01        19.00 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
        3.02        19.00        12.03        12.00        24.95         1.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
       40.01        22.98        30.02        54.08         4.01        49.05 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-70-6722 TCGA-77-6843 
        6.64         6.94        13.35        16.18        12.07        73.12 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7335 TCGA-77-7338 TCGA-77-8008 TCGA-77-8128 
       75.09       140.09        70.13         0.16        86.76        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8145 
      156.66        12.59        39.09        17.72        11.54         6.97 
TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GF 
       54.41        36.36       126.18        22.29        61.94        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       38.86         9.67        41.39        40.24         6.41        36.53 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       31.30         1.38        29.95        19.04        24.13        31.56 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 
       13.22        22.45        16.77         3.09         2.01        15.39 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC 
        7.76        36.59        12.59        22.59        30.28        19.86 
TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 
       24.36        16.21        15.29        29.92        24.92        11.77 
TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 
       20.22        10.59         2.70         4.01         2.30         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
        5.03        26.63        17.69        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       30.81        21.34        18.15        27.02        20.32        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HI 
       20.71        12.89        16.11        13.18         4.54        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NK-A5CR 
       13.74         4.21         2.89        49.28        25.32        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB 
        3.65        33.07         3.72        43.89        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                         173.82 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                          21.9                           21.7 
[1] "0.0 - 151.3 (21.9)" "0.1 - 173.8 (21.7)"
[1] "hr=" "1"  
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(11Q13.3) MUTATED         0       36       49        0        25
  AMP PEAK 15(11Q13.3) WILD-TYPE       2       53      103        2        40
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(11Q13.3) MUTATED          37         1         26          4
  AMP PEAK 15(11Q13.3) WILD-TYPE        58         2         37         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                             36                             53
  STAGE IB                             49                            103
  STAGE II                              0                              2
  STAGE IIA                            25                             40
  STAGE IIB                            37                             58
  STAGE III                             1                              2
  STAGE IIIA                           26                             37
  STAGE IIIB                            4                             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    46 105  28   6
  AMP PEAK 15(11Q13.3) WILD-TYPE  66 189  43  18
D15V4, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  T1                           46                             66
  T2                          105                            189
  T3                           28                             43
  T4                            6                             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 15(11Q13.3) MUTATED   113  50  16   3
  AMP PEAK 15(11Q13.3) WILD-TYPE 204  83  24   2
D15V5, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  N0                          113                            204
  N1                           50                             83
  N2                           16                             24
  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   155   4
  AMP PEAK 15(11Q13.3) WILD-TYPE 256   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED    155    4
  AMP PEAK 15(11Q13.3) WILD-TYPE  256    3
   clus
vv  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  0                          155                            256
  1                            4                              3
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED    41 144
  AMP PEAK 15(11Q13.3) WILD-TYPE  89 227
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED     41  144
  AMP PEAK 15(11Q13.3) WILD-TYPE   89  227
        clus
vv       AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  FEMALE                           41                             89
  MALE                            144                            227
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED   137  18
  AMP PEAK 15(11Q13.3) WILD-TYPE 247  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED    137   18
  AMP PEAK 15(11Q13.3) WILD-TYPE  247   35
     clus
vv    AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  NO                           137                            247
  YES                           18                             35
[1] 2 2
[1] FALSE
D15V9, 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 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                                                           178
  AMP PEAK 15(11Q13.3) WILD-TYPE                                                         301
D15V10, multiclass
                                                             clus
vv                                                            AMP PEAK 15(11Q13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          178
                                                             clus
vv                                                            AMP PEAK 15(11Q13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            301
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous
D15V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(11Q13.3) MUTATED   152   3   1   8
  AMP PEAK 15(11Q13.3) WILD-TYPE 247   9   3  15
D15V13, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  R0                          152                            247
  R1                            3                              9
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(11Q13.3) MUTATED       3                         8   130
  AMP PEAK 15(11Q13.3) WILD-TYPE     6                        23   219
D15V14, multiclass
                           clus
vv                          AMP PEAK 15(11Q13.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                              130
                           clus
vv                          AMP PEAK 15(11Q13.3) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             23
  WHITE                                                219
[1] 3 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     3 109
  AMP PEAK 15(11Q13.3) WILD-TYPE   5 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      3  109
  AMP PEAK 15(11Q13.3) WILD-TYPE    5  208
                        clus
vv                       AMP PEAK 15(11Q13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          109
                        clus
vv                       AMP PEAK 15(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            208
[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   139 111
  AMP PEAK 16(12P13.33) WILD-TYPE 141 103
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                            250                             244 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                            111                             103 
$`AMP PEAK 16(12P13.33) MUTATED`
TCGA-18-3410 TCGA-18-3416 TCGA-21-A5DI TCGA-33-4532 TCGA-33-6737 TCGA-34-2605 
        4.80        31.99        32.19       129.01        19.76        28.96 
TCGA-34-2609 TCGA-43-5668 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
       31.27        18.38        78.18         2.93        11.61        12.03 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A5DR TCGA-60-2711 
       13.05         3.45        17.00        16.77         0.13        41.42 
TCGA-60-2712 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-90-7964 
        9.01        66.61         8.02        20.78        42.08        14.07 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-J1-A4AH 
        0.16        18.38        16.14        57.07        19.36        19.10 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3412 TCGA-18-3417 
       39.85        40.90         0.43         8.58        11.34        36.07 
TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
       86.96       154.32        49.94       119.54        46.88        99.16 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-22-1012 
       34.78        31.73        43.23        31.63        33.93        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
       27.02        20.48        35.08        24.13        38.17        34.75 
TCGA-22-4604 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
       13.12        11.77        63.55        14.63        44.25        86.30 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4566 
       71.34        11.74        62.86        56.32        97.94       173.82 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI 
      103.53        14.07        54.44        63.35       110.99        44.19 
TCGA-33-AASJ TCGA-34-2596 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
      118.36         2.63        65.23        60.30        50.66        16.93 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-37-3792 TCGA-37-5819 
       39.32         1.12         4.04        26.43         0.39         3.39 
TCGA-37-A5EL TCGA-39-5019 TCGA-39-5021 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       37.58       111.35        68.58        36.39        68.38        71.18 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       55.56        17.06        38.66        39.12        33.11        27.91 
TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-46-3765 
       21.47         5.46        13.38        11.77         9.73        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       12.16        13.02         9.83         4.44        10.65        13.91 
TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
        0.39        29.95         5.46         8.75        27.45        28.96 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 
       18.25        21.90        18.48        14.53        19.76         6.51 
TCGA-56-7822 TCGA-56-8304 TCGA-56-8622 TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D 
       17.49         3.48         1.81        10.36        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-58-8387 TCGA-58-8391 TCGA-58-A46K TCGA-58-A46N 
       19.23        13.32        13.25        71.24        34.36        29.92 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 
       21.11        10.22        96.82        37.94        92.71        80.45 
TCGA-60-2719 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7022 
       42.64        35.90        26.83        11.77        70.13        68.15 
TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS 
      102.67        58.65        59.97        45.57        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2727 TCGA-66-2737 TCGA-66-2744 TCGA-66-2756 
       16.37        53.88        16.96         2.01         0.99         0.99 
TCGA-66-2758 TCGA-66-2767 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2785 
       21.01         2.01         3.02         2.01         3.98         1.97 
TCGA-66-2787 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-68-7755 TCGA-68-7756 
       40.01        30.02        10.06        54.08         2.73         6.64 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 TCGA-77-7139 
       13.35        16.18        14.73        12.07        29.56       140.09 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        0.49        73.22        70.13       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 
       32.55        55.73        37.81       156.66        53.92        17.72 
TCGA-77-8143 TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
       26.40        66.51        36.36       132.36       150.25        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 
        5.92        61.94        27.62        38.86        41.39        36.53 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
       34.95        32.91        29.95        18.94        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 
       24.13        31.56        10.09         0.76        22.45         5.29 
TCGA-85-8354 TCGA-85-8481 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN 
       32.71         7.76        12.59        18.08        22.59        34.13 
TCGA-85-A4JB TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L 
       30.97        19.73        15.85        14.96        15.29        12.39 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
        2.93        11.77        22.62        10.59         2.70         3.48 
TCGA-92-8064 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-98-8023 TCGA-98-A538 
        5.26        14.14        17.69        71.01        21.34        27.16 
TCGA-98-A53B TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
        2.01        20.71        16.11        13.18        13.41        11.84 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HQ 
       64.54         1.22        13.74         4.21        43.92        14.73 
TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52V TCGA-O2-A5IB 
       83.57        33.07        43.89        11.18 

$`AMP PEAK 16(12P13.33) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 
       12.20         4.47       123.19         6.18        27.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 
       48.82        60.66        64.93        22.06       133.74         1.55 
TCGA-34-2604 TCGA-39-5039 TCGA-43-2578 TCGA-43-7657 TCGA-56-7221 TCGA-56-A4BY 
       31.50        17.88        22.49         7.76        19.99        17.85 
TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2715 TCGA-60-2721 TCGA-77-A5GB TCGA-90-7766 
       21.04         3.58        35.34        32.32        30.81         9.50 
TCGA-94-7033 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE 
       21.04         2.76         5.69        21.21         0.07        76.80 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 
       65.65        16.80        75.75       117.57        23.54        92.15 
TCGA-18-3419 TCGA-18-4086 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 
       92.42         2.79        70.16        60.89        15.58       122.43 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 
        9.34       119.80        88.11        41.69        10.82        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-4594 TCGA-22-4596 
        7.33         4.31        64.21         1.74        48.33         0.56 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5478 TCGA-22-5481 TCGA-22-5483 
       32.02        19.30         9.57         0.79        79.20        18.84 
TCGA-22-5485 TCGA-22-5492 TCGA-33-4547 TCGA-33-4583 TCGA-33-A4WN TCGA-33-A5GW 
       30.12        16.64        79.53       151.27         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 
       36.62         6.94        27.16        61.61        32.88        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-A5IX 
       74.66         9.07        44.75         4.96        38.79        33.90 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        4.01         0.43         7.96         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 
        6.81         0.39        21.70       133.25       126.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-43-2576 TCGA-43-6143 TCGA-43-6647 TCGA-43-6773 TCGA-43-7656 TCGA-43-A56U 
       40.21        22.98        24.89         3.81        19.59        14.20 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7810 TCGA-56-5897 TCGA-56-7579 TCGA-56-7580 
        0.39        28.34        30.35        12.43        31.27        30.41 
TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 
        0.10        33.24        14.96         4.93        26.89        14.07 
TCGA-56-8503 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4ZK 
        1.35        22.75        13.81         9.93        20.25        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 
        0.26        14.47         0.03        13.55        29.95        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-60-2697 TCGA-60-2707 
       34.78        85.12        56.65        35.24        12.23        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-60-2722 TCGA-60-2724 TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MG 
       29.85        23.57        52.67        70.42        55.30        70.62 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2734 
       14.99        11.34        25.28        36.16        34.59        43.10 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 
       21.07         1.02         2.01         0.92        43.99        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-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 
       19.00        19.00        12.03        12.00        24.95        25.97 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2795 TCGA-66-2800 
       22.98         4.04        22.98         5.03         4.01        49.05 
TCGA-68-7757 TCGA-70-6723 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
        6.94        12.33        73.12        75.09        23.28        11.18 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 
        6.51        86.76        12.59        39.09       104.09        11.54 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ 
       27.39         6.97        54.41        65.49        60.53       126.18 
TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 
        9.67        40.24         6.41        31.30         1.38         1.15 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8288 TCGA-85-8351 TCGA-85-8353 
       26.79        30.64        34.52        13.22        16.77         3.09 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL TCGA-85-A4JC 
        2.01        15.39        36.59        38.14        30.28        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A513 TCGA-85-A5B5 
       24.36        30.48        27.16        16.21        29.92         3.65 
TCGA-90-6837 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 
       24.92        20.22         4.01         2.30         4.01         5.03 
TCGA-94-8491 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       26.63        18.31        17.46        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 
       30.67        18.15        27.02        20.32        18.58        12.89 
TCGA-NC-A5HF TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HT 
        4.54        57.30         2.89        49.28        25.32        26.43 
TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-XC-AA0X 
        3.65         3.72        12.72         0.20 

  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                           0.13                            0.03 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                         173.82                          151.27 
  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE 
                         22.095                          21.570 
[1] "0.1 - 173.8 (22.1)" "0.0 - 151.3 (21.6)"
[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        30
  AMP PEAK 16(12P13.33) WILD-TYPE       0       52       73        0        35
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(12P13.33) MUTATED          54         1         37          7
  AMP PEAK 16(12P13.33) WILD-TYPE        41         2         26         12
                                 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                              52
  STAGE IB                              79                              73
  STAGE II                               2                               0
  STAGE IIA                             30                              35
  STAGE IIB                             54                              41
  STAGE III                              1                               2
  STAGE IIIA                            37                              26
  STAGE IIIB                             7                              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 16(12P13.33) MUTATED    45 159  39  12
  AMP PEAK 16(12P13.33) WILD-TYPE  67 135  32  12
D16V4, multiclass
    clus
vv   AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  T1                            45                              67
  T2                           159                             135
  T3                            39                              32
  T4                            12                              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 16(12P13.33) MUTATED   157  74  22   1
  AMP PEAK 16(12P13.33) WILD-TYPE 160  59  18   4
D16V5, multiclass
    clus
vv   AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  N0                           157                             160
  N1                            74                              59
  N2                            22                              18
  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   207   2
  AMP PEAK 16(12P13.33) WILD-TYPE 204   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(12P13.33) MUTATED    207    2
  AMP PEAK 16(12P13.33) WILD-TYPE  204    5
   clus
vv  AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  0                           207                             204
  1                             2                               5
[1] 2 2
[1] FALSE
D16V7, binary
                                 cls
clus                                0   1
  AMP PEAK 16(12P13.33) MUTATED    55 200
  AMP PEAK 16(12P13.33) WILD-TYPE  75 171
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(12P13.33) MUTATED     55  200
  AMP PEAK 16(12P13.33) WILD-TYPE   75  171
        clus
vv       AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  FEMALE                            55                              75
  MALE                             200                             171
[1] 2 2
[1] FALSE
D16V8, binary
                                 cls
clus                                0   1
  AMP PEAK 16(12P13.33) MUTATED   198  28
  AMP PEAK 16(12P13.33) WILD-TYPE 186  25
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(12P13.33) MUTATED    198   28
  AMP PEAK 16(12P13.33) WILD-TYPE  186   25
     clus
vv    AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  NO                            198                             186
  YES                            28                              25
[1] 2 2
[1] FALSE
D16V9, 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 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                                                           244
  AMP PEAK 16(12P13.33) WILD-TYPE                                                         235
D16V10, multiclass
                                                             clus
vv                                                            AMP PEAK 16(12P13.33) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           244
                                                             clus
vv                                                            AMP PEAK 16(12P13.33) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             235
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
D16V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 16(12P13.33) MUTATED   198   6   1  13
  AMP PEAK 16(12P13.33) WILD-TYPE 201   6   3  10
D16V13, multiclass
    clus
vv   AMP PEAK 16(12P13.33) MUTATED AMP PEAK 16(12P13.33) WILD-TYPE
  R0                           198                             201
  R1                             6                               6
  R2                             1                               3
  RX                            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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(12P13.33) MUTATED       2                        18   186
  AMP PEAK 16(12P13.33) WILD-TYPE     7                        13   163
D16V14, multiclass
                           clus
vv                          AMP PEAK 16(12P13.33) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            18
  WHITE                                               186
                           clus
vv                          AMP PEAK 16(12P13.33) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              13
  WHITE                                                 163
[1] 3 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     4 162
  AMP PEAK 16(12P13.33) WILD-TYPE   4 155
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 16(12P13.33) MUTATED      4  162
  AMP PEAK 16(12P13.33) WILD-TYPE    4  155
                        clus
vv                       AMP PEAK 16(12P13.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           162
                        clus
vv                       AMP PEAK 16(12P13.33) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             155
[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    96  80
  AMP PEAK 17(12Q15) WILD-TYPE 184 134
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                         176                          318 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                          80                          134 
$`AMP PEAK 17(12Q15) MUTATED`
TCGA-18-3410 TCGA-21-A5DI TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 
        4.80        32.19        48.82        60.66        22.06       129.01 
TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-43-5668 TCGA-43-8118 TCGA-56-8201 
       19.76        28.96        31.27        18.38         2.93        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
        3.45        17.00         0.13        41.42         9.01        35.34 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-94-7557 TCGA-94-7943 
       66.61         8.02        20.78        42.08         0.16        18.38 
TCGA-98-8020 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-18-3412 
        2.76        19.10         0.07        39.85        40.90        11.34 
TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
       36.07        86.96       154.32       119.54        46.88        99.16 
TCGA-21-1077 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-1016 
       34.78       119.80        43.23        33.93        10.82        27.02 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4601 TCGA-22-4604 TCGA-22-5473 TCGA-22-5477 
       35.08        48.33        34.75        13.12        63.55        44.25 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5491 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 
       86.30        71.34        56.32        97.94       103.53       151.27 
TCGA-33-4586 TCGA-33-A5GW TCGA-34-2596 TCGA-34-5231 TCGA-34-5239 TCGA-34-5241 
       14.07         0.30         2.63        65.23        60.30        16.93 
TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 
        1.12         4.04        26.43         0.39         8.12         7.82 
TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5019 TCGA-39-5034 
        3.39        37.58        21.70       133.25       111.35        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-43-3394 TCGA-43-6770 TCGA-43-6771 TCGA-43-8115 
       68.38        71.18        39.12        21.47         5.46        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-52-7809 
       11.77         9.73         9.83        10.65         0.39         5.46 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 
        8.75        27.45        28.96        18.25        21.90        14.53 
TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 TCGA-56-A49D TCGA-56-A4BX TCGA-58-A46K 
       19.76         6.51         3.48        20.94        13.32        34.36 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2719 
       21.11        10.22        37.94        92.71        80.45        42.64 
TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MJ 
       35.90        23.57        26.83        11.77       102.67        59.97 
TCGA-63-A5ML TCGA-63-A5MR TCGA-66-2744 TCGA-66-2754 TCGA-66-2756 TCGA-66-2758 
       45.57        89.29         0.99         2.01         0.99        21.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2773 TCGA-66-2781 TCGA-66-2793 TCGA-66-2794 
        1.02         2.01         3.02         3.98        10.06        54.08 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-70-6723 
       49.05         2.73         6.64        13.35        16.18        12.33 
TCGA-77-6842 TCGA-77-7142 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
       29.56        73.22        46.78        32.55        55.73        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        66.51        54.41        60.53 
TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GF TCGA-85-6175 TCGA-85-7950 TCGA-85-8048 
      150.25         5.92        27.62         9.67        18.94        25.15 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8353 
       24.13        31.56        34.52        10.09        22.45         3.09 
TCGA-85-8354 TCGA-85-8479 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CN TCGA-85-A4JC 
       32.71        15.39        12.59        18.08        34.13        19.86 
TCGA-85-A4QR TCGA-85-A510 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
       19.73        15.85        29.92         3.65         2.93        11.77 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-98-8023 TCGA-98-A53B 
       22.62        10.59         2.70         3.48        21.34         2.01 
TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK 
       16.11        13.18        64.54         1.22        13.74         4.21 
TCGA-NC-A5HQ TCGA-O2-A52Q 
       14.73         3.72 

$`AMP PEAK 17(12Q15) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19        31.99         6.18        27.19 
TCGA-22-1000 TCGA-22-5472 TCGA-33-4533 TCGA-33-4589 TCGA-34-2604 TCGA-39-5039 
       14.93        64.93       133.74         1.55        31.50        17.88 
TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
       22.49         7.76        78.18        11.61        12.03        19.99 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2721 TCGA-77-A5GB 
       16.77        17.85        21.04         3.58        32.32        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
        9.50        14.07        21.04        16.14        57.07        19.36 
TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE 
        5.69        21.21        76.80        65.65        16.80         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 
        8.58        75.75       117.57        23.54        92.15        92.42 
TCGA-18-4086 TCGA-18-5592 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 
        2.79        49.94        70.16        60.89        15.58        31.73 
TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 
      122.43         9.34        31.63        88.11        41.69        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 
        7.33         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-22-5474 TCGA-22-5478 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
       11.77        14.63         0.79        79.20        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4587 
       30.12        62.86        16.64        79.53       173.82        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI 
       63.35         4.70        36.62         6.94       110.99        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 
      118.36        27.16        61.61        32.88        81.24        74.66 
TCGA-34-5236 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 
        9.07        50.66        44.75        39.32         4.96        38.79 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 
       33.90         4.01         0.43         7.96         7.46         6.81 
TCGA-37-4141 TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        0.39       126.58        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5037 TCGA-39-5040 
        1.71        24.33         1.94        60.53        55.56        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       40.21        38.66        33.11        27.91        22.98        24.89 
TCGA-43-6773 TCGA-43-7656 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
        3.81        19.59        14.20        13.32        12.16        13.02 
TCGA-46-3769 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 
        4.44        13.91         0.39        29.95        28.34        30.35 
TCGA-56-5897 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 
       12.43        18.48        31.27        30.41         0.10        17.49 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       33.24        14.96         4.93        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
        1.81        22.75        13.81        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       15.81        19.23        18.74         0.26        14.47         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-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2703 
       85.12        56.65        35.24        29.92        12.23        96.82 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       21.93        49.48        66.54        56.91        50.33        48.49 
TCGA-60-2720 TCGA-60-2722 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
        3.19        29.85        52.67        70.13        70.42        68.15 
TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       55.30        70.62        58.65        14.99        11.34        25.28 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       78.28        16.37        36.16        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2755 TCGA-66-2757 
       43.10         2.01        21.07         1.02         0.92        43.99 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 
       25.05         0.99         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-66-2795 TCGA-68-7757 TCGA-68-A59J TCGA-70-6722 
        5.03        30.02         4.01         6.94        14.73        12.07 
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       140.09         0.49 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 
       70.13       106.95         0.16         6.51        86.76       156.66 
TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8145 
       12.59        39.09        17.72       104.09        11.54         6.97 
TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G8 
       65.49        36.36       126.18       132.36        22.29        61.94 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       38.86        41.39        40.24         6.41        36.53        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 
       31.30        32.91         1.38         1.15        29.95        19.04 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 
       26.79        30.64         0.76        13.22        16.77         5.29 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CL 
        2.01         7.76        36.59        38.14        22.59        30.28 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
       30.97        24.36        30.48        27.16        16.21        14.96 
TCGA-85-A512 TCGA-85-A53L TCGA-90-6837 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8064 
       15.29        12.39        24.92        20.22         4.01         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        2.30         4.01         5.03        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       71.01        18.31        17.46        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       30.67        27.16        18.15        27.02        20.32        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HI 
       20.71        12.89        13.41        11.84         4.54        57.30 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR 
        2.89        49.28        43.92        25.32        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
        3.65        33.07        12.72        43.89        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                       173.82 
  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE 
                      21.405                       22.140 
[1] "0.1 - 154.3 (21.4)" "0.0 - 173.8 (22.1)"
[1] "hr=" "1.1"
D17V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(12Q15) MUTATED         0       32       48        1        24
  AMP PEAK 17(12Q15) WILD-TYPE       2       57      104        1        41
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(12Q15) MUTATED          32         1         29          7
  AMP PEAK 17(12Q15) WILD-TYPE        63         2         34         12
                              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                           32                           57
  STAGE IB                           48                          104
  STAGE II                            1                            1
  STAGE IIA                          24                           41
  STAGE IIB                          32                           63
  STAGE III                           1                            2
  STAGE IIIA                         29                           34
  STAGE IIIB                          7                           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 17(12Q15) MUTATED    38 102  27  11
  AMP PEAK 17(12Q15) WILD-TYPE  74 192  44  13
D17V4, multiclass
    clus
vv   AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  T1                         38                           74
  T2                        102                          192
  T3                         27                           44
  T4                         11                           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   107  50  18   1
  AMP PEAK 17(12Q15) WILD-TYPE 210  83  22   4
D17V5, multiclass
    clus
vv   AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  N0                        107                          210
  N1                         50                           83
  N2                         18                           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   151   2
  AMP PEAK 17(12Q15) WILD-TYPE 260   5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED    151    2
  AMP PEAK 17(12Q15) WILD-TYPE  260    5
   clus
vv  AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  0                        151                          260
  1                          2                            5
[1] 2 2
[1] FALSE
D17V7, binary
                              cls
clus                             0   1
  AMP PEAK 17(12Q15) MUTATED    38 140
  AMP PEAK 17(12Q15) WILD-TYPE  92 231
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED     38  140
  AMP PEAK 17(12Q15) WILD-TYPE   92  231
        clus
vv       AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  FEMALE                         38                           92
  MALE                          140                          231
[1] 2 2
[1] FALSE
D17V8, binary
                              cls
clus                             0   1
  AMP PEAK 17(12Q15) MUTATED   133  21
  AMP PEAK 17(12Q15) WILD-TYPE 251  32
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED    133   21
  AMP PEAK 17(12Q15) WILD-TYPE  251   32
     clus
vv    AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  NO                         133                          251
  YES                         21                           32
[1] 2 2
[1] FALSE
D17V9, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 17(12Q15) MUTATED                                       6
  AMP PEAK 17(12Q15) WILD-TYPE                                     9
                              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                                                           169
  AMP PEAK 17(12Q15) WILD-TYPE                                                         310
D17V10, multiclass
                                                             clus
vv                                                            AMP PEAK 17(12Q15) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        169
                                                             clus
vv                                                            AMP PEAK 17(12Q15) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          310
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
D17V12, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 17(12Q15) MUTATED   144   4   1   8
  AMP PEAK 17(12Q15) WILD-TYPE 255   8   3  15
D17V13, multiclass
    clus
vv   AMP PEAK 17(12Q15) MUTATED AMP PEAK 17(12Q15) WILD-TYPE
  R0                        144                          255
  R1                          4                            8
  R2                          1                            3
  RX                          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                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(12Q15) MUTATED       2                        10   134
  AMP PEAK 17(12Q15) WILD-TYPE     7                        21   215
D17V14, multiclass
                           clus
vv                          AMP PEAK 17(12Q15) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                         10
  WHITE                                            134
                           clus
vv                          AMP PEAK 17(12Q15) WILD-TYPE
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                           21
  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"
D17V15, binary
                              cls
clus                             0   1
  AMP PEAK 17(12Q15) MUTATED     4 115
  AMP PEAK 17(12Q15) WILD-TYPE   4 202
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(12Q15) MUTATED      4  115
  AMP PEAK 17(12Q15) WILD-TYPE    4  202
                        clus
vv                       AMP PEAK 17(12Q15) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        115
                        clus
vv                       AMP PEAK 17(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          202
[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  39
  AMP PEAK 18(13Q34) WILD-TYPE 228 175
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          91                          403 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                          39                          175 
$`AMP PEAK 18(13Q34) MUTATED`
TCGA-18-3407 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A56V TCGA-56-8201 
        4.47         7.76        78.18         2.93        12.03        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-63-A5MH TCGA-94-7943 TCGA-98-8020 TCGA-NK-A7XE 
        3.45        17.00        66.61        18.38         2.76         0.43 
TCGA-18-3411 TCGA-21-1070 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 
      117.57       119.54        31.73         9.34       119.80        31.63 
TCGA-21-5786 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-5479 
       33.93        35.08        48.33        24.13        38.17        86.30 
TCGA-33-4538 TCGA-33-4587 TCGA-33-AASB TCGA-34-8455 TCGA-34-A5IX TCGA-37-4130 
       97.94        54.44         6.94         4.04        33.90         8.12 
TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5021 TCGA-39-5024 
        3.39        37.58        21.70       133.25        68.58        82.52 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-43-2576 TCGA-43-6143 TCGA-43-8115 
       36.39        68.38        55.56        40.21        22.98        13.38 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 
       29.95         5.46        30.35        12.43        18.25        14.53 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8626 TCGA-56-A4BX TCGA-56-A4ZK TCGA-58-A46N 
       17.49        33.24         9.93        13.32        18.74        29.92 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2714 
       21.11        10.22        37.94        92.71        80.45        50.33 
TCGA-63-A5MS TCGA-63-A5MT TCGA-66-2737 TCGA-66-2763 TCGA-66-2766 TCGA-66-2791 
       78.28        16.37         2.01         0.99         1.02         5.03 
TCGA-70-6723 TCGA-77-6845 TCGA-77-7138 TCGA-77-7337 TCGA-77-8133 TCGA-77-8156 
       12.33        23.28        11.18       106.95        53.92        36.36 
TCGA-77-A5G1 TCGA-77-A5GH TCGA-85-6798 TCGA-85-7696 TCGA-85-7843 TCGA-85-7950 
      132.36        38.86         6.41        36.53         1.15        18.94 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8353 TCGA-85-8479 TCGA-85-A4JC TCGA-90-A59Q 
       30.64        10.09         3.09        15.39        19.86        10.59 
TCGA-92-8065 TCGA-98-A53C TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HH 
        2.30        27.02        12.89        13.41        11.84         1.22 
TCGA-NC-A5HJ 
       13.74 

$`AMP PEAK 18(13Q34) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20       123.19         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
      129.01       133.74         1.55        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-A474 TCGA-56-7221 
       31.27        17.88        22.49        18.38        11.61        19.99 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       16.77        17.85        21.04         0.13         3.58        41.42 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
        9.01        35.34        32.32         8.02        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-A5I4 
       30.81         9.50        14.07        21.04         0.16        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       57.07        19.36         5.69        21.21        19.10         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W 
       76.80        39.85        40.90        65.65        16.80         8.58 
TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
       75.75        11.34        23.54        92.15        36.07        92.42 
TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 
       86.96         2.79       154.32        49.94        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-22-0940 TCGA-22-0944 TCGA-22-1002 
       88.11        41.69        10.82        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4596 
       64.21         1.74        14.10        27.02        20.48         0.56 
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-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
       63.55        14.63        44.25         0.79        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-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 
       79.53       173.82       103.53       151.27        14.07        63.35 
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-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       27.16         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 
       39.32         4.96         1.12        38.79        26.43         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         0.39         7.96         7.46         7.82         6.81 
TCGA-37-4141 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 
        0.39       126.58       111.35        55.20       102.18         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5040 TCGA-43-2581 
       24.33         1.94        60.53        71.18        17.06        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       39.12        33.11        27.91        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 
        3.81        19.59        11.77         9.73        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       12.16        13.02         9.83         4.44        10.65        13.91 
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-56-6545 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
       21.90        18.48        31.27        30.41        19.76         6.51 
TCGA-56-7731 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
        0.10        14.96         4.93         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 
        1.35         1.81        22.75        13.81        10.36        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       15.81        20.94        19.23         0.26        14.47         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-60-2697 TCGA-60-2703 
       85.12        34.36        56.65        35.24        12.23        96.82 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2719 
       21.93        49.48        66.54        56.91        48.49        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-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB 
       52.67        70.13        70.42        68.15        55.30       102.67 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
       70.62        58.65        59.97        45.57        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       25.28        89.29        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-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 
        6.94        13.35        16.18        14.73        12.07        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       73.12        75.09       140.09         0.49        73.22        70.13 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        0.16        46.78        32.55         6.51        86.76        55.73 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       37.81       156.66        12.59        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        66.51        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       65.49        60.53       126.18       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 
       61.94        27.62         9.67        41.39        40.24        34.95 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 
       31.30        32.91         1.38        29.95        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
       24.13        31.56        26.79        34.52         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 
       22.45        16.77         5.29        32.71         2.01         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       36.59        38.14        12.59        18.08        22.59        30.28 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       34.13        30.97        24.36        30.48        19.73        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       16.21        15.85        14.96        15.29        29.92        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-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-8035 TCGA-94-8490 
        2.70         3.48         4.01         5.26         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        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       27.68        21.44        30.81        30.67        21.34        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 
       18.15         2.01        20.32        18.58        20.71        16.11 
TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL 
       13.18         4.54        64.54        57.30         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
       49.28        43.92        25.32        14.73        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
        3.65        33.07         3.72        12.72        43.89        11.18 
TCGA-XC-AA0X 
        0.20 

  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                        0.43                         0.03 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                      133.25                       173.82 
  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE 
                       19.86                        21.99 
[1] "0.4 - 133.2 (19.9)" "0.0 - 173.8 (22.0)"
[1] "hr=" "1"  
D18V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(13Q34) MUTATED         0       17       23        0        10
  AMP PEAK 18(13Q34) WILD-TYPE       2       72      129        2        55
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(13Q34) MUTATED          19         0         18          3
  AMP PEAK 18(13Q34) WILD-TYPE        76         3         45         16
                              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                           17                           72
  STAGE IB                           23                          129
  STAGE II                            0                            2
  STAGE IIA                          10                           55
  STAGE IIB                          19                           76
  STAGE III                           0                            3
  STAGE IIIA                         18                           45
  STAGE IIIB                          3                           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
  AMP PEAK 18(13Q34) MUTATED    20  47  21   3
  AMP PEAK 18(13Q34) WILD-TYPE  92 247  50  21
D18V4, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  T1                         20                           92
  T2                         47                          247
  T3                         21                           50
  T4                          3                           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    56  21  12   1
  AMP PEAK 18(13Q34) WILD-TYPE 261 112  28   4
D18V5, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  N0                         56                          261
  N1                         21                          112
  N2                         12                           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    74   1
  AMP PEAK 18(13Q34) WILD-TYPE 337   6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     74    1
  AMP PEAK 18(13Q34) WILD-TYPE  337    6
   clus
vv  AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  0                         74                          337
  1                          1                            6
[1] 2 2
[1] FALSE
D18V7, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED    26  65
  AMP PEAK 18(13Q34) WILD-TYPE 104 306
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     26   65
  AMP PEAK 18(13Q34) WILD-TYPE  104  306
        clus
vv       AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  FEMALE                         26                          104
  MALE                           65                          306
[1] 2 2
[1] FALSE
D18V8, binary
                              cls
clus                             0   1
  AMP PEAK 18(13Q34) MUTATED    68  10
  AMP PEAK 18(13Q34) WILD-TYPE 316  43
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED     68   10
  AMP PEAK 18(13Q34) WILD-TYPE  316   43
     clus
vv    AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  NO                          68                          316
  YES                         10                           43
[1] 2 2
[1] FALSE
D18V9, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 18(13Q34) MUTATED                                       5
  AMP PEAK 18(13Q34) WILD-TYPE                                    10
                              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                                                            83
  AMP PEAK 18(13Q34) WILD-TYPE                                                         396
D18V10, multiclass
                                                             clus
vv                                                            AMP PEAK 18(13Q34) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         83
                                                             clus
vv                                                            AMP PEAK 18(13Q34) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          396
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
D18V12, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 18(13Q34) MUTATED    69   3   0   6
  AMP PEAK 18(13Q34) WILD-TYPE 330   9   4  17
D18V13, multiclass
    clus
vv   AMP PEAK 18(13Q34) MUTATED AMP PEAK 18(13Q34) WILD-TYPE
  R0                         69                          330
  R1                          3                            9
  R2                          0                            4
  RX                          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                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(13Q34) MUTATED       2                         7    68
  AMP PEAK 18(13Q34) WILD-TYPE     7                        24   281
D18V14, multiclass
                           clus
vv                          AMP PEAK 18(13Q34) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                          7
  WHITE                                             68
                           clus
vv                          AMP PEAK 18(13Q34) WILD-TYPE
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                           24
  WHITE                                              281
[1] 3 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  65
  AMP PEAK 18(13Q34) WILD-TYPE   7 252
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(13Q34) MUTATED      1   65
  AMP PEAK 18(13Q34) WILD-TYPE    7  252
                        clus
vv                       AMP PEAK 18(13Q34) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         65
                        clus
vv                       AMP PEAK 18(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          252
[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    95  61
  AMP PEAK 19(14Q13.3) WILD-TYPE 185 153
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                           156                            338 
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                            61                            153 
$`AMP PEAK 19(14Q13.3) MUTATED`
TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 
       48.82        60.66        22.06       129.01       133.74         1.55 
TCGA-33-6737 TCGA-39-5039 TCGA-43-2578 TCGA-43-8118 TCGA-43-A56V TCGA-56-8201 
       19.76        17.88        22.49         2.93        12.03        13.05 
TCGA-56-8504 TCGA-90-7766 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HM 
       16.77         9.50        19.36         2.76         5.69        39.85 
TCGA-NC-A5HR TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 
       40.90         8.58        75.75       117.57        11.34        92.15 
TCGA-18-3421 TCGA-18-5592 TCGA-21-1076 TCGA-21-1079 TCGA-21-1082 TCGA-21-5782 
       86.96        49.94        60.89        31.73       119.80        31.63 
TCGA-21-5786 TCGA-22-1011 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4604 
       33.93         1.74        20.48        48.33        24.13        13.12 
TCGA-22-4613 TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 
       11.77        97.94       173.82       103.53        14.07        63.35 
TCGA-33-AASD TCGA-33-AASI TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3792 
      110.99        44.19         4.04        26.43         4.01         0.39 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 
        3.39       133.25       111.35        24.33        60.53        55.56 
TCGA-43-6143 TCGA-43-6771 TCGA-46-3769 TCGA-46-6025 TCGA-51-4081 TCGA-52-7622 
       22.98         5.46         4.44        10.65        29.95        28.34 
TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7580 TCGA-56-7730 
        8.75        28.96        18.25        21.90        30.41         6.51 
TCGA-56-7823 TCGA-56-8304 TCGA-56-8624 TCGA-56-8629 TCGA-56-A49D TCGA-56-A62T 
       33.24         3.48        13.81        15.81        20.94        14.47 
TCGA-58-8387 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46N TCGA-60-2698 TCGA-60-2706 
       13.25        34.78        85.12        29.92        10.22        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 TCGA-60-2724 
       21.93        80.45        50.33        42.64        29.85        23.57 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MI 
       11.77        52.67        70.13        68.15        70.62        58.65 
TCGA-63-A5ML TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2744 TCGA-66-2756 TCGA-66-2763 
       45.57        16.37        34.59         0.99         0.99         0.99 
TCGA-66-2765 TCGA-66-2771 TCGA-66-2782 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 
        2.01        19.00        12.00        22.98         5.03        30.02 
TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-70-6722 TCGA-70-6723 
       10.06         4.01        49.05         2.73        12.07        12.33 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 
       23.28        11.18         0.49        73.22       106.95        46.78 
TCGA-77-8007 TCGA-77-8130 TCGA-77-8136 TCGA-77-8139 TCGA-77-8143 TCGA-77-8148 
        6.51       156.66        39.09       104.09        26.40        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-85-6175 TCGA-85-6560 
       54.41        65.49       150.25        61.94         9.67        41.39 
TCGA-85-6561 TCGA-85-7698 TCGA-85-7843 TCGA-85-8276 TCGA-85-8353 TCGA-85-8355 
       40.24        31.30         1.15        34.52         3.09         2.01 
TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A510 TCGA-85-A5B5 TCGA-92-7340 
       30.97        30.48        27.16        15.85         3.65         2.70 
TCGA-92-7341 TCGA-92-8064 TCGA-94-A4VJ TCGA-98-A538 TCGA-98-A53I TCGA-L3-A4E7 
        3.48         5.26        14.14        27.16        18.58        12.89 
TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
       11.84        64.54        57.30        43.92        25.32        14.73 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
        3.65        33.07         3.72        12.72        43.89         0.20 

$`AMP PEAK 19(14Q13.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-5472 TCGA-34-2604 TCGA-34-2605 
       27.19        32.19        14.93        64.93        31.50        28.96 
TCGA-34-2609 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-56-7221 
       31.27        18.38         7.76        78.18        11.61        19.99 
TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
        3.45        17.00        17.85        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 
       41.42         9.01        35.34        32.32        66.61         8.02 
TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       20.78        42.08        30.81        14.07        21.04         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       18.38        16.14        57.07        21.21        19.10         0.07 
TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3414 TCGA-18-3417 
       76.80        65.65        16.80         0.43        23.54        36.07 
TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
       92.42         2.79       154.32       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 
       70.16        34.78        15.58       122.43         9.34        43.23 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       88.11        41.69        10.82        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 
       64.21        14.10        27.02        35.08         0.56        38.17 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5473 TCGA-22-5474 
       34.75        32.02        19.30         9.57        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        86.30        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-34-2608 TCGA-34-5231 
      118.36        27.16         2.63        61.61        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       81.24        74.66         9.07        60.30        50.66        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-A5IX 
       44.75        39.32         4.96         1.12        38.79        33.90 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         7.96         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 
        0.39        37.58        21.70       126.58        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
       82.52       102.18         1.71         1.94        36.39        68.38 
TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       71.18        17.06        40.21        38.66        39.12        33.11 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       27.91        24.89        21.47         3.81        19.59        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       11.77         9.73        14.20        13.32        12.16        13.02 
TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 
        9.83        13.91         0.39         0.39         5.46        30.35 
TCGA-52-7812 TCGA-56-5897 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
       27.45        12.43        18.48        14.53        31.27        19.76 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 
        0.10        17.49        14.96         4.93        26.89        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-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 TCGA-58-8388 
       19.23        13.32        18.74         0.26         0.03        13.55 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       29.95        71.24        16.47        34.36        56.65        35.24 
TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 
       21.11        12.23        96.82        37.94        49.48        66.54 
TCGA-60-2713 TCGA-60-2716 TCGA-60-2720 TCGA-60-2723 TCGA-60-2725 TCGA-63-7021 
       56.91        48.49         3.19        35.90        26.83        70.42 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       55.30       102.67        59.97        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 
       89.29        78.28        36.16        53.88        16.96        43.10 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
        2.01        21.07         1.02         2.01         0.92        43.99 
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-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
       23.01         3.02         2.01        19.00        12.03         3.98 
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-66-2794 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
       54.08         6.64         6.94        13.35        16.18        14.73 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7335 TCGA-77-7338 
       29.56        73.12        75.09       140.09        70.13         0.16 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 
       32.55        86.76        55.73        37.81        12.59        53.92 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 TCGA-77-8156 
       17.72        11.54        27.39         6.97        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH 
      126.18       132.36        22.29         5.92        27.62        38.86 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
        6.41        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-85-8071 
       18.94        25.15        19.04        24.13        31.56        26.79 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       30.64        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-85-8582 
        5.29        32.71        15.39         7.76        36.59        38.14 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC 
       12.59        18.08        22.59        30.28        34.13        19.86 
TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
       24.36        19.73        16.21        14.96        15.29        29.92 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
       12.39        24.92         2.93        11.77        20.22        22.62 
TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
       10.59         4.01         2.30         4.01         5.03        26.63 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       17.69        71.01        18.31        17.46        27.68        21.44 
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-A53H TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF 
       20.32        20.71        16.11        13.18        13.41         4.54 
TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HT 
        1.22        13.74         4.21         2.89        49.28        26.43 
TCGA-NK-A5CR TCGA-O2-A5IB 
       83.57        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 
                        173.82                         154.32 
  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE 
                         23.85                          21.04 
[1] "0.2 - 173.8 (23.9)" "0.0 - 154.3 (21.0)"
[1] "hr=" "1.4"
D19V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(14Q13.3) MUTATED         2       21       44        1        24
  AMP PEAK 19(14Q13.3) WILD-TYPE       0       68      108        1        41
                                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        64         1         38         14
                                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                             68
  STAGE IB                             44                            108
  STAGE II                              1                              1
  STAGE IIA                            24                             41
  STAGE IIB                            31                             64
  STAGE III                             2                              1
  STAGE IIIA                           25                             38
  STAGE IIIB                            5                             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 19(14Q13.3) MUTATED    29  96  27   7
  AMP PEAK 19(14Q13.3) WILD-TYPE  83 198  44  17
D19V4, multiclass
    clus
vv   AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  T1                           29                             83
  T2                           96                            198
  T3                           27                             44
  T4                            7                             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 19(14Q13.3) MUTATED    97  41  19   1
  AMP PEAK 19(14Q13.3) WILD-TYPE 220  92  21   4
D19V5, multiclass
    clus
vv   AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  N0                           97                            220
  N1                           41                             92
  N2                           19                             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"
D19V6, binary
                                cls
clus                               0   1
  AMP PEAK 19(14Q13.3) MUTATED   132   2
  AMP PEAK 19(14Q13.3) WILD-TYPE 279   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(14Q13.3) MUTATED    132    2
  AMP PEAK 19(14Q13.3) WILD-TYPE  279    5
   clus
vv  AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  0                          132                            279
  1                            2                              5
[1] 2 2
[1] FALSE
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(14Q13.3) MUTATED    42 117
  AMP PEAK 19(14Q13.3) WILD-TYPE  88 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(14Q13.3) MUTATED     42  117
  AMP PEAK 19(14Q13.3) WILD-TYPE   88  254
        clus
vv       AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  FEMALE                           42                             88
  MALE                            117                            254
[1] 2 2
[1] FALSE
D19V8, binary
                                cls
clus                               0   1
  AMP PEAK 19(14Q13.3) MUTATED   125  18
  AMP PEAK 19(14Q13.3) WILD-TYPE 259  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(14Q13.3) MUTATED    125   18
  AMP PEAK 19(14Q13.3) WILD-TYPE  259   35
     clus
vv    AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  NO                           125                            259
  YES                           18                             35
[1] 2 2
[1] FALSE
D19V9, 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 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                                                           154
  AMP PEAK 19(14Q13.3) WILD-TYPE                                                         325
D19V10, multiclass
                                                             clus
vv                                                            AMP PEAK 19(14Q13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          154
                                                             clus
vv                                                            AMP PEAK 19(14Q13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            325
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
D19V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(14Q13.3) MUTATED   124   5   1  10
  AMP PEAK 19(14Q13.3) WILD-TYPE 275   7   3  13
D19V13, multiclass
    clus
vv   AMP PEAK 19(14Q13.3) MUTATED AMP PEAK 19(14Q13.3) WILD-TYPE
  R0                          124                            275
  R1                            5                              7
  R2                            1                              3
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(14Q13.3) MUTATED       3                        10   108
  AMP PEAK 19(14Q13.3) WILD-TYPE     6                        21   241
D19V14, multiclass
                           clus
vv                          AMP PEAK 19(14Q13.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              108
                           clus
vv                          AMP PEAK 19(14Q13.3) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             21
  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"
D19V15, binary
                                cls
clus                               0   1
  AMP PEAK 19(14Q13.3) MUTATED     6  90
  AMP PEAK 19(14Q13.3) WILD-TYPE   2 227
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(14Q13.3) MUTATED      6   90
  AMP PEAK 19(14Q13.3) WILD-TYPE    2  227
                        clus
vv                       AMP PEAK 19(14Q13.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                           90
                        clus
vv                       AMP PEAK 19(14Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            227
[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    91  62
  AMP PEAK 20(14Q32.33) WILD-TYPE 189 152
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                            153                             341 
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                             62                             152 
$`AMP PEAK 20(14Q32.33) MUTATED`
TCGA-18-4083 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 
        6.18        60.66        22.06       129.01       133.74         1.55 
TCGA-43-2578 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-8504 TCGA-77-7140 
       22.49         2.93        11.61        12.03        16.77        20.78 
TCGA-94-7033 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HM 
       21.04        19.36         2.76         5.69         0.07        39.85 
TCGA-NC-A5HR TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 
       40.90         8.58        75.75       117.57        11.34        92.15 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       92.42        86.96         2.79       154.32        49.94       119.54 
TCGA-21-1076 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-5783 TCGA-21-5786 
       60.89        31.73         9.34       119.80        88.11        33.93 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4595 TCGA-22-5473 TCGA-22-5482 TCGA-22-5483 
       27.02        20.48        24.13        63.55        11.74        18.84 
TCGA-33-4566 TCGA-33-4582 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-5240 
      173.82       103.53       110.99        44.19       118.36        50.66 
TCGA-34-5241 TCGA-34-8455 TCGA-34-8456 TCGA-37-3789 TCGA-37-3792 TCGA-37-4133 
       16.93         4.04        26.43         0.43         0.39         7.82 
TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 
        3.39        37.58       133.25        24.33        60.53        71.18 
TCGA-39-5037 TCGA-43-6143 TCGA-43-6771 TCGA-43-A475 TCGA-46-6025 TCGA-51-4081 
       55.56        22.98         5.46         9.73        10.65        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 TCGA-56-7580 TCGA-56-7730 
       28.34         5.46         8.75        18.25        30.41         6.51 
TCGA-56-7823 TCGA-56-8304 TCGA-56-8624 TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T 
       33.24         3.48        13.81        20.94        18.74        14.47 
TCGA-58-8386 TCGA-58-8391 TCGA-58-A46N TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
        0.03        71.24        29.92        92.71        21.93        80.45 
TCGA-60-2722 TCGA-60-2724 TCGA-63-7020 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MI 
       29.85        23.57        70.13        68.15        70.62        58.65 
TCGA-66-2744 TCGA-66-2756 TCGA-66-2763 TCGA-66-2771 TCGA-66-2781 TCGA-66-2782 
        0.99         0.99         0.99        19.00         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-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-70-6723 TCGA-77-6845 TCGA-77-7138 
        6.94        16.18        14.73        12.33        23.28        11.18 
TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 TCGA-77-8130 TCGA-77-8136 TCGA-77-8139 
      106.95        46.78         6.51       156.66        39.09       104.09 
TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 
       26.40        66.51        54.41        65.49        60.53       150.25 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 
       22.29        61.94        27.62         9.67        40.24         6.41 
TCGA-85-7698 TCGA-85-7843 TCGA-85-8071 TCGA-85-8353 TCGA-85-8355 TCGA-85-8582 
       31.30         1.15        26.79         3.09         2.01        38.14 
TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A5B5 TCGA-90-7769 TCGA-92-7340 
       30.97        30.48        27.16         3.65        11.77         2.70 
TCGA-92-7341 TCGA-94-8491 TCGA-98-A538 TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW 
        3.48        26.63        27.16        12.89        16.11        13.41 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ 
       64.54        57.30         2.89        49.28        25.32        14.73 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52Q 
       83.57         3.65         3.72 

$`AMP PEAK 20(14Q32.33) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 
       12.20         4.47       123.19         4.80        31.99        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5472 TCGA-33-6737 TCGA-34-2604 
       32.19        14.93        48.82        64.93        19.76        31.50 
TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       28.96        31.27        17.88        18.38         7.76        78.18 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A4ZJ 
       19.99        13.05         3.45        17.00        17.85        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 
        0.13         3.58        41.42         9.01        35.34        32.32 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 
       66.61         8.02        42.08        30.81         9.50        14.07 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-98-A53D TCGA-J1-A4AH 
        0.16        18.38        16.14        57.07        21.21        19.10 
TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3414 TCGA-18-3417 
       76.80        65.65        16.80         0.43        23.54        36.07 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 
       46.88        99.16        70.16        34.78        15.58       122.43 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
       43.23        31.63        41.69        10.82        21.99         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4594 
        4.31        64.21         1.74        14.10        35.08        48.33 
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-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
        9.57        11.77        14.63        44.25         0.79        86.30 
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-33-6738 
       97.94        79.53       151.27        14.07        54.44        63.35 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASL TCGA-34-2596 
        4.70         0.30        36.62         6.94        27.16         2.63 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       61.61        32.88        65.23        81.24        74.66         9.07 
TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       60.30        44.75        39.32         4.96         1.12        38.79 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 
       33.90         4.01         7.96         8.12         7.46         6.81 
TCGA-37-4141 TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        0.39        21.70       126.58       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
       82.52       102.18         1.71         1.94        36.39        68.38 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       17.06        40.21        38.66        39.12        33.11        27.91 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       24.89        21.47         3.81        19.59        13.38        11.77 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
       14.20        13.32        12.16        13.02         9.83         4.44 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 
       13.91         0.39         0.39        30.35        27.45        28.96 
TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
       12.43        21.90        18.48        14.53        31.27        19.76 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 
        0.10        17.49        14.96         4.93        26.89        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-A4BW TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 
       15.81        19.23        13.32         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-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       35.24        21.11        12.23        10.22        96.82        37.94 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       49.48        66.54        56.91        50.33        48.49        42.64 
TCGA-60-2720 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 
        3.19        35.90        26.83        11.77        52.67        70.42 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
       55.30       102.67        59.97        45.57        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       25.28        89.29        78.28        16.37        36.16        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-66-2755 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 
        2.01         0.92        43.99        21.01        25.05         2.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 
        1.02         2.01         2.01         7.07        23.01         3.02 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 
        2.01        19.00        12.03        24.95         1.97        25.97 
TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7756 
       40.01        22.98         5.03        54.08         4.01         6.64 
TCGA-68-8251 TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 
       13.35        12.07        29.56        73.12        75.09       140.09 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 
        0.49        73.22        70.13         0.16        32.55        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 
       55.73        37.81        12.59        53.92        17.72        11.54 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 
       27.39         6.97        36.36       126.18       132.36         5.92 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 
       38.86        41.39        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-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       30.64        34.52        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        15.39         7.76        36.59 
TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC 
       12.59        18.08        22.59        30.28        34.13        19.86 
TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 
       24.36        19.73        16.21        15.85        14.96        15.29 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE 
       29.92        12.39        24.92         2.93        20.22        22.62 
TCGA-90-A59Q TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 
       10.59         4.01         5.26         2.30         4.01         5.03 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
       14.14        17.69        71.01        18.31        17.46        27.68 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B 
       21.44        30.81        30.67        21.34        18.15         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-LA-A446 TCGA-MF-A522 
       27.02        20.32        18.58        20.71        13.18        11.84 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HT 
        4.54         1.22        13.74         4.21        43.92        26.43 
TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       33.07        12.72        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 
                         173.82                          151.27 
  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE 
                          23.57                           21.04 
[1] "0.0 - 173.8 (23.6)" "0.1 - 151.3 (21.0)"
[1] "hr=" "1.4"
D20V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(14Q32.33) MUTATED         1       19       46        0        22
  AMP PEAK 20(14Q32.33) WILD-TYPE       1       70      106        2        43
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(14Q32.33) MUTATED          36         1         25          4
  AMP PEAK 20(14Q32.33) WILD-TYPE        59         2         38         15
                                 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                              19                              70
  STAGE IB                              46                             106
  STAGE II                               0                               2
  STAGE IIA                             22                              43
  STAGE IIB                             36                              59
  STAGE III                              1                               2
  STAGE IIIA                            25                              38
  STAGE IIIB                             4                              15
  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    26  96  31   5
  AMP PEAK 20(14Q32.33) WILD-TYPE  86 198  40  19
D20V4, multiclass
    clus
vv   AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  T1                            26                              86
  T2                            96                             198
  T3                            31                              40
  T4                             5                              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
  AMP PEAK 20(14Q32.33) MUTATED    96  45  14   1
  AMP PEAK 20(14Q32.33) WILD-TYPE 221  88  26   4
D20V5, multiclass
    clus
vv   AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  N0                            96                             221
  N1                            45                              88
  N2                            14                              26
  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   132   3
  AMP PEAK 20(14Q32.33) WILD-TYPE 279   4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(14Q32.33) MUTATED    132    3
  AMP PEAK 20(14Q32.33) WILD-TYPE  279    4
   clus
vv  AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  0                           132                             279
  1                             3                               4
[1] 2 2
[1] FALSE
D20V7, binary
                                 cls
clus                                0   1
  AMP PEAK 20(14Q32.33) MUTATED    36 122
  AMP PEAK 20(14Q32.33) WILD-TYPE  94 249
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(14Q32.33) MUTATED     36  122
  AMP PEAK 20(14Q32.33) WILD-TYPE   94  249
        clus
vv       AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  FEMALE                            36                              94
  MALE                             122                             249
[1] 2 2
[1] FALSE
D20V8, binary
                                 cls
clus                                0   1
  AMP PEAK 20(14Q32.33) MUTATED   120  19
  AMP PEAK 20(14Q32.33) WILD-TYPE 264  34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(14Q32.33) MUTATED    120   19
  AMP PEAK 20(14Q32.33) WILD-TYPE  264   34
     clus
vv    AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  NO                            120                             264
  YES                            19                              34
[1] 2 2
[1] FALSE
D20V9, 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 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                                                           151
  AMP PEAK 20(14Q32.33) WILD-TYPE                                                         328
D20V10, multiclass
                                                             clus
vv                                                            AMP PEAK 20(14Q32.33) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           151
                                                             clus
vv                                                            AMP PEAK 20(14Q32.33) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
D20V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 20(14Q32.33) MUTATED   129   5   1   6
  AMP PEAK 20(14Q32.33) WILD-TYPE 270   7   3  17
D20V13, multiclass
    clus
vv   AMP PEAK 20(14Q32.33) MUTATED AMP PEAK 20(14Q32.33) WILD-TYPE
  R0                           129                             270
  R1                             5                               7
  R2                             1                               3
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(14Q32.33) MUTATED       2                        11   103
  AMP PEAK 20(14Q32.33) WILD-TYPE     7                        20   246
D20V14, multiclass
                           clus
vv                          AMP PEAK 20(14Q32.33) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               103
                           clus
vv                          AMP PEAK 20(14Q32.33) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              20
  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"
D20V15, binary
                                 cls
clus                                0   1
  AMP PEAK 20(14Q32.33) MUTATED     5  90
  AMP PEAK 20(14Q32.33) WILD-TYPE   3 227
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(14Q32.33) MUTATED      5   90
  AMP PEAK 20(14Q32.33) WILD-TYPE    3  227
                        clus
vv                       AMP PEAK 20(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                            90
                        clus
vv                       AMP PEAK 20(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             227
[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    97  78
  AMP PEAK 21(15Q26.3) WILD-TYPE 183 136
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                           175                            319 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                            78                            136 
$`AMP PEAK 21(15Q26.3) MUTATED`
TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-22-5472 TCGA-33-4532 TCGA-33-4589 
        4.80        31.99         6.18        64.93       129.01         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 TCGA-56-8308 
       19.76        31.50        28.96        31.27        22.49        17.00 
TCGA-56-8504 TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-63-A5MH TCGA-77-7140 
       16.77         0.13         3.58        41.42        66.61        20.78 
TCGA-90-7766 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-98-8020 
        9.50         0.16        18.38        16.14        57.07         2.76 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3411 
        0.07        76.80        40.90        16.80         0.43       117.57 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-4086 TCGA-21-1072 TCGA-21-1077 
       23.54        92.15        36.07         2.79        99.16        34.78 
TCGA-21-1079 TCGA-21-1082 TCGA-21-5786 TCGA-22-0944 TCGA-22-4591 TCGA-22-4593 
       31.73       119.80        33.93         7.33        20.48        35.08 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5474 TCGA-22-5482 TCGA-22-5483 
       13.12        32.02        11.77        14.63        11.74        18.84 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-AASD TCGA-33-AASI 
       97.94        79.53       173.82       151.27       110.99        44.19 
TCGA-34-2596 TCGA-34-2600 TCGA-34-5231 TCGA-34-5234 TCGA-34-5240 TCGA-34-5929 
        2.63        61.61        65.23        74.66        50.66         4.96 
TCGA-34-8455 TCGA-34-8456 TCGA-37-3789 TCGA-37-3792 TCGA-37-A5EL TCGA-37-A5EN 
        4.04        26.43         0.43         0.39        37.58        21.70 
TCGA-39-5031 TCGA-39-5037 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 
       60.53        55.56        39.12        27.91        22.98        21.47 
TCGA-43-A475 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-6025 TCGA-46-6026 
        9.73        13.32        12.16        13.02        10.65        13.91 
TCGA-52-7809 TCGA-56-5898 TCGA-56-7222 TCGA-56-7582 TCGA-56-7730 TCGA-56-8082 
        5.46        18.25        18.48        19.76         6.51        14.96 
TCGA-56-8626 TCGA-56-A4BW TCGA-56-A4ZK TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
        9.93        19.23        18.74        29.95        71.24        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-60-2695 TCGA-60-2706 TCGA-60-2710 TCGA-60-2722 
       85.12        34.36        21.11        92.71        66.54        29.85 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7022 TCGA-63-A5MB 
       23.57        26.83        11.77        70.13        68.15       102.67 
TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV 
       58.65        45.57        25.28        89.29        78.28        36.16 
TCGA-63-A5MY TCGA-66-2734 TCGA-66-2754 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       34.59        43.10         2.01         2.01         1.02         2.01 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2781 TCGA-66-2787 TCGA-66-2789 
        7.07        23.01         3.02         3.98        40.01         4.04 
TCGA-66-2791 TCGA-66-2795 TCGA-68-7755 TCGA-68-A59I TCGA-68-A59J TCGA-77-7141 
        5.03         4.01         2.73        16.18        14.73         0.49 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8133 TCGA-77-8136 
        0.16        46.78        32.55        55.73        53.92        39.09 
TCGA-77-8143 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5GF 
       26.40        54.41        65.49       132.36       150.25        27.62 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
       40.24         6.41        36.53        29.95        18.94        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8351 TCGA-85-8352 
       24.13        31.56        34.52        10.09        16.77         5.29 
TCGA-85-8354 TCGA-85-8481 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JC 
       32.71         7.76        12.59        18.08        30.28        19.86 
TCGA-85-A50Z TCGA-85-A510 TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-94-8491 
       16.21        15.85        10.59         3.48         4.01        26.63 
TCGA-94-A5I6 TCGA-96-7544 TCGA-98-A538 TCGA-98-A53B TCGA-L3-A524 TCGA-LA-A446 
       17.69        71.01        27.16         2.01        16.11        13.18 
TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HN TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52V 
       64.54        13.74        49.28        26.43        83.57        43.89 
TCGA-O2-A5IB 
       11.18 

$`AMP PEAK 21(15Q26.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
       12.20         4.47       123.19        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4533 TCGA-39-5039 TCGA-43-5668 
       48.82        60.66        22.06       133.74        17.88        18.38 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
        7.76        78.18         2.93        11.61        12.03        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2712 TCGA-60-2715 
       13.05         3.45        17.85        21.04         9.01        35.34 
TCGA-60-2721 TCGA-68-8250 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 
       32.32         8.02        42.08        30.81        14.07        21.04 
TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HM TCGA-NK-A5CT 
       19.36         5.69        21.21        19.10        39.85        65.65 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3412 TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 
        8.58        75.75        11.34        92.42        86.96       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1076 TCGA-21-1078 
       49.94       119.54        46.88        70.16        60.89        15.58 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 
      122.43         9.34        43.23        31.63        88.11        41.69 
TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       10.82        21.99         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-22-4607 TCGA-22-4609 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       19.30         9.57        63.55        44.25         0.79        86.30 
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-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
      103.53        14.07        54.44        63.35         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-2608 TCGA-34-5232 
       36.62         6.94       118.36        27.16        32.88        81.24 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 
        9.07        60.30        16.93        44.75        39.32         1.12 
TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       38.79        33.90         4.01         7.96         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       133.25       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      111.35        68.58        55.20        82.52       102.18         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 
       24.33         1.94        36.39        68.38        71.18        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 
       40.21        38.66        33.11        24.89         5.46         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3768 TCGA-46-3769 
       19.59        13.38        11.77        14.20         9.83         4.44 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 
        0.39         0.39        29.95        28.34        30.35         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7223 TCGA-56-7579 
       27.45        28.96        12.43        21.90        14.53        31.27 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 
       30.41         0.10        17.49        33.24         4.93         3.48 
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        13.81 
TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A5DS 
       10.36        20.25        15.81        20.94        13.32         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8392 TCGA-58-A46L 
       14.47         0.03        13.25        13.55        16.47        56.65 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       35.24        29.92        12.23        10.22        96.82        37.94 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       21.93        80.45        49.48        56.91        50.33        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 
       42.64         3.19        35.90        52.67        70.42        55.30 
TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MT TCGA-63-A5MW 
       70.62        59.97        14.99        11.34        16.37        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-68-8251 TCGA-70-6722 
       54.08        49.05         6.64         6.94        13.35        12.07 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       12.33        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8007 TCGA-77-8008 
      140.09        73.22        70.13       106.95         6.51        86.76 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       37.81       156.66        12.59        17.72       104.09        11.54 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       27.39         6.97        66.51        60.53        36.36       126.18 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       22.29         5.92        61.94        38.86         9.67        41.39 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 
       34.95        31.30        32.91         1.38         1.15        25.15 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8353 
       26.79        30.64         0.76        13.22        22.45         3.09 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CN 
        2.01        15.39        36.59        38.14        22.59        34.13 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A511 
       30.97        24.36        30.48        19.73        27.16        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 
       15.29        29.92        12.39         3.65        24.92         2.93 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 
       11.77        20.22        22.62         2.70         5.26         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
        4.01         5.03        14.14        18.31        17.46        27.68 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53C 
       21.44        30.81        30.67        21.34        18.15        27.02 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 
       20.32        18.58        20.71        12.89        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO 
        4.54         1.22        57.30         4.21         2.89        43.92 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       25.32        14.73         3.65        33.07         3.72        12.72 
TCGA-XC-AA0X 
        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 
                        173.82                         156.66 
  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE 
                         23.01                          21.21 
[1] "0.1 - 173.8 (23.0)" "0.0 - 156.7 (21.2)"
[1] "hr=" "1"  
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(15Q26.3) MUTATED         0       26       54        1        29
  AMP PEAK 21(15Q26.3) WILD-TYPE       2       63       98        1        36
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(15Q26.3) MUTATED          34         1         23          8
  AMP PEAK 21(15Q26.3) WILD-TYPE        61         2         40         11
                                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                             63
  STAGE IB                             54                             98
  STAGE II                              1                              1
  STAGE IIA                            29                             36
  STAGE IIB                            34                             61
  STAGE III                             1                              2
  STAGE IIIA                           23                             40
  STAGE IIIB                            8                             11
  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    33 115  24   7
  AMP PEAK 21(15Q26.3) WILD-TYPE  79 179  47  17
D21V4, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  T1                           33                             79
  T2                          115                            179
  T3                           24                             47
  T4                            7                             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   102  57  15   3
  AMP PEAK 21(15Q26.3) WILD-TYPE 215  76  25   2
D21V5, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  N0                          102                            215
  N1                           57                             76
  N2                           15                             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   154   3
  AMP PEAK 21(15Q26.3) WILD-TYPE 257   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED    154    3
  AMP PEAK 21(15Q26.3) WILD-TYPE  257    4
   clus
vv  AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  0                          154                            257
  1                            3                              4
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED    43 136
  AMP PEAK 21(15Q26.3) WILD-TYPE  87 235
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED     43  136
  AMP PEAK 21(15Q26.3) WILD-TYPE   87  235
        clus
vv       AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  FEMALE                           43                             87
  MALE                            136                            235
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED   138  19
  AMP PEAK 21(15Q26.3) WILD-TYPE 246  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED    138   19
  AMP PEAK 21(15Q26.3) WILD-TYPE  246   34
     clus
vv    AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  NO                           138                            246
  YES                           19                             34
[1] 2 2
[1] FALSE
D21V9, 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 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                                                           169
  AMP PEAK 21(15Q26.3) WILD-TYPE                                                         310
D21V10, multiclass
                                                             clus
vv                                                            AMP PEAK 21(15Q26.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          169
                                                             clus
vv                                                            AMP PEAK 21(15Q26.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            310
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
D21V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(15Q26.3) MUTATED   139   7   1  10
  AMP PEAK 21(15Q26.3) WILD-TYPE 260   5   3  13
D21V13, multiclass
    clus
vv   AMP PEAK 21(15Q26.3) MUTATED AMP PEAK 21(15Q26.3) WILD-TYPE
  R0                          139                            260
  R1                            7                              5
  R2                            1                              3
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(15Q26.3) MUTATED       1                        11   121
  AMP PEAK 21(15Q26.3) WILD-TYPE     8                        20   228
D21V14, multiclass
                           clus
vv                          AMP PEAK 21(15Q26.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              121
                           clus
vv                          AMP PEAK 21(15Q26.3) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             20
  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"
D21V15, binary
                                cls
clus                               0   1
  AMP PEAK 21(15Q26.3) MUTATED     2 111
  AMP PEAK 21(15Q26.3) WILD-TYPE   6 206
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(15Q26.3) MUTATED      2  111
  AMP PEAK 21(15Q26.3) WILD-TYPE    6  206
                        clus
vv                       AMP PEAK 21(15Q26.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          111
                        clus
vv                       AMP PEAK 21(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            206
[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   134  99
  AMP PEAK 22(17Q25.1) WILD-TYPE 146 115
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                           233                            261 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                            99                            115 
$`AMP PEAK 22(17Q25.1) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-22-5471 
       12.20         4.47         4.80        31.99         6.18        60.66 
TCGA-33-4532 TCGA-34-2604 TCGA-34-2609 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 
      129.01        31.50        31.27        22.49        18.38         7.76 
TCGA-43-A56V TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY 
       12.03        13.05         3.45        17.00        16.77        17.85 
TCGA-56-A4ZJ TCGA-60-2711 TCGA-60-2715 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 
       21.04        41.42        35.34        66.61         8.02        20.78 
TCGA-77-A5GA TCGA-94-7033 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-J1-A4AH 
       42.08        21.04        16.14        57.07        19.36        19.10 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 
       39.85        40.90         0.43       117.57        11.34        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
       36.07        92.42        86.96        46.88        99.16        70.16 
TCGA-21-1077 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
       34.78         9.34       119.80        43.23        33.93        10.82 
TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
       14.10        20.48        35.08        48.33        24.13        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 
       34.75        13.12        19.30         9.57        11.77        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5483 TCGA-22-5491 TCGA-33-4582 
       44.25         0.79        86.30        18.84        56.32       103.53 
TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 
       14.07        63.35         4.70        44.19       118.36         2.63 
TCGA-34-5231 TCGA-34-5236 TCGA-34-5240 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 
       65.23         9.07        50.66         4.04        26.43         4.01 
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-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5027 
       37.58        21.70       126.58       111.35        55.20       102.18 
TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       68.38        55.56        17.06        40.21        38.66        39.12 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6770 TCGA-43-8115 TCGA-43-A475 TCGA-46-3768 
       33.11        27.91        21.47        13.38         9.73         9.83 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 TCGA-52-7812 TCGA-56-1622 TCGA-56-7222 
       10.65        13.91         0.39        27.45        28.96        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-8304 TCGA-56-8629 
       14.53        31.27        19.76         6.51         3.48        15.81 
TCGA-56-A4BX TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J 
       13.32         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-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
       80.45        29.85        35.90        26.83        11.77        52.67 
TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MV 
       70.42        68.15       102.67        58.65        59.97        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2742 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 
       53.88        34.59        21.07         2.01         0.99        43.99 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 
       21.01         0.99         2.01        23.01        19.00         2.01 
TCGA-66-2781 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
        3.98        40.01        22.98         4.04        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 
       30.02        10.06         4.01         2.73         6.64        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 
       16.18        14.73        12.33        29.56        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 
      140.09         0.49        73.22        32.55         6.51        55.73 
TCGA-77-8128 TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8144 TCGA-77-8153 
       37.81        53.92        39.09       104.09        27.39        65.49 
TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-85-6175 
       36.36       150.25        22.29         5.92        27.62         9.67 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7843 TCGA-85-7844 TCGA-85-8070 TCGA-85-8072 
       41.39        36.53         1.15        29.95        31.56        30.64 
TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       10.09        22.45        16.77         5.29         3.09        32.71 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QR 
       18.08        22.59        30.28        34.13        19.86        19.73 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
       16.21        15.85        12.39         3.65         2.93        11.77 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-94-8491 
       20.22        22.62        10.59         2.70         3.48        26.63 
TCGA-94-A4VJ TCGA-96-7544 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53I 
       14.14        71.01        21.34        27.16        18.15        18.58 
TCGA-98-A53J TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HL TCGA-NC-A5HN 
       20.71        16.11        11.84        64.54         2.89        49.28 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52S 
       14.73        26.43        83.57        33.07        12.72 

$`AMP PEAK 22(17Q25.1) WILD-TYPE`
TCGA-18-3409 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5472 
      123.19        27.19        32.19        14.93        48.82        64.93 
TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-39-5039 
       22.06       133.74         1.55        19.76        28.96        17.88 
TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 TCGA-56-A5DR TCGA-60-2696 
       78.18         2.93        11.61        19.99         0.13         3.58 
TCGA-60-2712 TCGA-60-2721 TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7557 
        9.01        32.32        30.81         9.50        14.07         0.16 
TCGA-94-7943 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE 
       18.38         2.76         5.69        21.21         0.07        76.80 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3408 TCGA-18-3414 TCGA-18-4086 
       65.65        16.80         8.58        75.75        23.54         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 
      154.32        49.94       119.54        60.89        15.58        31.73 
TCGA-21-1080 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 
      122.43        31.63        88.11        41.69        21.99         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4596 TCGA-22-4605 
        4.31        64.21         1.74        27.02         0.56        32.02 
TCGA-22-5473 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
       63.55        71.34        79.20        11.74        30.12        62.86 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 
       16.64        97.94        79.53       173.82       151.27        54.44 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASL TCGA-34-2600 
        0.30        36.62         6.94       110.99        27.16        61.61 
TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 
       32.88        81.24        74.66        60.30        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3789 
       39.32         4.96         1.12        38.79        33.90         0.43 
TCGA-37-4129 TCGA-37-4130 TCGA-39-5011 TCGA-39-5021 TCGA-39-5024 TCGA-39-5028 
        7.96         8.12       133.25        68.58        82.52         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-43-6143 
       24.33         1.94        60.53        36.39        71.18        22.98 
TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8116 TCGA-43-A56U 
       24.89         5.46         3.81        19.59        11.77        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-51-4079 TCGA-51-4081 
       13.32        12.16        13.02         4.44         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-5897 TCGA-56-5898 
       28.34         5.46        30.35         8.75        12.43        18.25 
TCGA-56-6545 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       21.90        30.41         0.10        17.49        33.24        14.96 
TCGA-56-8083 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
        4.93        26.89        14.07         1.35         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW 
       13.81        10.36         9.93        20.25        20.94        19.23 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8388 TCGA-58-8392 TCGA-58-8393 
       18.74         0.26        14.47        13.55        16.47        34.78 
TCGA-58-A46L TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2709 
       56.65        21.11        12.23        10.22        37.94        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       66.54        56.91        50.33        48.49        42.64         3.19 
TCGA-60-2724 TCGA-63-7020 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5ML TCGA-63-A5MM 
       23.57        70.13        55.30        70.62        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-66-2727 
       11.34        25.28        89.29        78.28        16.37        16.96 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2759 
       43.10         2.01         0.99         1.02         0.92        25.05 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2773 TCGA-66-2778 
        2.01         1.02         2.01         7.07         3.02        19.00 
TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2794 
       12.03        12.00        24.95         1.97        25.97        54.08 
TCGA-66-2800 TCGA-68-7757 TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 TCGA-77-7335 
       49.05         6.94        12.07        73.12        75.09        70.13 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 
      106.95         0.16        46.78        86.76       156.66        12.59 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       17.72        11.54        26.40         6.97        66.51        54.41 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6561 
       60.53       126.18       132.36        61.94        38.86        40.24 
TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 
        6.41        34.95        31.30        32.91         1.38        18.94 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 
       25.15        19.04        24.13        26.79        34.52         0.76 
TCGA-85-8288 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       13.22         2.01        15.39         7.76        36.59        38.14 
TCGA-85-8584 TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 
       12.59        30.97        24.36        30.48        27.16        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 
       15.29        29.92        24.92         4.01         5.26         2.30 
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        27.68 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       21.44        30.81        30.67         2.01        27.02        20.32 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI 
       12.89        13.18        13.41         4.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NK-A5CX TCGA-O2-A52Q 
       13.74         4.21        43.92        25.32         3.65         3.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        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 
                        150.25                         173.82 
  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE 
                         22.29                          21.21 
[1] "0.0 - 150.2 (22.3)" "0.1 - 173.8 (21.2)"
[1] "hr=" "1"  
D22V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(17Q25.1) MUTATED         1       31       68        0        39
  AMP PEAK 22(17Q25.1) WILD-TYPE       1       58       84        2        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(17Q25.1) MUTATED          48         1         33          9
  AMP PEAK 22(17Q25.1) WILD-TYPE        47         2         30         10
                                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                             58
  STAGE IB                             68                             84
  STAGE II                              0                              2
  STAGE IIA                            39                             26
  STAGE IIB                            48                             47
  STAGE III                             1                              2
  STAGE IIIA                           33                             30
  STAGE IIIB                            9                             10
  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    39 158  28  11
  AMP PEAK 22(17Q25.1) WILD-TYPE  73 136  43  13
D22V4, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  T1                           39                             73
  T2                          158                            136
  T3                           28                             43
  T4                           11                             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   131  77  24   3
  AMP PEAK 22(17Q25.1) WILD-TYPE 186  56  16   2
D22V5, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  N0                          131                            186
  N1                           77                             56
  N2                           24                             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   195   5
  AMP PEAK 22(17Q25.1) WILD-TYPE 216   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED    195    5
  AMP PEAK 22(17Q25.1) WILD-TYPE  216    2
   clus
vv  AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  0                          195                            216
  1                            5                              2
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED    46 190
  AMP PEAK 22(17Q25.1) WILD-TYPE  84 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED     46  190
  AMP PEAK 22(17Q25.1) WILD-TYPE   84  181
        clus
vv       AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  FEMALE                           46                             84
  MALE                            190                            181
[1] 2 2
[1] FALSE
D22V8, binary
                                cls
clus                               0   1
  AMP PEAK 22(17Q25.1) MUTATED   173  32
  AMP PEAK 22(17Q25.1) WILD-TYPE 211  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED    173   32
  AMP PEAK 22(17Q25.1) WILD-TYPE  211   21
     clus
vv    AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  NO                           173                            211
  YES                           32                             21
[1] 2 2
[1] FALSE
D22V9, 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 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                                                           228
  AMP PEAK 22(17Q25.1) WILD-TYPE                                                         251
D22V10, multiclass
                                                             clus
vv                                                            AMP PEAK 22(17Q25.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          228
                                                             clus
vv                                                            AMP PEAK 22(17Q25.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            251
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
D22V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 22(17Q25.1) MUTATED   192   5   2   8
  AMP PEAK 22(17Q25.1) WILD-TYPE 207   7   2  15
D22V13, multiclass
    clus
vv   AMP PEAK 22(17Q25.1) MUTATED AMP PEAK 22(17Q25.1) WILD-TYPE
  R0                          192                            207
  R1                            5                              7
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(17Q25.1) MUTATED       3                        12   163
  AMP PEAK 22(17Q25.1) WILD-TYPE     6                        19   186
D22V14, multiclass
                           clus
vv                          AMP PEAK 22(17Q25.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              163
                           clus
vv                          AMP PEAK 22(17Q25.1) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             19
  WHITE                                                186
[1] 3 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     3 143
  AMP PEAK 22(17Q25.1) WILD-TYPE   5 174
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 22(17Q25.1) MUTATED      3  143
  AMP PEAK 22(17Q25.1) WILD-TYPE    5  174
                        clus
vv                       AMP PEAK 22(17Q25.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          143
                        clus
vv                       AMP PEAK 22(17Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            174
[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   100  75
  AMP PEAK 23(18P11.32) WILD-TYPE 180 139
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                            175                             319 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                             75                             139 
$`AMP PEAK 23(18P11.32) MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-18-4083 TCGA-22-5471 TCGA-33-4532 TCGA-33-6737 
        4.47        31.99         6.18        60.66       129.01        19.76 
TCGA-34-2604 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       31.50        22.49        18.38         7.76        78.18         2.93 
TCGA-43-A474 TCGA-43-A56V TCGA-56-A4BY TCGA-56-A5DR TCGA-60-2711 TCGA-63-A5MH 
       11.61        12.03        17.85         0.13        41.42        66.61 
TCGA-68-8250 TCGA-77-7140 TCGA-90-7766 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
        8.02        20.78         9.50        16.14        57.07        19.36 
TCGA-J1-A4AH TCGA-18-3411 TCGA-18-3412 TCGA-21-1075 TCGA-21-1079 TCGA-21-1082 
       19.10       117.57        11.34        70.16        31.73       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-4591 
       43.23        31.63        41.69        33.93         7.33        20.48 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4604 TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 
       35.08        24.13        13.12        71.34        18.84        62.86 
TCGA-22-5491 TCGA-33-4566 TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 
       56.32       173.82        36.62       110.99        44.19         2.63 
TCGA-34-5231 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-A5IX 
       65.23         9.07        60.30        50.66        16.93        33.90 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL 
        0.43         0.39         8.12         6.81         0.39        37.58 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 
      126.58       111.35        68.58       102.18        24.33        60.53 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-5670 TCGA-43-6143 TCGA-43-A475 
       55.56        17.06        40.21        27.91        22.98         9.73 
TCGA-46-3768 TCGA-46-6026 TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 
        9.83        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 
       18.48        14.53        30.41         6.51         3.48        14.07 
TCGA-56-A49D TCGA-56-A5DS TCGA-58-8386 TCGA-58-8391 TCGA-58-8392 TCGA-60-2698 
       20.94         0.26         0.03        71.24        16.47        10.22 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7023 
       29.85        35.90        26.83        11.77        70.13        55.30 
TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 
      102.67        58.65        45.57        53.88        16.96        43.10 
TCGA-66-2742 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 TCGA-66-2769 
       21.07        21.01        25.05         0.99         2.01         7.07 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2781 TCGA-66-2783 TCGA-66-2787 TCGA-66-2789 
       23.01         2.01         3.98        24.95        40.01         4.04 
TCGA-66-2794 TCGA-66-2800 TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-7141 
       54.08        49.05        14.73        12.07        12.33         0.49 
TCGA-77-7335 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       70.13        46.78        32.55        55.73        37.81       156.66 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 
       11.54        26.40        54.41        65.49        36.36       150.25 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 
       27.62        40.24         6.41         1.15        29.95        19.04 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8352 TCGA-85-8353 
       31.56        26.79        34.52        10.09         5.29         3.09 
TCGA-85-8354 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
       32.71        36.59        18.08        22.59        34.13        30.97 
TCGA-85-A50M TCGA-85-A510 TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q 
       27.16        15.85         3.65        11.77        22.62        10.59 
TCGA-92-8064 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-8169 TCGA-98-8021 TCGA-98-A538 
        5.26        26.63        14.14        18.31        30.81        27.16 
TCGA-98-A53B TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HH 
        2.01        18.58        12.89        16.11        11.84         1.22 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52N 
       57.30         2.89        14.73        26.43         3.65        33.07 
TCGA-O2-A5IB 
       11.18 

$`AMP PEAK 23(18P11.32) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
       12.20       123.19         4.80        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-34-2605 
       48.82        64.93        22.06       133.74         1.55        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 
       31.27        17.88        19.99        13.05         3.45        17.00 
TCGA-56-8504 TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 
       16.77        21.04         3.58         9.01        35.34        32.32 
TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       42.08        30.81        14.07        21.04         0.16        18.38 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        2.76         5.69        21.21         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 
       40.90        65.65        16.80         0.43         8.58        75.75 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       23.54        92.15        36.07        92.42        86.96         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 
      154.32        49.94       119.54        46.88        99.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-5783 TCGA-21-5787 
       34.78        15.58       122.43         9.34        88.11        10.82 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       21.99         4.31        64.21         1.74        14.10        27.02 
TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 
       48.33         0.56        38.17        34.75        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
        9.57        11.77        63.55        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 TCGA-33-4538 
       86.30        79.20        11.74        30.12        16.64        97.94 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 
       79.53       103.53       151.27        14.07        54.44        63.35 
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-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       32.88        81.24        74.66        44.75        39.32         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-4129 
        1.12        38.79         4.04        26.43         4.01         7.96 
TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5022 
        7.46         7.82         3.39        21.70       133.25        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       82.52         1.71         1.94        36.39        68.38        71.18 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       38.66        39.12        33.11        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 
        3.81        19.59        13.38        11.77        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 
       12.16        13.02         4.44        10.65         0.39         0.39 
TCGA-52-7622 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
       28.34        30.35        27.45        28.96        12.43        21.90 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       31.27        19.76         0.10        17.49        33.24        14.96 
TCGA-56-8083 TCGA-56-8307 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
        4.93        26.89         1.35         1.81        22.75        13.81 
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-A4ZK TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 
       18.74        14.47        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-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       12.23        96.82        37.94        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       49.48        66.54        56.91        50.33        48.49        42.64 
TCGA-60-2720 TCGA-60-2724 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MG 
        3.19        23.57        52.67        70.42        68.15        70.62 
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-A5MV TCGA-63-A5MY TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 
       16.37        36.16        34.59         2.01         0.99         1.02 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 
        2.01         0.92         0.99        43.99         2.01         1.02 
TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
        2.01        19.00         3.02        19.00        12.03        12.00 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
        1.97        25.97        22.98        22.98         5.03        30.02 
TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
       10.06         4.01         2.73         6.64         6.94        13.35 
TCGA-68-A59I TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       16.18        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 
      140.09        73.22       106.95         0.16         6.51        86.76 
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-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
        6.97        66.51        60.53       126.18       132.36        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 
        5.92        61.94        38.86         9.67        41.39        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 
       34.95        31.30        32.91         1.38        18.94        25.15 
TCGA-85-8052 TCGA-85-8072 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       24.13        30.64         0.76        13.22        22.45        16.77 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL 
        2.01        15.39         7.76        38.14        12.59        30.28 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 
       19.86        24.36        30.48        19.73        16.21        14.96 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED 
       15.29        29.92        12.39        24.92         2.93        20.22 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 
        2.70         3.48         4.01         2.30         4.01         5.03 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 
       17.69        71.01        17.46        27.68        21.44        30.67 
TCGA-98-8023 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-LA-A446 
       21.34        18.15        27.02        20.32        20.71        13.18 
TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN 
       13.41         4.54        64.54        13.74         4.21        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NK-A5CR TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       43.92        25.32        83.57         3.72        12.72        43.89 
TCGA-XC-AA0X 
        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 
                         173.82                          154.32 
  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE 
                          22.62                           21.44 
[1] "0.0 - 173.8 (22.6)" "0.1 - 154.3 (21.4)"
[1] "hr=" "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        27
  AMP PEAK 23(18P11.32) WILD-TYPE       1       60       95        2        38
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(18P11.32) MUTATED          28         1         26          7
  AMP PEAK 23(18P11.32) WILD-TYPE        67         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                              60
  STAGE IB                              57                              95
  STAGE II                               0                               2
  STAGE IIA                             27                              38
  STAGE IIB                             28                              67
  STAGE III                              1                               2
  STAGE IIIA                            26                              37
  STAGE IIIB                             7                              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  23   5
  AMP PEAK 23(18P11.32) WILD-TYPE  75 180  48  19
D23V4, multiclass
    clus
vv   AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  T1                            37                              75
  T2                           114                             180
  T3                            23                              48
  T4                             5                              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
  AMP PEAK 23(18P11.32) MUTATED   107  50  17   3
  AMP PEAK 23(18P11.32) WILD-TYPE 210  83  23   2
D23V5, multiclass
    clus
vv   AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  N0                           107                             210
  N1                            50                              83
  N2                            17                              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"
D23V6, binary
                                 cls
clus                                0   1
  AMP PEAK 23(18P11.32) MUTATED   149   2
  AMP PEAK 23(18P11.32) WILD-TYPE 262   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED    149    2
  AMP PEAK 23(18P11.32) WILD-TYPE  262    5
   clus
vv  AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  0                           149                             262
  1                             2                               5
[1] 2 2
[1] FALSE
D23V7, binary
                                 cls
clus                                0   1
  AMP PEAK 23(18P11.32) MUTATED    41 138
  AMP PEAK 23(18P11.32) WILD-TYPE  89 233
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED     41  138
  AMP PEAK 23(18P11.32) WILD-TYPE   89  233
        clus
vv       AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  FEMALE                            41                              89
  MALE                             138                             233
[1] 2 2
[1] FALSE
D23V8, binary
                                 cls
clus                                0   1
  AMP PEAK 23(18P11.32) MUTATED   134  24
  AMP PEAK 23(18P11.32) WILD-TYPE 250  29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED    134   24
  AMP PEAK 23(18P11.32) WILD-TYPE  250   29
     clus
vv    AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  NO                            134                             250
  YES                            24                              29
[1] 2 2
[1] FALSE
D23V9, 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 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                                                           173
  AMP PEAK 23(18P11.32) WILD-TYPE                                                         306
D23V10, multiclass
                                                             clus
vv                                                            AMP PEAK 23(18P11.32) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           173
                                                             clus
vv                                                            AMP PEAK 23(18P11.32) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             306
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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 260   9   1  14
D23V13, multiclass
    clus
vv   AMP PEAK 23(18P11.32) MUTATED AMP PEAK 23(18P11.32) WILD-TYPE
  R0                           139                             260
  R1                             3                               9
  R2                             3                               1
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(18P11.32) MUTATED       4                         6   129
  AMP PEAK 23(18P11.32) WILD-TYPE     5                        25   220
D23V14, multiclass
                           clus
vv                          AMP PEAK 23(18P11.32) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                               129
                           clus
vv                          AMP PEAK 23(18P11.32) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                              25
  WHITE                                                 220
[1] 3 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     2 111
  AMP PEAK 23(18P11.32) WILD-TYPE   6 206
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(18P11.32) MUTATED      2  111
  AMP PEAK 23(18P11.32) WILD-TYPE    6  206
                        clus
vv                       AMP PEAK 23(18P11.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           111
                        clus
vv                       AMP PEAK 23(18P11.32) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             206
[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    83  66
  AMP PEAK 24(18Q11.2) WILD-TYPE 197 148
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           149                            345 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                            66                            148 
$`AMP PEAK 24(18Q11.2) MUTATED`
TCGA-18-3407 TCGA-18-4083 TCGA-22-5471 TCGA-33-4532 TCGA-34-2609 TCGA-43-2578 
        4.47         6.18        60.66       129.01        31.27        22.49 
TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A56V TCGA-60-2711 
       18.38         7.76        78.18         2.93        12.03        41.42 
TCGA-60-2712 TCGA-77-7140 TCGA-96-7545 TCGA-J1-A4AH TCGA-18-3411 TCGA-18-3412 
        9.01        20.78        57.07        19.10       117.57        11.34 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 TCGA-22-1012 TCGA-22-4595 
      119.80        43.23        88.11        41.69        14.10        24.13 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 
       38.17        13.12        11.77         0.79        71.34        79.20 
TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-33-4566 TCGA-33-4586 TCGA-33-AASD 
       18.84        62.86        56.32       173.82        14.07       110.99 
TCGA-33-AASI TCGA-34-2596 TCGA-34-5231 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       44.19         2.63        65.23         9.07        60.30        50.66 
TCGA-34-8456 TCGA-37-3789 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
       26.43         0.43         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 
        0.39        37.58       133.25       111.35        68.58       102.18 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5037 TCGA-39-5040 TCGA-43-3920 TCGA-43-6647 
       24.33        60.53        55.56        17.06        33.11        24.89 
TCGA-43-8115 TCGA-43-A475 TCGA-46-3769 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 
       13.38         9.73         4.44        13.91         0.39        29.95 
TCGA-52-7809 TCGA-52-7811 TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 
        5.46         8.75        18.25        14.53        30.41         6.51 
TCGA-56-8304 TCGA-56-A49D TCGA-56-A4BX TCGA-58-8391 TCGA-58-8392 TCGA-58-A46M 
        3.48        20.94        13.32        71.24        16.47        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 
       29.92        21.11        29.85        35.90        26.83        11.77 
TCGA-63-7020 TCGA-63-7023 TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-66-2734 
       70.13        55.30        59.97        45.57        25.28        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-70-6723 TCGA-77-6842 TCGA-77-7463 TCGA-77-7465 
       49.05         2.73        12.33        29.56        46.78        32.55 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8140 TCGA-77-8143 TCGA-77-8150 
       55.73        37.81       156.66        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        36.36       150.25        27.62        38.86        40.24 
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        26.79 
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        18.08        34.13 
TCGA-85-A4JB TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8064 TCGA-98-8021 
       30.97        11.77        22.62        10.59         5.26        30.81 
TCGA-98-8022 TCGA-98-A53I TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HG 
       30.67        18.58        12.89        13.41        11.84        64.54 
TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A5IB 
        2.89        14.73         3.65        12.72        11.18 

$`AMP PEAK 24(18Q11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI 
       12.20       123.19         4.80        31.99        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 
       14.93        48.82        64.93        22.06       133.74         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-39-5039 TCGA-43-A474 TCGA-56-7221 
       19.76        31.50        28.96        17.88        11.61        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ 
       13.05         3.45        17.00        16.77        17.85        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 
        0.13         3.58        35.34        32.32        66.61         8.02 
TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       42.08        30.81         9.50        14.07        21.04         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D 
       18.38        16.14        19.36         2.76         5.69        21.21 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 
        0.07        76.80        39.85        40.90        65.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
        0.43         8.58        75.75        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       92.42        86.96         2.79       154.32        49.94       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-21-5782 TCGA-21-5786 TCGA-21-5787 
       31.73       122.43         9.34        31.63        33.93        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
       21.99         7.33         4.31        64.21         1.74        27.02 
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-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 
       19.30         9.57        63.55        14.63        44.25        86.30 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
       11.74        30.12        16.64        97.94        79.53       103.53 
TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      151.27        54.44        63.35         4.70         0.30        36.62 
TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 
        6.94       118.36        27.16        61.61        32.88        81.24 
TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       74.66        16.93        44.75        39.32         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 
       38.79         4.04        33.90         4.01         0.39         7.96 
TCGA-37-5819 TCGA-37-A5EN TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
        3.39        21.70       126.58        55.20        82.52         1.71 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-43-2576 TCGA-43-2581 
        1.94        36.39        68.38        71.18        40.21        38.66 
TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       39.12        27.91        22.98        21.47         5.46         3.81 
TCGA-43-7656 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       19.59        11.77        14.20        13.32        12.16        13.02 
TCGA-46-3768 TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7810 TCGA-52-7812 
        9.83        10.65         0.39        28.34        30.35        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 
       28.96        12.43        21.90        18.48        31.27        19.76 
TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 
        0.10        17.49        33.24        14.96         4.93        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS 
        9.93        20.25        15.81        19.23        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8393 
       14.47         0.03        13.25        13.55        29.95        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       85.12        34.36        56.65        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-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2724 
       56.91        50.33        48.49        42.64         3.19        23.57 
TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       52.67        70.42        68.15       102.67        70.62        58.65 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       14.99        11.34        89.29        78.28        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       53.88        34.59        16.96         2.01        21.07         0.99 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2763 
        1.02         2.01         0.92         0.99        43.99         0.99 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 
        2.01         1.02         2.01        19.00         3.02        19.00 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 
       12.03         3.98        12.00        24.95         1.97        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2795 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
        4.04         5.03         4.01         6.64         6.94        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       16.18        14.73        12.07        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       140.09         0.49        73.22        70.13       106.95 
TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
        0.16         6.51        86.76        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 
       17.72       104.09        27.39         6.97        66.51        60.53 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-85-6175 
      126.18       132.36        22.29         5.92        61.94         9.67 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
       41.39        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        30.64         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        15.39         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JC 
       36.59        38.14        12.59        22.59        30.28        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       24.36        30.48        19.73        27.16        16.21        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       14.96        15.29        29.92        12.39         3.65        24.92 
TCGA-90-7767 TCGA-90-A4ED TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 
        2.93        20.22         2.70         3.48         4.01         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        4.01         5.03        26.63        14.14        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-98-A538 
       18.31        17.46        27.68        21.44        21.34        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-L3-A524 
       18.15         2.01        27.02        20.32        20.71        16.11 
TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK 
       13.18         4.54         1.22        57.30        13.74         4.21 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N 
       49.28        43.92        25.32        26.43        83.57        33.07 
TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
        3.72        43.89         0.20 

  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                          0.39                           0.03 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                        173.82                         154.32 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                         24.89                          21.04 
[1] "0.4 - 173.8 (24.9)" "0.0 - 154.3 (21.0)"
[1] "hr=" "1.1"
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(18Q11.2) MUTATED         0       24       43        0        23
  AMP PEAK 24(18Q11.2) WILD-TYPE       2       65      109        2        42
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(18Q11.2) MUTATED          31         2         21          4
  AMP PEAK 24(18Q11.2) WILD-TYPE        64         1         42         15
                                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                             65
  STAGE IB                             43                            109
  STAGE II                              0                              2
  STAGE IIA                            23                             42
  STAGE IIB                            31                             64
  STAGE III                             2                              1
  STAGE IIIA                           21                             42
  STAGE IIIB                            4                             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
  AMP PEAK 24(18Q11.2) MUTATED    32  97  14   8
  AMP PEAK 24(18Q11.2) WILD-TYPE  80 197  57  16
D24V4, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  T1                           32                             80
  T2                           97                            197
  T3                           14                             57
  T4                            8                             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 24(18Q11.2) MUTATED    83  52  15   0
  AMP PEAK 24(18Q11.2) WILD-TYPE 234  81  25   5
D24V5, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  N0                           83                            234
  N1                           52                             81
  N2                           15                             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"
D24V6, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED   127   1
  AMP PEAK 24(18Q11.2) WILD-TYPE 284   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED    127    1
  AMP PEAK 24(18Q11.2) WILD-TYPE  284    6
   clus
vv  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  0                          127                            284
  1                            1                              6
[1] 2 2
[1] FALSE
D24V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED    39 112
  AMP PEAK 24(18Q11.2) WILD-TYPE  91 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED     39  112
  AMP PEAK 24(18Q11.2) WILD-TYPE   91  259
        clus
vv       AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  FEMALE                           39                             91
  MALE                            112                            259
[1] 2 2
[1] FALSE
D24V8, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED   108  25
  AMP PEAK 24(18Q11.2) WILD-TYPE 276  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED    108   25
  AMP PEAK 24(18Q11.2) WILD-TYPE  276   28
     clus
vv    AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  NO                           108                            276
  YES                           25                             28
[1] 2 2
[1] FALSE
D24V9, 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 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                                                           145
  AMP PEAK 24(18Q11.2) WILD-TYPE                                                         334
D24V10, multiclass
                                                             clus
vv                                                            AMP PEAK 24(18Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          145
                                                             clus
vv                                                            AMP PEAK 24(18Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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 277   8   2  18
D24V13, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  R0                          122                            277
  R1                            4                              8
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(18Q11.2) MUTATED       2                         6   108
  AMP PEAK 24(18Q11.2) WILD-TYPE     7                        25   241
D24V14, multiclass
                           clus
vv                          AMP PEAK 24(18Q11.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                              108
                           clus
vv                          AMP PEAK 24(18Q11.2) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             25
  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"
D24V15, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED     2  94
  AMP PEAK 24(18Q11.2) WILD-TYPE   6 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED      2   94
  AMP PEAK 24(18Q11.2) WILD-TYPE    6  223
                        clus
vv                       AMP PEAK 24(18Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       AMP PEAK 24(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            223
[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   127  93
  AMP PEAK 25(19Q12) WILD-TYPE 153 121
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         220                          274 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          93                          121 
$`AMP PEAK 25(19Q12) MUTATED`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 
        4.47         4.80        31.99        48.82        60.66        22.06 
TCGA-33-4533 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 
      133.74        19.76        31.50        28.96        17.88        22.49 
TCGA-43-5668 TCGA-43-7657 TCGA-43-A56V TCGA-56-8308 TCGA-56-A4BY TCGA-56-A5DR 
       18.38         7.76        12.03        17.00        17.85         0.13 
TCGA-60-2712 TCGA-63-A5MH TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-98-8020 
        9.01        66.61        18.38        16.14        57.07         2.76 
TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A7XE TCGA-O2-A52W 
       19.10         0.07        40.90        65.65         0.43         8.58 
TCGA-18-3411 TCGA-18-3417 TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1080 
      117.57        36.07       119.54        46.88        60.89       122.43 
TCGA-21-1081 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-1011 TCGA-22-4591 
        9.34        33.93        10.82        21.99         1.74        20.48 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-5474 TCGA-22-5477 
       35.08        24.13        38.17        34.75        14.63        44.25 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4538 TCGA-33-4566 
       79.20        18.84        30.12        62.86        97.94       173.82 
TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 
      103.53        14.07        63.35       110.99        44.19         2.63 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 
       61.61        32.88        65.23        60.30        50.66        39.32 
TCGA-34-7107 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4130 TCGA-37-5819 
        1.12        26.43        33.90         0.39         8.12         3.39 
TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5029 
       37.58        21.70       133.25       126.58       111.35        24.33 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 
       60.53        36.39        68.38        17.06        40.21        39.12 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-A475 TCGA-46-3768 
       33.11        27.91        22.98        19.59         9.73         9.83 
TCGA-46-6026 TCGA-52-7809 TCGA-56-6545 TCGA-56-7580 TCGA-56-7582 TCGA-56-8082 
       13.91         5.46        21.90        30.41        19.76        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-58-8386 
        4.93         3.48        15.81        20.94        13.32         0.03 
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-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2719 TCGA-60-2722 
       10.22        37.94        92.71        80.45        42.64        29.85 
TCGA-60-2723 TCGA-63-7020 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       35.90        70.13        68.15       102.67        70.62        58.65 
TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MV TCGA-66-2742 TCGA-66-2756 TCGA-66-2758 
       45.57        89.29        36.16        21.07         0.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2770 TCGA-66-2777 TCGA-66-2781 
       25.05         0.99         1.02        23.01         2.01         3.98 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 
       12.00         1.97        40.01        22.98         5.03        30.02 
TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
       10.06         4.01        49.05        13.35        16.18        14.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 
       12.07        12.33        29.56        73.12        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7465 TCGA-77-8008 
      140.09         0.49        73.22        70.13        32.55        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8136 TCGA-77-8138 TCGA-77-8145 
       55.73        37.81       156.66        39.09        17.72         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
       66.51        54.41        65.49       132.36       150.25        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6798 
        5.92        61.94        27.62        38.86         9.67         6.41 
TCGA-85-7696 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 TCGA-85-8070 TCGA-85-8072 
       36.53        32.91         1.15        25.15        31.56        30.64 
TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8582 
       10.09        22.45        16.77         3.09        32.71        38.14 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 
       12.59        30.28        34.13        19.73        27.16        15.85 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       12.39         3.65        11.77        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-98-8021 
        3.48         4.01         5.26        14.14        17.69        30.81 
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-A446 TCGA-LA-A7SW TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP 
       13.18        13.41        13.74         2.89        49.28        25.32 
TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52N TCGA-XC-AA0X 
       14.73         3.65        33.07         0.20 

$`AMP PEAK 25(19Q12) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
       12.20       123.19         6.18        27.19        32.19        14.93 
TCGA-22-5472 TCGA-33-4532 TCGA-33-4589 TCGA-34-2609 TCGA-43-7658 TCGA-43-8118 
       64.93       129.01         1.55        31.27        78.18         2.93 
TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8504 TCGA-56-A4ZJ 
       11.61        19.99        13.05         3.45        16.77        21.04 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 
        3.58        41.42        35.34        32.32         8.02        20.78 
TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       42.08        30.81         9.50        14.07        21.04         0.16 
TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5D1 
       19.36         5.69        21.21        76.80        39.85        16.80 
TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 
       75.75        11.34        23.54        92.15        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 
        2.79       154.32        49.94        99.16        70.16        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       15.58        31.73       119.80        43.23        31.63        88.11 
TCGA-21-5784 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 
       41.69         7.33         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-22-5473 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 
       11.77        63.55         0.79        86.30        71.34        11.74 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 TCGA-33-4583 TCGA-33-4587 TCGA-33-A4WN 
       56.32        16.64        79.53       151.27        54.44         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ TCGA-33-AASL TCGA-34-5232 
        0.30        36.62         6.94       118.36        27.16        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 
       74.66         9.07        16.93        44.75         4.96        38.79 
TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
        4.04         4.01         0.43         7.96         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
        6.81         0.39        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5030 TCGA-39-5036 TCGA-39-5037 TCGA-43-2581 TCGA-43-6647 
        1.71         1.94        71.18        55.56        38.66        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U 
       21.47         5.46         3.81        13.38        11.77        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 
       13.32        12.16        13.02         4.44        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-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       28.96        12.43        18.25        18.48        14.53        31.27 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8307 TCGA-56-8309 
        6.51         0.10        17.49        33.24        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        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 
       20.25        19.23        18.74         0.26        14.47        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-60-2697 
       13.55        29.95        71.24        16.47        85.12        12.23 
TCGA-60-2703 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       96.82        21.93        49.48        66.54        56.91        50.33 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
       48.49         3.19        23.57        26.83        11.77        52.67 
TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       70.42        55.30        59.97        14.99        11.34        25.28 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       78.28        16.37        53.88        34.59        16.96        43.10 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
        2.01         0.99         1.02         2.01         0.92        43.99 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 
        2.01         2.01         2.01         7.07        19.00         3.02 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2783 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 
       19.00        12.03        24.95        25.97         4.04        22.98 
TCGA-66-2794 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-77-6844 TCGA-77-7337 
       54.08         2.73         6.64         6.94        75.09       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8131 TCGA-77-8133 TCGA-77-8139 
        0.16        46.78         6.51        12.59        53.92       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       11.54        26.40        27.39        60.53        36.36       126.18 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 
       41.39        40.24        34.95        31.30         1.38        29.95 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 
       18.94        19.04        24.13        26.79        34.52         0.76 
TCGA-85-8288 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
       13.22         5.29         2.01        15.39         7.76        36.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       18.08        22.59        30.97        19.86        24.36        30.48 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7767 
       16.21        14.96        15.29        29.92        24.92         2.93 
TCGA-90-A4ED TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 
       20.22         2.30         4.01         5.03        26.63        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 
       18.31        17.46        27.68        21.44        30.67        21.34 
TCGA-98-A538 TCGA-98-A53C TCGA-98-A53H TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG 
       27.16        27.02        20.32        11.84         4.54        64.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CR 
        1.22        57.30         4.21        43.92        26.43        83.57 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
        3.72        12.72        43.89        11.18 

  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                        0.03                         0.10 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                      173.82                       154.32 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                      22.995                       20.235 
[1] "0.0 - 173.8 (23.0)" "0.1 - 154.3 (20.2)"
[1] "hr=" "1.2"
D25V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(19Q12) MUTATED         2       37       59        1        33
  AMP PEAK 25(19Q12) WILD-TYPE       0       52       93        1        32
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(19Q12) MUTATED          40         0         38         10
  AMP PEAK 25(19Q12) WILD-TYPE        55         3         25          9
                              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                           37                           52
  STAGE IB                           59                           93
  STAGE II                            1                            1
  STAGE IIA                          33                           32
  STAGE IIB                          40                           55
  STAGE III                           0                            3
  STAGE IIIA                         38                           25
  STAGE IIIB                         10                            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
  AMP PEAK 25(19Q12) MUTATED    44 139  30  12
  AMP PEAK 25(19Q12) WILD-TYPE  68 155  41  12
D25V4, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  T1                         44                           68
  T2                        139                          155
  T3                         30                           41
  T4                         12                           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   135  60  27   1
  AMP PEAK 25(19Q12) WILD-TYPE 182  73  13   4
D25V5, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  N0                        135                          182
  N1                         60                           73
  N2                         27                           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   187   4
  AMP PEAK 25(19Q12) WILD-TYPE 224   3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED    187    4
  AMP PEAK 25(19Q12) WILD-TYPE  224    3
   clus
vv  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  0                        187                          224
  1                          4                            3
[1] 2 2
[1] FALSE
D25V7, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED    53 172
  AMP PEAK 25(19Q12) WILD-TYPE  77 199
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     53  172
  AMP PEAK 25(19Q12) WILD-TYPE   77  199
        clus
vv       AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  FEMALE                         53                           77
  MALE                          172                          199
[1] 2 2
[1] FALSE
D25V8, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED   172  28
  AMP PEAK 25(19Q12) WILD-TYPE 212  25
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED    172   28
  AMP PEAK 25(19Q12) WILD-TYPE  212   25
     clus
vv    AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  NO                         172                          212
  YES                         28                           25
[1] 2 2
[1] FALSE
D25V9, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 25(19Q12) MUTATED                                       9
  AMP PEAK 25(19Q12) WILD-TYPE                                     6
                              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                                                           214
  AMP PEAK 25(19Q12) WILD-TYPE                                                         265
D25V10, multiclass
                                                             clus
vv                                                            AMP PEAK 25(19Q12) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        214
                                                             clus
vv                                                            AMP PEAK 25(19Q12) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          265
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
D25V12, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 25(19Q12) MUTATED   177   5   2  13
  AMP PEAK 25(19Q12) WILD-TYPE 222   7   2  10
D25V13, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  R0                        177                          222
  R1                          5                            7
  R2                          2                            2
  RX                         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                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(19Q12) MUTATED       5                        15   151
  AMP PEAK 25(19Q12) WILD-TYPE     4                        16   198
D25V14, multiclass
                           clus
vv                          AMP PEAK 25(19Q12) MUTATED
  ASIAN                                              5
  BLACK OR AFRICAN AMERICAN                         15
  WHITE                                            151
                           clus
vv                          AMP PEAK 25(19Q12) WILD-TYPE
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              198
[1] 3 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     3 133
  AMP PEAK 25(19Q12) WILD-TYPE   5 184
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED      3  133
  AMP PEAK 25(19Q12) WILD-TYPE    5  184
                        clus
vv                       AMP PEAK 25(19Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        133
                        clus
vv                       AMP PEAK 25(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          184
[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   134  96
  AMP PEAK 26(19Q13.2) WILD-TYPE 146 118
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                           230                            264 
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                            96                            118 
$`AMP PEAK 26(19Q13.2) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 
       12.20         4.47         4.80        60.66        22.06       129.01 
TCGA-33-4533 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 
      133.74        19.76        31.50        28.96        31.27        17.88 
TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-56-8308 TCGA-56-A4BY TCGA-56-A5DR 
       22.49        18.38         7.76        17.00        17.85         0.13 
TCGA-60-2712 TCGA-63-A5MH TCGA-77-A5GA TCGA-90-7964 TCGA-94-7943 TCGA-94-A5I4 
        9.01        66.61        42.08        14.07        18.38        16.14 
TCGA-96-7545 TCGA-98-8020 TCGA-J1-A4AH TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A7XE 
       57.07         2.76        19.10        40.90        65.65         0.43 
TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3417 TCGA-18-3421 TCGA-21-1070 
        8.58       117.57        11.34        36.07        86.96       119.54 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1080 TCGA-21-1081 TCGA-21-5783 TCGA-21-5786 
       46.88        60.89       122.43         9.34        88.11        33.93 
TCGA-21-5787 TCGA-22-0940 TCGA-22-1005 TCGA-22-1011 TCGA-22-4591 TCGA-22-4593 
       10.82        21.99        64.21         1.74        20.48        35.08 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       24.13        38.17        34.75        63.55        14.63        44.25 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4538 TCGA-33-4582 
       79.20        18.84        30.12        62.86        97.94       103.53 
TCGA-33-4586 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 
       14.07        63.35       110.99        44.19         2.63        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 
       32.88        65.23        60.30        50.66        16.93        39.32 
TCGA-34-7107 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4130 TCGA-37-5819 
        1.12        26.43        33.90         0.39         8.12         3.39 
TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 TCGA-39-5029 TCGA-39-5034 TCGA-39-5035 
       21.70       126.58       111.35        24.33        36.39        68.38 
TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       17.06        40.21        39.12        33.11        27.91        22.98 
TCGA-43-A475 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-52-7809 TCGA-56-1622 
        9.73         9.83        10.65        13.91         5.46        28.96 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7580 TCGA-56-7582 TCGA-56-8083 TCGA-56-8304 
       18.25        21.90        30.41        19.76         4.93         3.48 
TCGA-56-8622 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-58-8392 TCGA-58-8393 
        1.81        15.81        20.94        13.32        16.47        34.78 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2698 
       34.36        56.65        35.24        29.92        21.11        10.22 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2719 TCGA-60-2722 
       37.94        92.71        80.45        49.48        42.64        29.85 
TCGA-60-2723 TCGA-63-7020 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       35.90        70.13        68.15       102.67        70.62        58.65 
TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2742 
       45.57        89.29        78.28        36.16        34.59        21.07 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 
        0.99        21.01        25.05         0.99         1.02         2.01 
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-70-6722 TCGA-77-6842 TCGA-77-6843 
       13.35        16.18        14.73        12.07        29.56        73.12 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       23.28        11.18       140.09         0.49        73.22        70.13 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8136 
       32.55        86.76        55.73        37.81       156.66        39.09 
TCGA-77-8138 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5G3 
       17.72         6.97        66.51        54.41       132.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       22.29         5.92        61.94        27.62        38.86         9.67 
TCGA-85-7696 TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 TCGA-85-8070 TCGA-85-8276 
       36.53        32.91         1.15        25.15        31.56        34.52 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8582 
       22.45        16.77         3.09        32.71         2.01        38.14 
TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A50M 
       12.59        18.08        30.28        34.13        30.97        27.16 
TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE 
       15.85        29.92        12.39         3.65        11.77        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-A4VJ 
       10.59         2.70         3.48         4.01         5.26        14.14 
TCGA-94-A5I6 TCGA-98-8021 TCGA-98-8022 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I 
       17.69        30.81        30.67        18.15         2.01        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HH 
       20.71        12.89        16.11        13.18        13.41         1.22 
TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CX 
       13.74         2.89        49.28        25.32        14.73         3.65 
TCGA-O2-A52N TCGA-XC-AA0X 
       33.07         0.20 

$`AMP PEAK 26(19Q13.2) WILD-TYPE`
TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
      123.19        31.99         6.18        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5472 TCGA-33-4589 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 
       48.82        64.93         1.55        78.18         2.93        11.61 
TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8504 TCGA-56-A4ZJ 
       12.03        19.99        13.05         3.45        16.77        21.04 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 
        3.58        41.42        35.34        32.32         8.02        20.78 
TCGA-77-A5GB TCGA-90-7766 TCGA-94-7033 TCGA-94-7557 TCGA-96-A4JK TCGA-98-A539 
       30.81         9.50        21.04         0.16        19.36         5.69 
TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5D1 TCGA-18-3408 
       21.21         0.07        76.80        39.85        16.80        75.75 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       23.54        92.15        92.42         2.79       154.32        49.94 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 
       99.16        70.16        34.78        15.58        31.73       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 
       43.23        31.63        41.69         7.33         4.31        14.10 
TCGA-22-1016 TCGA-22-4594 TCGA-22-4596 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       27.02        48.33         0.56        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 
        9.57        11.77         0.79        86.30        71.34        11.74 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 
       56.32        16.64        79.53       173.82       151.27        54.44 
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-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 
       81.24        74.66         9.07        44.75         4.96        38.79 
TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
        4.04         4.01         0.43         7.96         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 
        6.81         0.39        37.58       133.25        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 
       82.52       102.18         1.71         1.94        60.53        71.18 
TCGA-39-5037 TCGA-43-2581 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       55.56        38.66        24.89        21.47         5.46         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       19.59        13.38        11.77        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3769 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       13.02         4.44         0.39         0.39        29.95        28.34 
TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-7222 TCGA-56-7223 
       30.35         8.75        27.45        12.43        18.48        14.53 
TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       31.27         6.51         0.10        17.49        33.24        14.96 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       26.89        14.07         1.35        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
        9.93        20.25        19.23        18.74         0.26        14.47 
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-60-2697 TCGA-60-2703 TCGA-60-2707 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       12.23        96.82        21.93        66.54        56.91        50.33 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
       48.49         3.19        23.57        26.83        11.77        52.67 
TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       70.42        55.30        59.97        14.99        11.34        25.28 
TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 
       16.37        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-70-6723 TCGA-77-6844 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        6.94        12.33        75.09       106.95         0.16        46.78 
TCGA-77-8007 TCGA-77-8131 TCGA-77-8133 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
        6.51        12.59        53.92       104.09        11.54        26.40 
TCGA-77-8144 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-85-6560 
       27.39        65.49        60.53        36.36       126.18        41.39 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 
       40.24         6.41        34.95        31.30         1.38        29.95 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 
       18.94        19.04        24.13        26.79        30.64        10.09 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8352 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
        0.76        13.22         5.29        15.39         7.76        36.59 
TCGA-85-8666 TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z 
       22.59        19.86        24.36        30.48        19.73        16.21 
TCGA-85-A511 TCGA-85-A512 TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-92-8065 
       14.96        15.29        24.92         2.93        20.22         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
        4.01         5.03        26.63        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53C TCGA-98-A53H 
       27.68        21.44        21.34        27.16        27.02        20.32 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HO 
       11.84         4.54        64.54        57.30         4.21        43.92 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       26.43        83.57         3.72        12.72        43.89        11.18 

  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                          0.13                           0.03 
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                        156.66                         173.82 
  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE 
                        23.705                         19.925 
[1] "0.1 - 156.7 (23.7)" "0.0 - 173.8 (19.9)"
[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       40       67        1        32
  AMP PEAK 26(19Q13.2) WILD-TYPE       0       49       85        1        33
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(19Q13.2) MUTATED          41         0         35         11
  AMP PEAK 26(19Q13.2) WILD-TYPE        54         3         28          8
                                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                             40                             49
  STAGE IB                             67                             85
  STAGE II                              1                              1
  STAGE IIA                            32                             33
  STAGE IIB                            41                             54
  STAGE III                             0                              3
  STAGE IIIA                           35                             28
  STAGE IIIB                           11                              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
  AMP PEAK 26(19Q13.2) MUTATED    48 148  26  12
  AMP PEAK 26(19Q13.2) WILD-TYPE  64 146  45  12
D26V4, multiclass
    clus
vv   AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  T1                           48                             64
  T2                          148                            146
  T3                           26                             45
  T4                           12                             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   143  61  26   2
  AMP PEAK 26(19Q13.2) WILD-TYPE 174  72  14   3
D26V5, multiclass
    clus
vv   AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  N0                          143                            174
  N1                           61                             72
  N2                           26                             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   198   3
  AMP PEAK 26(19Q13.2) WILD-TYPE 213   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19Q13.2) MUTATED    198    3
  AMP PEAK 26(19Q13.2) WILD-TYPE  213    4
   clus
vv  AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  0                          198                            213
  1                            3                              4
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  AMP PEAK 26(19Q13.2) MUTATED    49 185
  AMP PEAK 26(19Q13.2) WILD-TYPE  81 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19Q13.2) MUTATED     49  185
  AMP PEAK 26(19Q13.2) WILD-TYPE   81  186
        clus
vv       AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  FEMALE                           49                             81
  MALE                            185                            186
[1] 2 2
[1] FALSE
D26V8, binary
                                cls
clus                               0   1
  AMP PEAK 26(19Q13.2) MUTATED   182  26
  AMP PEAK 26(19Q13.2) WILD-TYPE 202  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19Q13.2) MUTATED    182   26
  AMP PEAK 26(19Q13.2) WILD-TYPE  202   27
     clus
vv    AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  NO                           182                            202
  YES                           26                             27
[1] 2 2
[1] FALSE
D26V9, 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 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                                                           223
  AMP PEAK 26(19Q13.2) WILD-TYPE                                                         256
D26V10, multiclass
                                                             clus
vv                                                            AMP PEAK 26(19Q13.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          223
                                                             clus
vv                                                            AMP PEAK 26(19Q13.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            256
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
D26V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 26(19Q13.2) MUTATED   190   5   2  11
  AMP PEAK 26(19Q13.2) WILD-TYPE 209   7   2  12
D26V13, multiclass
    clus
vv   AMP PEAK 26(19Q13.2) MUTATED AMP PEAK 26(19Q13.2) WILD-TYPE
  R0                          190                            209
  R1                            5                              7
  R2                            2                              2
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(19Q13.2) MUTATED       5                        15   160
  AMP PEAK 26(19Q13.2) WILD-TYPE     4                        16   189
D26V14, multiclass
                           clus
vv                          AMP PEAK 26(19Q13.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           15
  WHITE                                              160
                           clus
vv                          AMP PEAK 26(19Q13.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             16
  WHITE                                                189
[1] 3 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     3 142
  AMP PEAK 26(19Q13.2) WILD-TYPE   5 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 26(19Q13.2) MUTATED      3  142
  AMP PEAK 26(19Q13.2) WILD-TYPE    5  175
                        clus
vv                       AMP PEAK 26(19Q13.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          142
                        clus
vv                       AMP PEAK 26(19Q13.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            175
[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   144 131
  AMP PEAK 27(20P12.2) WILD-TYPE 136  83
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           275                            219 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                           131                             83 
$`AMP PEAK 27(20P12.2) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-21-A5DI TCGA-22-5471 TCGA-22-5472 
        4.47       123.19         4.80        32.19        60.66        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 
       22.06       129.01         1.55        28.96        17.88        22.49 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 
        7.76        78.18         2.93        11.61        12.03        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2711 
        3.45        17.00        16.77        21.04         0.13        41.42 
TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       35.34        32.32         8.02        20.78        42.08        30.81 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
        0.16        18.38        16.14        57.07        19.36         2.76 
TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 
        5.69        19.10         0.07         0.43         8.58       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-5592 TCGA-21-1070 
       11.34        23.54        92.15        36.07        49.94       119.54 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 
       46.88        60.89        34.78       122.43         9.34       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-22-1011 
       43.23        31.63        88.11        41.69        33.93         1.74 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4604 
       27.02        20.48        35.08        48.33        38.17        13.12 
TCGA-22-4605 TCGA-22-4609 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       32.02         9.57        63.55        14.63        44.25         0.79 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-33-4538 
       71.34        11.74        18.84        30.12        56.32        97.94 
TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
      103.53        54.44        63.35       110.99        44.19       118.36 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5239 TCGA-34-5240 
        2.63        61.61        32.88        65.23        60.30        50.66 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
       39.32         1.12         4.04        26.43        33.90         4.01 
TCGA-37-4130 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 
        8.12         0.39         3.39        37.58        21.70       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 
      111.35        68.58         1.71        24.33        60.53        71.18 
TCGA-39-5037 TCGA-43-2576 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6773 
       55.56        40.21        33.11        27.91        22.98         3.81 
TCGA-43-7656 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       19.59        13.02         9.83        10.65        13.91         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 
       29.95        28.34         5.46         8.75        28.96        18.25 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
       21.90        18.48        14.53        31.27        30.41        19.76 
TCGA-56-7730 TCGA-56-7822 TCGA-56-7823 TCGA-56-8622 TCGA-56-8624 TCGA-56-A49D 
        6.51        17.49        33.24         1.81        13.81        20.94 
TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8391 TCGA-58-8392 
       19.23        18.74        14.47         0.03        71.24        16.47 
TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 
       34.78        34.36        35.24        21.11        10.22        96.82 
TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       37.94        21.93        80.45        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2726 TCGA-63-7020 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ 
       35.90        11.77        70.13       102.67        70.62        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 
       45.57        14.99        78.28        36.16        53.88        16.96 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        2.01        21.07         0.99        21.01        25.05         0.99 
TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 
        7.07        23.01         3.02         2.01        12.03         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2787 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 
       12.00        24.95        40.01        22.98         5.03        30.02 
TCGA-66-2793 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-70-6722 
       10.06        49.05         6.64        13.35        16.18        12.07 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       12.33        29.56        75.09        23.28        11.18       140.09 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        0.49        73.22         0.16         6.51        86.76        55.73 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 
      156.66        53.92        39.09        11.54        26.40         6.97 
TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
       36.36       150.25        22.29         5.92        61.94        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 
       38.86         9.67         6.41        36.53        31.30         1.15 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 
       18.94        19.04        24.13        31.56        34.52        10.09 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8353 TCGA-85-8354 TCGA-85-8481 TCGA-85-8664 
        0.76        22.45         3.09        32.71         7.76        18.08 
TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50M 
       22.59        34.13        30.97        19.86        30.48        27.16 
TCGA-85-A510 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
       15.85        12.39         3.65         2.93        11.77        20.22 
TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-8490 TCGA-94-A5I6 TCGA-98-8021 
       22.62         3.48         5.26         5.03        17.69        30.81 
TCGA-98-8022 TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 
       30.67         2.01        18.58        20.71        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI 
       13.18        13.41        11.84         4.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ 
       13.74         4.21         2.89        49.28        25.32        14.73 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       83.57         3.65        33.07         3.72        12.72 

$`AMP PEAK 27(20P12.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 
       12.20        31.99         6.18        27.19        14.93        48.82 
TCGA-33-4533 TCGA-33-6737 TCGA-34-2604 TCGA-34-2609 TCGA-43-5668 TCGA-56-7221 
      133.74        19.76        31.50        31.27        18.38        19.99 
TCGA-56-A4BY TCGA-60-2696 TCGA-60-2712 TCGA-63-A5MH TCGA-90-7766 TCGA-90-7964 
       17.85         3.58         9.01        66.61         9.50        14.07 
TCGA-94-7033 TCGA-98-A53D TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT 
       21.04        21.21        76.80        39.85        40.90        65.65 
TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       16.80        75.75        92.42        86.96         2.79       154.32 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 TCGA-21-1079 TCGA-21-5787 TCGA-22-0940 
       99.16        70.16        15.58        31.73        10.82        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-4595 TCGA-22-4596 
        7.33         4.31        64.21        14.10        24.13         0.56 
TCGA-22-4601 TCGA-22-4607 TCGA-22-4613 TCGA-22-5479 TCGA-22-5481 TCGA-22-5489 
       34.75        19.30        11.77        86.30        79.20        62.86 
TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-A4WN 
       16.64        79.53       173.82       151.27        14.07         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASL TCGA-34-5232 TCGA-34-5234 
        0.30        36.62         6.94        27.16        81.24        74.66 
TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-37-3789 
        9.07        16.93        44.75         4.96        38.79         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-39-5011 
        0.39         7.96         7.46         7.82         6.81       133.25 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
       55.20        82.52       102.18         1.94        36.39        68.38 
TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       17.06        38.66        39.12        24.89        21.47         5.46 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       13.38        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3769 TCGA-51-4080 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 TCGA-56-7731 
        4.44         0.39        30.35        27.45        12.43         0.10 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       14.96         4.93         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-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J TCGA-58-A46L 
        0.26        13.25        13.55        29.95        85.12        56.65 
TCGA-58-A46N TCGA-60-2697 TCGA-60-2706 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       29.92        12.23        92.71        49.48        66.54        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7021 
       50.33        48.49        23.57        26.83        52.67        70.42 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MI TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       68.15        55.30        58.65        11.34        25.28        89.29 
TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 
       16.37        34.59        43.10         0.99         1.02         2.01 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 
        0.92        43.99         2.01         1.02         2.01         2.01 
TCGA-66-2771 TCGA-66-2778 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 
       19.00        19.00         1.97        25.97         4.04        22.98 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59J TCGA-77-6843 
       54.08         4.01         2.73         6.94        14.73        73.12 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8128 TCGA-77-8131 
       70.13       106.95        46.78        32.55        37.81        12.59 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 
       17.72       104.09        27.39        66.51        54.41        65.49 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 
       60.53       126.18       132.36        41.39        40.24        34.95 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 
       32.91         1.38        29.95        25.15        26.79        30.64 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 
       13.22        16.77         5.29         2.01        15.39        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z 
       38.14        12.59        30.28        24.36        19.73        16.21 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-A59Q TCGA-92-7340 
       14.96        15.29        29.92        24.92        10.59         2.70 
TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 
        4.01         2.30         4.01        26.63        14.14        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-98-A538 
       18.31        17.46        27.68        21.44        21.34        27.16 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-NC-A5HG TCGA-NC-A5HO TCGA-NC-A5HT 
       18.15        27.02        20.32        64.54        43.92        26.43 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       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 
                        156.66                         173.82 
  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE 
                         21.90                          21.47 
[1] "0.0 - 156.7 (21.9)" "0.1 - 173.8 (21.5)"
[1] "hr=" "1.3"
D27V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(20P12.2) MUTATED         2       41       91        1        33
  AMP PEAK 27(20P12.2) WILD-TYPE       0       48       61        1        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(20P12.2) MUTATED          58         2         33         11
  AMP PEAK 27(20P12.2) WILD-TYPE        37         1         30          8
                                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                             41                             48
  STAGE IB                             91                             61
  STAGE II                              1                              1
  STAGE IIA                            33                             32
  STAGE IIB                            58                             37
  STAGE III                             2                              1
  STAGE IIIA                           33                             30
  STAGE IIIB                           11                              8
  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    49 175  41  15
  AMP PEAK 27(20P12.2) WILD-TYPE  63 119  30   9
D27V4, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  T1                           49                             63
  T2                          175                            119
  T3                           41                             30
  T4                           15                              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   180  74  21   2
  AMP PEAK 27(20P12.2) WILD-TYPE 137  59  19   3
D27V5, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  N0                          180                            137
  N1                           74                             59
  N2                           21                             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   233   6
  AMP PEAK 27(20P12.2) WILD-TYPE 178   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED    233    6
  AMP PEAK 27(20P12.2) WILD-TYPE  178    1
   clus
vv  AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  0                          233                            178
  1                            6                              1
[1] 2 2
[1] FALSE
D27V7, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED    58 222
  AMP PEAK 27(20P12.2) WILD-TYPE  72 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED     58  222
  AMP PEAK 27(20P12.2) WILD-TYPE   72  149
        clus
vv       AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  FEMALE                           58                             72
  MALE                            222                            149
[1] 2 2
[1] FALSE
D27V8, binary
                                cls
clus                               0   1
  AMP PEAK 27(20P12.2) MUTATED   217  32
  AMP PEAK 27(20P12.2) WILD-TYPE 167  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED    217   32
  AMP PEAK 27(20P12.2) WILD-TYPE  167   21
     clus
vv    AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  NO                           217                            167
  YES                           32                             21
[1] 2 2
[1] FALSE
D27V9, 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 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                                                           269
  AMP PEAK 27(20P12.2) WILD-TYPE                                                         210
D27V10, multiclass
                                                             clus
vv                                                            AMP PEAK 27(20P12.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          269
                                                             clus
vv                                                            AMP PEAK 27(20P12.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            210
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
D27V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 27(20P12.2) MUTATED   219   8   3  14
  AMP PEAK 27(20P12.2) WILD-TYPE 180   4   1   9
D27V13, multiclass
    clus
vv   AMP PEAK 27(20P12.2) MUTATED AMP PEAK 27(20P12.2) WILD-TYPE
  R0                          219                            180
  R1                            8                              4
  R2                            3                              1
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20P12.2) MUTATED       6                        16   194
  AMP PEAK 27(20P12.2) WILD-TYPE     3                        15   155
D27V14, multiclass
                           clus
vv                          AMP PEAK 27(20P12.2) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              194
                           clus
vv                          AMP PEAK 27(20P12.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                155
[1] 3 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     7 171
  AMP PEAK 27(20P12.2) WILD-TYPE   1 146
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 27(20P12.2) MUTATED      7  171
  AMP PEAK 27(20P12.2) WILD-TYPE    1  146
                        clus
vv                       AMP PEAK 27(20P12.2) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          171
                        clus
vv                       AMP PEAK 27(20P12.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            146
[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   164 138
  AMP PEAK 28(20Q11.21) WILD-TYPE 116  76
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                            302                             192 
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                            138                              76 
$`AMP PEAK 28(20Q11.21) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-21-A5DI TCGA-22-5471 
       12.20         4.47       123.19         4.80        32.19        60.66 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 
       64.93        22.06       129.01         1.55        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       31.27        17.88        22.49        18.38         7.76        78.18 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 TCGA-56-8305 TCGA-56-8504 
        2.93        11.61        12.03        13.05         3.45        16.77 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 TCGA-68-8250 
       21.04         0.13         3.58        41.42        35.34         8.02 
TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
       20.78        42.08        30.81         0.16        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD 
       57.07        19.36         2.76         5.69        19.10         0.07 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 
       39.85        40.90        16.80         0.43         8.58       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-5592 
       11.34        23.54        92.15        36.07        92.42        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 
      119.54        46.88        60.89        34.78        15.58        31.73 
TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 
        9.34       119.80        43.23        88.11        41.69        33.93 
TCGA-21-5787 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       10.82         1.74        14.10        27.02        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4604 TCGA-22-4605 TCGA-22-5477 TCGA-22-5478 
       48.33        24.13        13.12        32.02        44.25         0.79 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-33-4538 
       71.34        11.74        18.84        30.12        56.32        97.94 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-33-AAS8 TCGA-33-AASD 
      103.53       151.27        14.07        63.35        36.62       110.99 
TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 
       44.19       118.36         2.63        61.61        32.88        65.23 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 
       60.30        50.66        39.32         1.12         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 
       33.90         4.01         0.39         8.12         7.82         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 
        0.39         3.39        37.58        21.70       133.25       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 TCGA-39-5031 TCGA-39-5036 
      111.35        68.58         1.71        24.33        60.53        71.18 
TCGA-39-5037 TCGA-43-2576 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6771 
       55.56        40.21        33.11        27.91        22.98         5.46 
TCGA-43-6773 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
        3.81        13.02         9.83         4.44        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-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
       21.90        18.48        14.53        31.27        30.41        19.76 
TCGA-56-7822 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8629 
       17.49         1.81        13.81        10.36         9.93        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8390 
       20.94        19.23        18.74        14.47         0.03        29.95 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 TCGA-60-2698 
       71.24        34.78        34.36        35.24        21.11        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 
       96.82        37.94        92.71        21.93        80.45        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2726 TCGA-63-7020 TCGA-63-A5MB 
       42.64         3.19        29.85        11.77        70.13       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-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
       49.05         6.64        13.35        16.18        14.73        12.07 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
       29.56        73.12        23.28        11.18       140.09         0.49 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       73.22       106.95         0.16        46.78        32.55         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8143 
       86.76        55.73       156.66        53.92        39.09        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 
       27.39         6.97        66.51        36.36       150.25        22.29 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       61.94        27.62        38.86         9.67        41.39        40.24 
TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 
       36.53        31.30         1.15        29.95        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 
       31.56        26.79        34.52        10.09         0.76        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8481 TCGA-85-8582 
       16.77         5.29         3.09        32.71         7.76        38.14 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR 
       18.08        22.59        30.97        19.86        30.48        19.73 
TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 
       27.16        15.85        14.96        12.39         3.65         2.93 
TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-A4VJ 
       11.77        20.22        22.62         3.48         5.26        14.14 
TCGA-94-A5I6 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J 
       17.69        30.67        27.16         2.01        18.58        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF 
       12.89        16.11        13.18        13.41        11.84         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
       64.54         1.22        57.30        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N 
       49.28        25.32        14.73        83.57         3.65        33.07 
TCGA-O2-A52Q TCGA-O2-A52S 
        3.72        12.72 

$`AMP PEAK 28(20Q11.21) WILD-TYPE`
TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-33-4533 
       31.99         6.18        27.19        14.93        48.82       133.74 
TCGA-33-6737 TCGA-56-7221 TCGA-56-8308 TCGA-56-A4BY TCGA-60-2712 TCGA-60-2721 
       19.76        19.99        17.00        17.85         9.01        32.32 
TCGA-63-A5MH TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-98-A53D TCGA-NC-A5HE 
       66.61         9.50        14.07        21.04        21.21        76.80 
TCGA-NK-A5CT TCGA-18-3408 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1072 
       65.65        75.75        86.96         2.79       154.32        99.16 
TCGA-21-1075 TCGA-21-1080 TCGA-21-5782 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       70.16       122.43        31.63        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 
       64.21         0.56        38.17        34.75        19.30         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5481 TCGA-22-5489 
       11.77        63.55        14.63        86.30        79.20        62.86 
TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW 
       16.64        79.53       173.82        54.44         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        81.24        74.66         9.07        16.93 
TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-37-3789 TCGA-37-4129 TCGA-37-4132 
       44.75         4.96        38.79         0.43         7.96         7.46 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
       55.20        82.52       102.18         1.94        36.39        68.38 
TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 
       17.06        38.66        39.12        24.89        21.47        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       13.38        11.77         9.73        14.20        13.32        12.16 
TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7812 TCGA-56-5897 TCGA-56-7730 
        0.39         0.39        29.95        27.45        12.43         6.51 
TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
        0.10        33.24        14.96         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 TCGA-56-8628 TCGA-56-A4BX TCGA-56-A5DS 
       14.07         1.35        22.75        20.25        13.32         0.26 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N 
       13.25        13.55        16.47        85.12        56.65        29.92 
TCGA-60-2697 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2723 
       12.23        49.48        66.54        56.91        48.49        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       23.57        26.83        52.67        70.42        68.15        55.30 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-66-2727 TCGA-66-2734 
       11.34        25.28        89.29        16.37        16.96        43.10 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 
        2.01         0.92         2.01         2.01         2.01        19.00 
TCGA-66-2778 TCGA-66-2783 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
       19.00        24.95        25.97         4.04        22.98         5.03 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-70-6723 
       30.02        54.08         4.01         2.73         6.94        12.33 
TCGA-77-6844 TCGA-77-7335 TCGA-77-8128 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 
       75.09        70.13        37.81        12.59        17.72       104.09 
TCGA-77-8140 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
       11.54        54.41        65.49        60.53       126.18       132.36 
TCGA-77-A5G7 TCGA-85-6798 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 
        5.92         6.41        34.95        32.91         1.38        18.94 
TCGA-85-8048 TCGA-85-8072 TCGA-85-8288 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 
       25.15        30.64        13.22         2.01        15.39        36.59 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A512 
       12.59        30.28        34.13        24.36        16.21        15.29 
TCGA-85-A513 TCGA-90-6837 TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 
       29.92        24.92        10.59         2.70         4.01         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
        4.01         5.03        26.63        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53C 
       27.68        21.44        30.81        21.34        18.15        27.02 
TCGA-98-A53H TCGA-NC-A5HO TCGA-NC-A5HT TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       20.32        43.92        26.43        43.89        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 
                         156.66                          173.82 
  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE 
                         22.175                          21.275 
[1] "0.0 - 156.7 (22.2)" "0.1 - 173.8 (21.3)"
[1] "hr=" "1.2"
D28V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(20Q11.21) MUTATED         2       47       94        1        41
  AMP PEAK 28(20Q11.21) WILD-TYPE       0       42       58        1        24
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 28(20Q11.21) MUTATED          60         2         42          9
  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                              47                              42
  STAGE IB                              94                              58
  STAGE II                               1                               1
  STAGE IIA                             41                              24
  STAGE IIB                             60                              35
  STAGE III                              2                               1
  STAGE IIIA                            42                              21
  STAGE IIIB                             9                              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    58 189  42  17
  AMP PEAK 28(20Q11.21) WILD-TYPE  54 105  29   7
D28V4, multiclass
    clus
vv   AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  T1                            58                              54
  T2                           189                             105
  T3                            42                              29
  T4                            17                               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   191  84  27   0
  AMP PEAK 28(20Q11.21) WILD-TYPE 126  49  13   5
D28V5, multiclass
    clus
vv   AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  N0                           191                             126
  N1                            84                              49
  N2                            27                              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   256   6
  AMP PEAK 28(20Q11.21) WILD-TYPE 155   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.21) MUTATED    256    6
  AMP PEAK 28(20Q11.21) WILD-TYPE  155    1
   clus
vv  AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  0                           256                             155
  1                             6                               1
[1] 2 2
[1] FALSE
D28V7, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.21) MUTATED    60 246
  AMP PEAK 28(20Q11.21) WILD-TYPE  70 125
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.21) MUTATED     60  246
  AMP PEAK 28(20Q11.21) WILD-TYPE   70  125
        clus
vv       AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  FEMALE                            60                              70
  MALE                             246                             125
[1] 2 2
[1] FALSE
D28V8, binary
                                 cls
clus                                0   1
  AMP PEAK 28(20Q11.21) MUTATED   233  34
  AMP PEAK 28(20Q11.21) WILD-TYPE 151  19
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.21) MUTATED    233   34
  AMP PEAK 28(20Q11.21) WILD-TYPE  151   19
     clus
vv    AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  NO                            233                             151
  YES                            34                              19
[1] 2 2
[1] FALSE
D28V9, 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 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                                                           294
  AMP PEAK 28(20Q11.21) WILD-TYPE                                                         185
D28V10, multiclass
                                                             clus
vv                                                            AMP PEAK 28(20Q11.21) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           294
                                                             clus
vv                                                            AMP PEAK 28(20Q11.21) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
D28V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 28(20Q11.21) MUTATED   243   6   2  15
  AMP PEAK 28(20Q11.21) WILD-TYPE 156   6   2   8
D28V13, multiclass
    clus
vv   AMP PEAK 28(20Q11.21) MUTATED AMP PEAK 28(20Q11.21) WILD-TYPE
  R0                           243                             156
  R1                             6                               6
  R2                             2                               2
  RX                            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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(20Q11.21) MUTATED       5                        19   215
  AMP PEAK 28(20Q11.21) WILD-TYPE     4                        12   134
D28V14, multiclass
                           clus
vv                          AMP PEAK 28(20Q11.21) MUTATED
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            19
  WHITE                                               215
                           clus
vv                          AMP PEAK 28(20Q11.21) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                              12
  WHITE                                                 134
[1] 3 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     7 189
  AMP PEAK 28(20Q11.21) WILD-TYPE   1 128
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(20Q11.21) MUTATED      7  189
  AMP PEAK 28(20Q11.21) WILD-TYPE    1  128
                        clus
vv                       AMP PEAK 28(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           189
                        clus
vv                       AMP PEAK 28(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             128
[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   151 101
  AMP PEAK 29(22Q11.21) WILD-TYPE 129 113
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                            252                             242 
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                            101                             113 
$`AMP PEAK 29(22Q11.21) MUTATED`
TCGA-18-3409 TCGA-18-5595 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-34-2605 
      123.19        27.19        22.06       129.01         1.55        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 
       31.27        17.88        18.38         7.76         2.93        11.61 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ 
       19.99        13.05         3.45        17.00        16.77        21.04 
TCGA-56-A5DR TCGA-60-2711 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-94-7033 
        0.13        41.42        20.78        42.08        30.81        21.04 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 
       18.38        16.14        57.07        19.36         2.76         5.69 
TCGA-J1-A4AH TCGA-NC-A5HD TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 
       19.10         0.07         8.58        75.75       117.57        11.34 
TCGA-18-3414 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 
       23.54        86.96       154.32       119.54        99.16        70.16 
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-21-5784 TCGA-21-5786 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 
       41.69        33.93         4.31         1.74        14.10        20.48 
TCGA-22-4593 TCGA-22-4595 TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5473 
       35.08        24.13        13.12        32.02        11.77        63.55 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5491 
       44.25         0.79        86.30        79.20        11.74        56.32 
TCGA-22-5492 TCGA-33-4582 TCGA-33-4586 TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 
       16.64       103.53        14.07       110.99       118.36         2.63 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       61.61        32.88        65.23         9.07        60.30        50.66 
TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       16.93        39.32         1.12         4.04        26.43        33.90 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EN TCGA-39-5016 
        8.12         7.82         6.81         0.39        21.70       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5029 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 
      111.35        68.58        24.33        36.39        71.18        55.56 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-A475 
       33.11        27.91        22.98        24.89        21.47         9.73 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
       13.32        12.16        13.02         9.83         4.44        10.65 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 
       29.95         5.46        30.35         8.75        28.96        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 
       18.25        21.90        31.27        30.41        19.76         6.51 
TCGA-56-7731 TCGA-56-7822 TCGA-56-8083 TCGA-56-8304 TCGA-56-8503 TCGA-56-8622 
        0.10        17.49         4.93         3.48         1.35         1.81 
TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS 
        9.93        15.81        20.94        19.23        13.32         0.26 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
        0.03        13.25        29.95        35.24        29.92        21.11 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 
       96.82        37.94        92.71        21.93        80.45        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 
       42.64         3.19        29.85        35.90        26.83        11.77 
TCGA-63-7020 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ 
       70.13        55.30       102.67        70.62        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       45.57        25.28        78.28        16.37        36.16        53.88 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2766 
       43.10         2.01        21.07         0.99         0.92         1.02 
TCGA-66-2769 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2788 TCGA-66-2791 
        7.07         3.02         2.01         3.98        22.98         5.03 
TCGA-66-2792 TCGA-66-2800 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 
       30.02        49.05        16.18        14.73        12.07        12.33 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 
       29.56        23.28       140.09         0.49        73.22       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 
        0.16        46.78        32.55        86.76        37.81       156.66 
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        36.36       132.36       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 
       61.94        27.62        38.86         9.67        40.24        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-8052 TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 
       34.95        31.30        24.13        31.56        34.52        10.09 
TCGA-85-8350 TCGA-85-8354 TCGA-85-8580 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC 
       22.45        32.71        36.59        34.13        30.97        19.86 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A5B5 
       30.48        19.73        27.16        15.85        14.96         3.65 
TCGA-90-7767 TCGA-90-7769 TCGA-92-7341 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 
        2.93        11.77         3.48        14.14        17.69        18.31 
TCGA-96-8170 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 
       17.46        30.67        27.16        20.71        16.11        13.18 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
       64.54         1.22        57.30         4.21         2.89        49.28 
TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-XC-AA0X 
       25.32        26.43        83.57         3.65        33.07         0.20 

$`AMP PEAK 29(22Q11.21) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI 
       12.20         4.47         4.80        31.99         6.18        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-33-4533 TCGA-33-6737 
       14.93        48.82        60.66        64.93       133.74        19.76 
TCGA-34-2604 TCGA-43-2578 TCGA-43-7658 TCGA-43-A56V TCGA-56-A4BY TCGA-60-2696 
       31.50        22.49        78.18        12.03        17.85         3.58 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-90-7766 
        9.01        35.34        32.32        66.61         8.02         9.50 
TCGA-90-7964 TCGA-94-7557 TCGA-98-A53D TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR 
       14.07         0.16        21.21        76.80        39.85        40.90 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
       65.65        16.80         0.43        92.15        36.07        92.42 
TCGA-18-4086 TCGA-18-5592 TCGA-21-1071 TCGA-21-1078 TCGA-21-1080 TCGA-21-1082 
        2.79        49.94        46.88        15.58       122.43       119.80 
TCGA-21-5782 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-1016 
       31.63        10.82        21.99         7.33        64.21        27.02 
TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 
       48.33         0.56        38.17        34.75        19.30         9.57 
TCGA-22-5474 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4538 
       14.63        71.34        18.84        30.12        62.86        97.94 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
       79.53       173.82       151.27        54.44        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-5232 
        0.30        36.62         6.94        44.19        27.16        81.24 
TCGA-34-5234 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 
       74.66        44.75         4.96        38.79         4.01         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 
        0.39         7.96         7.46         3.39        37.58       133.25 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 
       55.20        82.52       102.18         1.71         1.94        60.53 
TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-6771 
       68.38        17.06        40.21        38.66        39.12         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-6026 
        3.81        19.59        13.38        11.77        14.20        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7812 TCGA-56-7222 TCGA-56-7223 
        0.39         0.39        28.34        27.45        18.48        14.53 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8307 TCGA-56-8309 TCGA-56-8623 TCGA-56-8624 
       33.24        14.96        26.89        14.07        22.75        13.81 
TCGA-56-8625 TCGA-56-8628 TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8388 TCGA-58-8391 
       10.36        20.25        18.74        14.47        13.55        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2697 
       16.47        34.78        85.12        34.36        56.65        12.23 
TCGA-60-2698 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2724 
       10.22        49.48        66.54        56.91        48.49        23.57 
TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR 
       52.67        70.42        68.15        14.99        11.34        89.29 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 
       34.59        16.96         1.02         2.01         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 
       21.01        25.05         0.99         2.01         2.01         2.01 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 
       23.01        19.00        19.00        12.03        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 
        1.97        25.97        40.01         4.04        22.98        10.06 
TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
       54.08         4.01         2.73         6.64         6.94        13.35 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7335 TCGA-77-8007 TCGA-77-8009 
       73.12        75.09        11.18        70.13         6.51        55.73 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8148 TCGA-77-8154 
       39.09        17.72       104.09        27.39        66.51        60.53 
TCGA-77-A5FZ TCGA-85-6560 TCGA-85-6798 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
      126.18        41.39         6.41        32.91         1.38         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 
       29.95        18.94        25.15        19.04        26.79        30.64 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 
        0.76        13.22        16.77         5.29         3.09         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
       15.39         7.76        38.14        12.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       30.28        24.36        16.21        15.29        29.92        12.39 
TCGA-90-6837 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
       24.92        20.22        22.62        10.59         2.70         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-96-7544 
        5.26         2.30         4.01         5.03        26.63        71.01 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B 
       27.68        21.44        30.81        21.34        18.15         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 
       27.02        20.32        18.58        12.89        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HJ TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-O2-A52Q TCGA-O2-A52S 
        4.54        13.74        43.92        14.73         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A5IB 
       43.89        11.18 

  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                           0.03                            0.16 
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                         156.66                          173.82 
  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE 
                          23.13                           19.99 
[1] "0.0 - 156.7 (23.1)" "0.2 - 173.8 (20.0)"
[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       39       82        1        33
  AMP PEAK 29(22Q11.21) WILD-TYPE       0       50       70        1        32
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 29(22Q11.21) MUTATED          59         0         27          6
  AMP PEAK 29(22Q11.21) WILD-TYPE        36         3         36         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                              39                              50
  STAGE IB                              82                              70
  STAGE II                               1                               1
  STAGE IIA                             33                              32
  STAGE IIB                             59                              36
  STAGE III                              0                               3
  STAGE IIIA                            27                              36
  STAGE IIIB                             6                              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    47 162  37  10
  AMP PEAK 29(22Q11.21) WILD-TYPE  65 132  34  14
D29V4, multiclass
    clus
vv   AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  T1                            47                              65
  T2                           162                             132
  T3                            37                              34
  T4                            10                              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   168  67  15   1
  AMP PEAK 29(22Q11.21) WILD-TYPE 149  66  25   4
D29V5, multiclass
    clus
vv   AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  N0                           168                             149
  N1                            67                              66
  N2                            15                              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   218   5
  AMP PEAK 29(22Q11.21) WILD-TYPE 193   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(22Q11.21) MUTATED    218    5
  AMP PEAK 29(22Q11.21) WILD-TYPE  193    2
   clus
vv  AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  0                           218                             193
  1                             5                               2
[1] 2 2
[1] FALSE
D29V7, binary
                                 cls
clus                                0   1
  AMP PEAK 29(22Q11.21) MUTATED    58 198
  AMP PEAK 29(22Q11.21) WILD-TYPE  72 173
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(22Q11.21) MUTATED     58  198
  AMP PEAK 29(22Q11.21) WILD-TYPE   72  173
        clus
vv       AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  FEMALE                            58                              72
  MALE                             198                             173
[1] 2 2
[1] FALSE
D29V8, binary
                                 cls
clus                                0   1
  AMP PEAK 29(22Q11.21) MUTATED   199  24
  AMP PEAK 29(22Q11.21) WILD-TYPE 185  29
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(22Q11.21) MUTATED    199   24
  AMP PEAK 29(22Q11.21) WILD-TYPE  185   29
     clus
vv    AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  NO                            199                             185
  YES                            24                              29
[1] 2 2
[1] FALSE
D29V9, 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 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                                                           246
  AMP PEAK 29(22Q11.21) WILD-TYPE                                                         233
D29V10, multiclass
                                                             clus
vv                                                            AMP PEAK 29(22Q11.21) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           246
                                                             clus
vv                                                            AMP PEAK 29(22Q11.21) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             233
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
D29V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 29(22Q11.21) MUTATED   211   8   0   9
  AMP PEAK 29(22Q11.21) WILD-TYPE 188   4   4  14
D29V13, multiclass
    clus
vv   AMP PEAK 29(22Q11.21) MUTATED AMP PEAK 29(22Q11.21) WILD-TYPE
  R0                           211                             188
  R1                             8                               4
  R2                             0                               4
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(22Q11.21) MUTATED       4                        10   184
  AMP PEAK 29(22Q11.21) WILD-TYPE     5                        21   165
D29V14, multiclass
                           clus
vv                          AMP PEAK 29(22Q11.21) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               184
                           clus
vv                          AMP PEAK 29(22Q11.21) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                              21
  WHITE                                                 165
[1] 3 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     4 160
  AMP PEAK 29(22Q11.21) WILD-TYPE   4 157
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 29(22Q11.21) MUTATED      4  160
  AMP PEAK 29(22Q11.21) WILD-TYPE    4  157
                        clus
vv                       AMP PEAK 29(22Q11.21) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           160
                        clus
vv                       AMP PEAK 29(22Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             157
[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    67  55
  AMP PEAK 30(XQ28) WILD-TYPE 213 159
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                        122                         372 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                         55                         159 
$`AMP PEAK 30(XQ28) MUTATED`
TCGA-18-3407 TCGA-18-5595 TCGA-22-A5C4 TCGA-33-4532 TCGA-34-2604 TCGA-34-2605 
        4.47        27.19        22.06       129.01        31.50        28.96 
TCGA-34-2609 TCGA-43-7657 TCGA-43-8118 TCGA-56-8504 TCGA-56-A5DR TCGA-77-7140 
       31.27         7.76         2.93        16.77         0.13        20.78 
TCGA-77-A5GA TCGA-94-7557 TCGA-94-A5I4 TCGA-96-A4JK TCGA-J1-A4AH TCGA-NK-A7XE 
       42.08         0.16        16.14        19.36        19.10         0.43 
TCGA-18-3408 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-21-1081 TCGA-22-0940 
       75.75        92.15        36.07        86.96         9.34        21.99 
TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-5473 
       14.10        20.48        35.08        48.33        24.13        63.55 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-33-4547 
       44.25         0.79        71.34        79.20        18.84        79.53 
TCGA-33-4566 TCGA-33-AASJ TCGA-34-2596 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 
      173.82       118.36         2.63        50.66        44.75        39.32 
TCGA-34-8454 TCGA-37-3792 TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 
       38.79         0.39         7.82         3.39        21.70       133.25 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5028 TCGA-39-5037 TCGA-43-5670 TCGA-43-A475 
      111.35        68.58         1.71        55.56        27.91         9.73 
TCGA-46-3769 TCGA-51-4079 TCGA-56-7222 TCGA-56-7223 TCGA-56-8082 TCGA-56-8624 
        4.44         0.39        18.48        14.53        14.96        13.81 
TCGA-56-8629 TCGA-56-A49D TCGA-58-8386 TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
       15.81        20.94         0.03        35.24        29.92        21.11 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2724 TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MT 
       80.45        49.48        23.57        58.65        25.28        16.37 
TCGA-63-A5MW TCGA-66-2753 TCGA-66-2756 TCGA-66-2758 TCGA-66-2766 TCGA-66-2769 
       53.88         1.02         0.99        21.01         1.02         7.07 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2781 TCGA-66-2782 TCGA-66-2792 TCGA-66-2793 
        3.02        19.00         3.98        12.00        30.02        10.06 
TCGA-68-7756 TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 
        6.64        12.33        29.56        23.28        11.18         0.49 
TCGA-77-7338 TCGA-77-8009 TCGA-77-8136 TCGA-77-8144 TCGA-77-8156 TCGA-77-A5G3 
        0.16        55.73        39.09        27.39        36.36       150.25 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-8070 TCGA-85-8351 
       27.62         9.67        40.24         6.41        31.56        16.77 
TCGA-85-8353 TCGA-85-8354 TCGA-85-A4QR TCGA-85-A50M TCGA-90-7769 TCGA-90-A4EE 
        3.09        32.71        19.73        27.16        11.77        22.62 
TCGA-92-8064 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-98-8023 TCGA-98-A53B 
        5.26        26.63        14.14        17.69        21.34         2.01 
TCGA-LA-A446 TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HQ 
       13.18         1.22        13.74         2.89        49.28        14.73 
TCGA-O2-A52Q TCGA-O2-A5IB 
        3.72        11.18 

$`AMP PEAK 30(XQ28) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI 
       12.20       123.19         4.80        31.99         6.18        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-33-4533 TCGA-33-4589 
       14.93        48.82        60.66        64.93       133.74         1.55 
TCGA-33-6737 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 TCGA-43-A474 
       19.76        17.88        22.49        18.38        78.18        11.61 
TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY 
       12.03        19.99        13.05         3.45        17.00        17.85 
TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 
       21.04         3.58        41.42         9.01        35.34        32.32 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
       66.61         8.02        30.81         9.50        14.07        21.04 
TCGA-94-7943 TCGA-96-7545 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD 
       18.38        57.07         2.76         5.69        21.21         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W 
       76.80        39.85        40.90        65.65        16.80         8.58 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 
      117.57        11.34        23.54        92.42         2.79       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
       49.94       119.54        46.88        99.16        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
       34.78        15.58        31.73       122.43       119.80        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
       31.63        88.11        41.69        33.93        10.82         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4596 TCGA-22-4599 
        4.31        64.21         1.74        27.02         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-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       14.63        86.30        11.74        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       16.64        97.94       103.53       151.27        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       63.35         4.70         0.30        36.62         6.94       110.99 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       44.19        27.16        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5929 TCGA-34-7107 
       74.66         9.07        60.30        16.93         4.96         1.12 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
        4.04        26.43        33.90         4.01         0.43         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-39-5016 
        8.12         7.46         6.81         0.39        37.58       126.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       55.20        82.52       102.18        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
       36.39        68.38        71.18        17.06        40.21        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       39.12        33.11        22.98        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 
        3.81        19.59        13.38        11.77        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4080 
       12.16        13.02         9.83        10.65        13.91         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-56-7579 TCGA-56-7580 
       28.96        12.43        18.25        21.90        31.27        30.41 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8083 
       19.76         6.51         0.10        17.49        33.24         4.93 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
        3.48        26.89        14.07         1.35         1.81        22.75 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK 
       10.36         9.93        20.25        19.23        13.32        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        0.26        14.47        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-60-2697 
       16.47        34.78        85.12        34.36        56.65        12.23 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2710 
       10.22        96.82        37.94        92.71        21.93        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 
       56.91        50.33        48.49        42.64         3.19        29.85 
TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
       35.90        26.83        11.77        52.67        70.13        70.42 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML 
       68.15        55.30       102.67        70.62        59.97        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MY 
       14.99        11.34        89.29        78.28        36.16        34.59 
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-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
        0.92        43.99        25.05         0.99         2.01         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2783 
        2.01        23.01        19.00         2.01        12.03        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-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 
        5.03        54.08         4.01        49.05         2.73         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 
       13.35        16.18        14.73        12.07        73.12        75.09 
TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 
      140.09        73.22        70.13       106.95        46.78        32.55 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
        6.51        86.76        37.81       156.66        12.59        53.92 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 
       17.72       104.09        11.54        26.40         6.97        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
       54.41        65.49        60.53       126.18       132.36        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 
        5.92        61.94        38.86        41.39        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-85-8049 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       25.15        19.04        24.13        26.79        30.64        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8355 
       10.09         0.76        13.22        22.45         5.29         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 
       15.39         7.76        36.59        38.14        12.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA 
       22.59        30.28        34.13        30.97        19.86        24.36 
TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
       30.48        16.21        15.85        14.96        15.29        29.92 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A59Q 
       12.39         3.65        24.92         2.93        20.22        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 
        2.70         3.48         4.01         2.30         4.01         5.03 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       71.01        18.31        17.46        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       30.67        27.16        18.15        27.02        20.32        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF 
       20.71        12.89        16.11        13.41        11.84         4.54 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT 
       64.54        57.30         4.21        43.92        25.32        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       83.57         3.65        33.07        12.72        43.89         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 
                     173.82                      156.66 
  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE 
                      20.63                       22.67 
[1] "0.0 - 173.8 (20.6)" "0.1 - 156.7 (22.7)"
[1] "hr=" "1.1"
D30V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 30(XQ28) MUTATED         0       10       38        0        19
  AMP PEAK 30(XQ28) WILD-TYPE       2       79      114        2        46
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 30(XQ28) MUTATED          26         2         17          7
  AMP PEAK 30(XQ28) WILD-TYPE        69         1         46         12
                             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                          79
  STAGE IB                          38                         114
  STAGE II                           0                           2
  STAGE IIA                         19                          46
  STAGE IIB                         26                          69
  STAGE III                          2                           1
  STAGE IIIA                        17                          46
  STAGE IIIB                         7                          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 30(XQ28) MUTATED    13  78  23  10
  AMP PEAK 30(XQ28) WILD-TYPE  99 216  48  14
D30V4, multiclass
    clus
vv   AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  T1                        13                          99
  T2                        78                         216
  T3                        23                          48
  T4                        10                          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    70  41  10   1
  AMP PEAK 30(XQ28) WILD-TYPE 247  92  30   4
D30V5, multiclass
    clus
vv   AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  N0                        70                         247
  N1                        41                          92
  N2                        10                          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   101   2
  AMP PEAK 30(XQ28) WILD-TYPE 310   5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED    101    2
  AMP PEAK 30(XQ28) WILD-TYPE  310    5
   clus
vv  AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  0                       101                         310
  1                         2                           5
[1] 2 2
[1] FALSE
D30V7, binary
                             cls
clus                            0   1
  AMP PEAK 30(XQ28) MUTATED    26  98
  AMP PEAK 30(XQ28) WILD-TYPE 104 273
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED     26   98
  AMP PEAK 30(XQ28) WILD-TYPE  104  273
        clus
vv       AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  FEMALE                        26                         104
  MALE                          98                         273
[1] 2 2
[1] FALSE
D30V8, binary
                             cls
clus                            0   1
  AMP PEAK 30(XQ28) MUTATED    99  10
  AMP PEAK 30(XQ28) WILD-TYPE 285  43
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED     99   10
  AMP PEAK 30(XQ28) WILD-TYPE  285   43
     clus
vv    AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  NO                         99                         285
  YES                        10                          43
[1] 2 2
[1] FALSE
D30V9, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  AMP PEAK 30(XQ28) MUTATED                                       4
  AMP PEAK 30(XQ28) WILD-TYPE                                    11
                             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                                                           119
  AMP PEAK 30(XQ28) WILD-TYPE                                                         360
D30V10, multiclass
                                                             clus
vv                                                            AMP PEAK 30(XQ28) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       119
                                                             clus
vv                                                            AMP PEAK 30(XQ28) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
D30V12, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 30(XQ28) MUTATED    98   4   1   5
  AMP PEAK 30(XQ28) WILD-TYPE 301   8   3  18
D30V13, multiclass
    clus
vv   AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  R0                        98                         301
  R1                         4                           8
  R2                         1                           3
  RX                         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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 30(XQ28) MUTATED       3                         6    84
  AMP PEAK 30(XQ28) WILD-TYPE     6                        25   265
D30V14, multiclass
                           clus
vv                          AMP PEAK 30(XQ28) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         6
  WHITE                                            84
                           clus
vv                          AMP PEAK 30(XQ28) WILD-TYPE
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          25
  WHITE                                             265
[1] 3 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  74
  AMP PEAK 30(XQ28) WILD-TYPE   8 243
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 30(XQ28) MUTATED      0   74
  AMP PEAK 30(XQ28) WILD-TYPE    8  243
                        clus
vv                       AMP PEAK 30(XQ28) MUTATED AMP PEAK 30(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             0                           8
  NOT HISPANIC OR LATINO                        74                         243
[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   131  94
  DEL PEAK  1(1P36.11) WILD-TYPE 149 120
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           225                            269 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            94                            120 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-18-3406 TCGA-18-4083 TCGA-22-1017 TCGA-22-5471 TCGA-33-4533 TCGA-34-2605 
       12.20         6.18        48.82        60.66       133.74        28.96 
TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 
        7.76         2.93        11.61        12.03        19.99         3.45 
TCGA-56-8308 TCGA-60-2711 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       17.00        41.42        18.38        16.14        57.07        19.36 
TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-18-3408 
        5.69        19.10        76.80        39.85        40.90        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-4721 TCGA-18-5592 
      117.57        11.34        23.54        92.15       154.32        49.94 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 TCGA-21-1082 
       46.88        99.16        70.16        34.78        31.73       119.80 
TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-4593 
       43.23        33.93        10.82        21.99         7.33        35.08 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4609 TCGA-22-5473 
        0.56        38.17        34.75        13.12         9.57        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5483 TCGA-22-5491 TCGA-33-4538 
       14.63        44.25        86.30        18.84        56.32        97.94 
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-34-2608 
        6.94        44.19        27.16         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-7107 TCGA-34-8456 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
       65.23         1.12        26.43         0.39         7.96         8.12 
TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5027 
        7.82         3.39        37.58        21.70       126.58       102.18 
TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       60.53        71.18        55.56        40.21        38.66        39.12 
TCGA-43-6770 TCGA-46-3765 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       21.47        13.32         9.83        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-56-7223 TCGA-56-7580 
       27.45        28.96        18.25        21.90        14.53        30.41 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-7823 TCGA-56-A4BX TCGA-56-A4ZK 
       19.76         6.51        17.49        33.24        13.32        18.74 
TCGA-56-A62T TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K 
       14.47        29.95        71.24        16.47        34.78        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       56.65        35.24        10.22        92.71        21.93        80.45 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2722 TCGA-60-2726 TCGA-63-7023 TCGA-63-A5MB 
       56.91        50.33        29.85        11.77        55.30       102.67 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MV TCGA-66-2737 
       59.97        45.57        25.28        89.29        36.16         2.01 
TCGA-66-2742 TCGA-66-2755 TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 
       21.07         0.92        21.01         1.02         2.01        23.01 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 TCGA-66-2787 
        3.02         2.01        12.03         3.98         1.97        40.01 
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-68-7757 TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 
       49.05         2.73         6.94        14.73        12.07        12.33 
TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
       73.12        23.28       140.09         0.49        73.22         0.16 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8144 TCGA-77-8145 
       32.55        55.73        37.81        53.92        27.39         6.97 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GF 
       66.51        54.41        65.49       150.25        61.94        27.62 
TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 TCGA-85-8049 
        9.67        40.24        36.53        31.30        32.91        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 
       24.13        31.56        26.79        30.64        10.09         0.76 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4CN 
       16.77         5.29         3.09        36.59        30.28        34.13 
TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 
       19.86        19.73        14.96        15.29        12.39         3.65 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-8490 TCGA-94-A5I6 
       20.22        22.62         3.48         5.26         5.03        17.69 
TCGA-98-8021 TCGA-98-8023 TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 
       30.81        21.34        18.58        20.71        16.11        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK 
       13.41        11.84         4.54        64.54        57.30         4.21 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR 
        2.89        49.28        43.92        25.32        14.73        83.57 
TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
        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-18-5595 TCGA-21-A5DI 
        4.47       123.19         4.80        31.99        27.19        32.19 
TCGA-22-1000 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 
       14.93        64.93        22.06       129.01         1.55        19.76 
TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 
       31.50        31.27        17.88        22.49        18.38        78.18 
TCGA-56-8201 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       13.05        16.77        17.85        21.04         0.13         3.58 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 
        9.01        35.34        32.32        66.61         8.02        20.78 
TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       42.08        30.81         9.50        14.07        21.04         0.16 
TCGA-98-8020 TCGA-98-A53D TCGA-NC-A5HD TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE 
        2.76        21.21         0.07        65.65        16.80         0.43 
TCGA-O2-A52W TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-21-1070 
        8.58        36.07        92.42        86.96         2.79       119.54 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-5782 TCGA-21-5783 
       60.89        15.58       122.43         9.34        31.63        88.11 
TCGA-21-5784 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       41.69         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-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
        0.79        71.34        79.20        11.74        30.12        62.86 
TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASD 
       16.64        79.53       173.82        63.35         4.70       110.99 
TCGA-33-AASJ TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
      118.36        81.24        74.66         9.07        60.30        50.66 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 
       16.93        44.75        39.32         4.96        38.79         4.04 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 
       33.90         4.01         0.43         7.46         6.81         0.39 
TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
      133.25       111.35        68.58        55.20        82.52         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-3920 
       24.33         1.94        36.39        68.38        17.06        33.11 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
       27.91        22.98        24.89         5.46         3.81        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 
       13.38        11.77         9.73        14.20        12.16        13.02 
TCGA-46-3769 TCGA-56-5897 TCGA-56-7222 TCGA-56-7579 TCGA-56-7731 TCGA-56-8082 
        4.44        12.43        18.48        31.27         0.10        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        4.93         3.48        26.89        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       22.75        13.81        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       20.94        19.23         0.26         0.03        13.25        13.55 
TCGA-58-A46J TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 
       85.12        29.92        21.11        12.23        96.82        37.94 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 
       49.48        66.54        48.49        42.64         3.19        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
       23.57        26.83        52.67        70.13        70.42        68.15 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MT 
       70.62        58.65        14.99        11.34        78.28        16.37 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 
       53.88        34.59        16.96        43.10         0.99         1.02 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        2.01         0.99        43.99        25.05         0.99         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 
        2.01         7.07        19.00        19.00        12.00        24.95 
TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I 
       25.97        22.98         4.04         6.64        13.35        16.18 
TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 
       29.56        75.09        11.18        70.13       106.95        46.78 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 
        6.51        86.76       156.66        12.59        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
      104.09        11.54        26.40        60.53        36.36       126.18 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
      132.36        22.29         5.92        38.86        41.39         6.41 
TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       34.95         1.38         1.15        29.95        18.94        25.15 
TCGA-85-8276 TCGA-85-8288 TCGA-85-8350 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
       34.52        13.22        22.45        32.71         2.01        15.39 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB 
        7.76        38.14        12.59        18.08        22.59        30.97 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 
       24.36        30.48        27.16        16.21        15.85        29.92 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
       24.92         2.93        11.77        10.59         2.70         4.01 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        2.30         4.01        26.63        14.14        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A 
       17.46        27.68        21.44        30.67        27.16        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 TCGA-NC-A5HH TCGA-NC-A5HJ 
        2.01        27.02        20.32        12.89         1.22        13.74 
TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A5IB TCGA-XC-AA0X 
       26.43         3.65        33.07        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                         173.82 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         23.28                          20.78 
[1] "0.2 - 154.3 (23.3)" "0.0 - 173.8 (20.8)"
[1] "hr=" "1.1"
D31V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.11) MUTATED         0       34       67        2        36
  DEL PEAK  1(1P36.11) WILD-TYPE       2       55       85        0        29
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED          39         2         31         11
  DEL PEAK  1(1P36.11) WILD-TYPE        56         1         32          8
                                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                             34                             55
  STAGE IB                             67                             85
  STAGE II                              2                              0
  STAGE IIA                            36                             29
  STAGE IIB                            39                             56
  STAGE III                             2                              1
  STAGE IIIA                           31                             32
  STAGE IIIB                           11                              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  1(1P36.11) MUTATED    46 136  32  14
  DEL PEAK  1(1P36.11) WILD-TYPE  66 158  39  10
D31V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                           46                             66
  T2                          136                            158
  T3                           32                             39
  T4                           14                             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   135  71  18   2
  DEL PEAK  1(1P36.11) WILD-TYPE 182  62  22   3
D31V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                          135                            182
  N1                           71                             62
  N2                           18                             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   193   3
  DEL PEAK  1(1P36.11) WILD-TYPE 218   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    193    3
  DEL PEAK  1(1P36.11) WILD-TYPE  218    4
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                          193                            218
  1                            3                              4
[1] 2 2
[1] FALSE
D31V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    49 179
  DEL PEAK  1(1P36.11) WILD-TYPE  81 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     49  179
  DEL PEAK  1(1P36.11) WILD-TYPE   81  192
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           49                             81
  MALE                            179                            192
[1] 2 2
[1] FALSE
D31V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   167  33
  DEL PEAK  1(1P36.11) WILD-TYPE 217  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    167   33
  DEL PEAK  1(1P36.11) WILD-TYPE  217   20
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                           167                            217
  YES                           33                             20
[1] 2 2
[1] FALSE
D31V9, 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 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                                                           219
  DEL PEAK  1(1P36.11) WILD-TYPE                                                         260
D31V10, multiclass
                                                             clus
vv                                                            DEL PEAK  1(1P36.11) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          219
                                                             clus
vv                                                            DEL PEAK  1(1P36.11) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            260
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
D31V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED   186   7   2  11
  DEL PEAK  1(1P36.11) WILD-TYPE 213   5   2  12
D31V13, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                          186                            213
  R1                            7                              5
  R2                            2                              2
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED       4                        15   162
  DEL PEAK  1(1P36.11) WILD-TYPE     5                        16   187
D31V14, multiclass
                           clus
vv                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           15
  WHITE                                              162
                           clus
vv                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             16
  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"
D31V15, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     5 141
  DEL PEAK  1(1P36.11) WILD-TYPE   3 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      5  141
  DEL PEAK  1(1P36.11) WILD-TYPE    3  176
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          141
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            176
[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   120  98
  DEL PEAK  2(1P13.1) WILD-TYPE 160 116
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          218                           276 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           98                           116 
$`DEL PEAK  2(1P13.1) MUTATED`
TCGA-18-3406 TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 TCGA-34-2605 TCGA-43-2578 
       12.20        48.82        60.66        22.06        28.96        22.49 
TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 
        7.76        78.18        11.61        12.03        19.99         3.45 
TCGA-56-8308 TCGA-60-2721 TCGA-77-A5GA TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 
       17.00        32.32        42.08        18.38        16.14        57.07 
TCGA-96-A4JK TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HR TCGA-18-3408 
       19.36         5.69        19.10        76.80        40.90        75.75 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 
       11.34        23.54        92.15        86.96       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-21-1079 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1012 TCGA-22-4593 
       31.73        33.93        21.99         7.33        14.10        35.08 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4609 TCGA-22-5473 
        0.56        38.17        34.75        13.12         9.57        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 
       14.63        44.25        86.30        79.20        18.84        30.12 
TCGA-22-5489 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-A4WN 
       62.86        97.94       103.53       151.27        14.07         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 
        0.30        36.62         6.94        44.19        27.16         2.63 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-7107 TCGA-34-8456 TCGA-37-4129 
       61.61        32.88        65.23         1.12        26.43         7.96 
TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5029 TCGA-39-5034 
        3.39        37.58        21.70       126.58        24.33        36.39 
TCGA-39-5037 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-46-3765 
       55.56        38.66        39.12        33.11        22.98        13.32 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        9.83        10.65        13.91         0.39         0.39        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-56-5898 TCGA-56-6545 TCGA-56-7223 TCGA-56-7730 TCGA-56-7822 TCGA-56-7823 
       18.25        21.90        14.53         6.51        17.49        33.24 
TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8391 
       10.36        20.94        13.32        18.74        14.47        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M TCGA-60-2698 TCGA-60-2707 
       16.47        34.78        56.65        35.24        10.22        21.93 
TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 TCGA-60-2722 TCGA-60-2726 TCGA-63-A5MB 
       80.45        50.33        42.64        29.85        11.77       102.67 
TCGA-63-A5MJ TCGA-63-A5MP TCGA-63-A5MR TCGA-66-2727 TCGA-66-2754 TCGA-66-2755 
       59.97        25.28        89.29        16.96         2.01         0.92 
TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 
        0.99        21.01         0.99         1.02         2.01        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2781 TCGA-66-2787 TCGA-66-2790 
       19.00         3.02         2.01         3.98        40.01        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-A59J TCGA-70-6723 TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 
        2.73        14.73        12.33        73.12        23.28       140.09 
TCGA-77-7141 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
        0.49         0.16        46.78        32.55        55.73        37.81 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8145 TCGA-77-8148 TCGA-77-8156 TCGA-77-A5G3 
       53.92        39.09         6.97        66.51        36.36       150.25 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 
       61.94        27.62        38.86         9.67        40.24        36.53 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
        1.38         1.15        18.94        19.04        24.13        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 
       30.64        34.52        10.09         0.76         5.29         3.09 
TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QR 
       12.59        18.08        30.28        34.13        30.97        19.73 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 
       16.21        14.96        15.29        12.39         3.65         2.93 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8064 TCGA-94-8035 TCGA-94-8490 
       22.62        10.59         3.48         5.26         4.01         5.03 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-98-8021 TCGA-98-8022 
       14.14        17.69        71.01        18.31        30.81        30.67 
TCGA-98-8023 TCGA-98-A53B TCGA-98-A53I TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HG 
       21.34         2.01        18.58        16.11        11.84        64.54 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
        4.21         2.89        49.28        43.92        25.32        14.73 
TCGA-O2-A52N TCGA-O2-A52S 
       33.07        12.72 

$`DEL PEAK  2(1P13.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
        4.47       123.19         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 
       32.19        14.93        64.93       129.01       133.74         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-8118 
       19.76        31.50        31.27        17.88        18.38         2.93 
TCGA-56-8201 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       13.05        16.77        17.85        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 
       41.42         9.01        35.34        66.61         8.02        20.78 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-98-8020 
       30.81         9.50        14.07        21.04         0.16         2.76 
TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE 
       21.21         0.07        39.85        65.65        16.80         0.43 
TCGA-O2-A52W TCGA-18-3411 TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-21-1078 
        8.58       117.57        36.07        92.42         2.79        15.58 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
      122.43         9.34       119.80        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5787 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 
       41.69        10.82         4.31        64.21         1.74        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-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 
        0.79        71.34        11.74        56.32        16.64        79.53 
TCGA-33-4566 TCGA-33-4587 TCGA-33-6738 TCGA-33-AASD TCGA-33-AASJ TCGA-34-5232 
      173.82        54.44        63.35       110.99       118.36        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 
       39.32         4.96        38.79         4.04        33.90         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         0.39         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        0.39       133.25       111.35        68.58        55.20        82.52 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
      102.18         1.71         1.94        60.53        68.38        71.18 
TCGA-39-5040 TCGA-43-2576 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       17.06        40.21        27.91        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
        3.81        19.59        13.38        11.77         9.73        14.20 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-56-5897 TCGA-56-7222 TCGA-56-7579 
       12.16        13.02         4.44        12.43        18.48        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 
       30.41        19.76         0.10        14.96         4.93         3.48 
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        13.81 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A5DS TCGA-58-8386 
        9.93        20.25        15.81        19.23         0.26         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46N 
       13.25        13.55        29.95        85.12        34.36        29.92 
TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2709 
       21.11        12.23        96.82        37.94        92.71        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 
       66.54        56.91        48.49         3.19        35.90        23.57 
TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       26.83        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MS 
       70.62        58.65        45.57        14.99        11.34        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 
       16.37        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-68-8251 TCGA-68-A59I TCGA-70-6722 TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 
       13.35        16.18        12.07        29.56        75.09        11.18 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8007 TCGA-77-8008 TCGA-77-8130 
       73.22        70.13       106.95         6.51        86.76       156.66 
TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       12.59        17.72       104.09        11.54        26.40        27.39 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 
       54.41        65.49        60.53       126.18       132.36        22.29 
TCGA-77-A5G7 TCGA-85-6560 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
        5.92        41.39         6.41        34.95        31.30        32.91 
TCGA-85-7844 TCGA-85-8048 TCGA-85-8070 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       29.95        25.15        31.56        13.22        22.45        16.77 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
       32.71         2.01        15.39         7.76        36.59        38.14 
TCGA-85-8666 TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A510 
       22.59        19.86        24.36        30.48        27.16        15.85 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-92-7340 TCGA-92-8063 
       29.92        24.92        11.77        20.22         2.70         4.01 
TCGA-92-8065 TCGA-94-8491 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-A538 
        2.30        26.63        17.46        27.68        21.44        27.16 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A446 
       18.15        27.02        20.32        20.71        12.89        13.18 
TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HT 
       13.41         4.54         1.22        57.30        13.74        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       83.57         3.65         3.72        43.89        11.18         0.20 

  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                         0.16                          0.03 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                       154.32                        173.82 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                       22.275                        21.090 
[1] "0.2 - 154.3 (22.3)" "0.0 - 173.8 (21.1)"
[1] "hr=" "1.1"
D32V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.1) MUTATED         1       33       59        1        37
  DEL PEAK  2(1P13.1) WILD-TYPE       1       56       93        1        28
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P13.1) MUTATED          46         1         27         11
  DEL PEAK  2(1P13.1) WILD-TYPE        49         2         36          8
                               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                            56
  STAGE IB                            59                            93
  STAGE II                             1                             1
  STAGE IIA                           37                            28
  STAGE IIB                           46                            49
  STAGE III                            1                             2
  STAGE IIIA                          27                            36
  STAGE IIIB                          11                             8
  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    47 130  32  12
  DEL PEAK  2(1P13.1) WILD-TYPE  65 164  39  12
D32V4, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  T1                          47                            65
  T2                         130                           164
  T3                          32                            39
  T4                          12                            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   127  73  17   2
  DEL PEAK  2(1P13.1) WILD-TYPE 190  60  23   3
D32V5, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  N0                         127                           190
  N1                          73                            60
  N2                          17                            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   189   2
  DEL PEAK  2(1P13.1) WILD-TYPE 222   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED    189    2
  DEL PEAK  2(1P13.1) WILD-TYPE  222    5
   clus
vv  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  0                         189                           222
  1                           2                             5
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED    52 169
  DEL PEAK  2(1P13.1) WILD-TYPE  78 202
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED     52  169
  DEL PEAK  2(1P13.1) WILD-TYPE   78  202
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  FEMALE                          52                            78
  MALE                           169                           202
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED   165  26
  DEL PEAK  2(1P13.1) WILD-TYPE 219  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED    165   26
  DEL PEAK  2(1P13.1) WILD-TYPE  219   27
     clus
vv    DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  NO                          165                           219
  YES                          26                            27
[1] 2 2
[1] FALSE
D32V9, 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 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                                                           212
  DEL PEAK  2(1P13.1) WILD-TYPE                                                         267
D32V10, multiclass
                                                             clus
vv                                                            DEL PEAK  2(1P13.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         212
                                                             clus
vv                                                            DEL PEAK  2(1P13.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           267
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
D32V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P13.1) MUTATED   179   7   2  12
  DEL PEAK  2(1P13.1) WILD-TYPE 220   5   2  11
D32V13, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  R0                         179                           220
  R1                           7                             5
  R2                           2                             2
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.1) MUTATED       3                        11   164
  DEL PEAK  2(1P13.1) WILD-TYPE     6                        20   185
D32V14, multiclass
                           clus
vv                          DEL PEAK  2(1P13.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             164
                           clus
vv                          DEL PEAK  2(1P13.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            20
  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"
D32V15, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED     6 136
  DEL PEAK  2(1P13.1) WILD-TYPE   2 181
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      6  136
  DEL PEAK  2(1P13.1) WILD-TYPE    2  181
                        clus
vv                       DEL PEAK  2(1P13.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         136
                        clus
vv                       DEL PEAK  2(1P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           181
[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  22
  DEL PEAK  3(2P25.3) WILD-TYPE 252 192
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           50                           444 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           22                           192 
$`DEL PEAK  3(2P25.3) MUTATED`
TCGA-18-3406 TCGA-43-2578 TCGA-43-7657 TCGA-77-7140 TCGA-NC-A5HM TCGA-18-3414 
       12.20        22.49         7.76        20.78        39.85        23.54 
TCGA-18-3421 TCGA-22-4594 TCGA-22-4601 TCGA-22-5489 TCGA-33-4587 TCGA-34-A5IX 
       86.96        48.33        34.75        62.86        54.44        33.90 
TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5028 TCGA-39-5029 
        6.81         3.39        21.70       133.25         1.71        24.33 
TCGA-39-5031 TCGA-39-5034 TCGA-52-7810 TCGA-56-1622 TCGA-56-8307 TCGA-56-A49D 
       60.53        36.39        30.35        28.96        26.89        20.94 
TCGA-58-8392 TCGA-60-2713 TCGA-60-2722 TCGA-60-2726 TCGA-63-A5ML TCGA-63-A5MP 
       16.47        56.91        29.85        11.77        45.57        25.28 
TCGA-63-A5MY TCGA-66-2756 TCGA-66-2766 TCGA-66-2780 TCGA-66-2781 TCGA-66-2791 
       34.59         0.99         1.02        12.03         3.98         5.03 
TCGA-68-A59J TCGA-77-7337 TCGA-77-8130 TCGA-77-8153 TCGA-77-A5GH TCGA-85-7699 
       14.73       106.95       156.66        65.49        38.86        32.91 
TCGA-85-7710 TCGA-85-8352 TCGA-85-8354 TCGA-85-A511 TCGA-92-8063 TCGA-96-A4JL 
        1.38         5.29        32.71        14.96         4.01        27.68 
TCGA-NC-A5HH TCGA-O2-A52S 
        1.22        12.72 

$`DEL PEAK  3(2P25.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
        4.47       123.19         4.80        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
      129.01       133.74         1.55        19.76        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 
       31.27        17.88        18.38        78.18         2.93        11.61 
TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
       12.03        19.99        13.05         3.45        17.00        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 
       17.85        21.04         0.13         3.58        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA TCGA-77-A5GB 
       35.34        32.32        66.61         8.02        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
        9.50        14.07        21.04         0.16        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH 
       57.07        19.36         2.76         5.69        21.21        19.10 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE 
        0.07        76.80        40.90        65.65        16.80         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 
        8.58        75.75       117.57        11.34        92.15        36.07 
TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       92.42         2.79       154.32        49.94       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-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
      122.43         9.34       119.80        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       41.69        33.93        10.82        21.99         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       64.21         1.74        14.10        27.02        20.48        35.08 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       24.13         0.56        38.17        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
        9.57        11.77        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 
       86.30        71.34        79.20        11.74        18.84        30.12 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
       56.32        16.64        97.94        79.53       173.82       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      151.27        14.07        63.35         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-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       61.61        32.88        65.23        81.24        74.66         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       60.30        50.66        16.93        44.75        39.32         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 
        1.12        38.79         4.04        26.43         4.01         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 
        0.39         7.96         8.12         7.46         7.82         0.39 
TCGA-37-A5EL TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
       37.58       126.58       111.35        68.58        55.20        82.52 
TCGA-39-5027 TCGA-39-5030 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
      102.18         1.94        68.38        71.18        55.56        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       40.21        38.66        39.12        33.11        27.91        22.98 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       24.89        21.47         5.46         3.81        19.59        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       11.77         9.73        14.20        13.32        12.16        13.02 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
        9.83         4.44        10.65        13.91         0.39         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 
       29.95        28.34         5.46         8.75        27.45        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       18.25        21.90        18.48        14.53        31.27        30.41 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       19.76         6.51         0.10        17.49        33.24        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
        4.93         3.48        14.07         1.35         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW 
       13.81        10.36         9.93        20.25        15.81        19.23 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       13.32        18.74         0.26        14.47         0.03        13.25 
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-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 
       56.65        35.24        29.92        21.11        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-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 
       66.54        50.33        48.49        42.64         3.19        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
       23.57        26.83        52.67        70.13        70.42        68.15 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM 
       55.30       102.67        70.62        58.65        59.97        14.99 
TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       11.34        89.29        78.28        16.37        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-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 
        2.01         0.92        43.99        21.01        25.05         0.99 
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-66-2782 TCGA-66-2783 TCGA-66-2785 
        3.02         2.01        19.00        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-68-8251 TCGA-68-A59I TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 
        6.94        13.35        16.18        12.07        12.33        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       140.09         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       73.22        70.13         0.16        46.78        32.55         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       86.76        55.73        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 
       66.51        54.41        60.53        36.36       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 
      150.25        22.29         5.92        61.94        27.62         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       41.39        40.24         6.41        36.53        34.95        31.30 
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-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       31.56        26.79        30.64        34.52        10.09         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 
       13.22        22.45        16.77         3.09         2.01        15.39 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        7.76        36.59        38.14        12.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       30.28        34.13        30.97        19.86        24.36        30.48 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 
       19.73        27.16        16.21        15.85        15.29        29.92 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
       12.39         3.65        24.92         2.93        11.77        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-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        4.01         5.03        26.63        14.14        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       18.31        17.46        21.44        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       27.16        18.15         2.01        27.02        20.32        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.71        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54        64.54        57.30        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
       49.28        43.92        25.32        14.73        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
        3.65        33.07         3.72        43.89        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 
                       156.66                        173.82 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                       24.805                        21.275 
[1] "1.0 - 156.7 (24.8)" "0.0 - 173.8 (21.3)"
[1] "hr=" "1"  
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(2P25.3) MUTATED         0        9       14        0         2
  DEL PEAK  3(2P25.3) WILD-TYPE       2       80      138        2        63
                               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        85         2         53         16
                               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                            80
  STAGE IB                            14                           138
  STAGE II                             0                             2
  STAGE IIA                            2                            63
  STAGE IIB                           10                            85
  STAGE III                            1                             2
  STAGE IIIA                          10                            53
  STAGE IIIB                           3                            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  3(2P25.3) MUTATED    10  27   6   7
  DEL PEAK  3(2P25.3) WILD-TYPE 102 267  65  17
D33V4, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  T1                          10                           102
  T2                          27                           267
  T3                           6                            65
  T4                           7                            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   8   1
  DEL PEAK  3(2P25.3) WILD-TYPE 287 122  32   4
D33V5, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  N0                          30                           287
  N1                          11                           122
  N2                           8                            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    43   1
  DEL PEAK  3(2P25.3) WILD-TYPE 368   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED     43    1
  DEL PEAK  3(2P25.3) WILD-TYPE  368    6
   clus
vv  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  0                          43                           368
  1                           1                             6
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED    16  34
  DEL PEAK  3(2P25.3) WILD-TYPE 114 337
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED     16   34
  DEL PEAK  3(2P25.3) WILD-TYPE  114  337
        clus
vv       DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  FEMALE                          16                           114
  MALE                            34                           337
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED    37   4
  DEL PEAK  3(2P25.3) WILD-TYPE 347  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED     37    4
  DEL PEAK  3(2P25.3) WILD-TYPE  347   49
     clus
vv    DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  NO                           37                           347
  YES                           4                            49
[1] 2 2
[1] FALSE
D33V9, 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 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                                                            48
  DEL PEAK  3(2P25.3) WILD-TYPE                                                         431
D33V10, multiclass
                                                             clus
vv                                                            DEL PEAK  3(2P25.3) MUTATED
  LUNG BASALOID 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)                          48
                                                             clus
vv                                                            DEL PEAK  3(2P25.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           431
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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 357  11   4  22
D33V13, multiclass
    clus
vv   DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  R0                          42                           357
  R1                           1                            11
  R2                           0                             4
  RX                           1                            22
[1] 4 2
[1] 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    35
  DEL PEAK  3(2P25.3) WILD-TYPE     7                        31   314
D33V14, multiclass
                           clus
vv                          DEL PEAK  3(2P25.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              35
                           clus
vv                          DEL PEAK  3(2P25.3) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            31
  WHITE                                               314
[1] 3 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  29
  DEL PEAK  3(2P25.3) WILD-TYPE   7 288
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      1   29
  DEL PEAK  3(2P25.3) WILD-TYPE    7  288
                        clus
vv                       DEL PEAK  3(2P25.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          29
                        clus
vv                       DEL PEAK  3(2P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           288
[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    76  54
  DEL PEAK  4(2Q22.1) WILD-TYPE 204 160
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                          130                           364 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                           54                           160 
$`DEL PEAK  4(2Q22.1) MUTATED`
TCGA-18-3406 TCGA-18-3416 TCGA-22-A5C4 TCGA-43-7657 TCGA-43-A474 TCGA-56-8305 
       12.20        31.99        22.06         7.76        11.61         3.45 
TCGA-56-A5DR TCGA-60-2715 TCGA-63-A5MH TCGA-94-A5I4 TCGA-NC-A5HR TCGA-NK-A5D1 
        0.13        35.34        66.61        16.14        40.90        16.80 
TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-21-1075 TCGA-21-1077 TCGA-21-1082 
       11.34        92.15        36.07        70.16        34.78       119.80 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
       31.63        88.11        33.93        10.82        21.99         7.33 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4604 TCGA-22-5474 TCGA-22-5477 
       35.08        48.33        24.13        13.12        14.63        44.25 
TCGA-22-5481 TCGA-33-4538 TCGA-33-4587 TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASJ 
       79.20        97.94        54.44        36.62         6.94       118.36 
TCGA-33-AASL TCGA-34-5231 TCGA-37-3783 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 
       27.16        65.23         4.01         8.12         6.81         0.39 
TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5035 TCGA-39-5037 TCGA-43-6770 
        3.39        37.58       133.25        68.38        55.56        21.47 
TCGA-43-8115 TCGA-43-8116 TCGA-46-3768 TCGA-46-6025 TCGA-51-4081 TCGA-52-7810 
       13.38        11.77         9.83        10.65        29.95        30.35 
TCGA-56-7223 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8503 TCGA-56-8629 
       14.53        17.49         3.48        26.89         1.35        15.81 
TCGA-56-A62T TCGA-58-8391 TCGA-58-8392 TCGA-58-A46K TCGA-58-A46M TCGA-60-2698 
       14.47        71.24        16.47        34.36        35.24        10.22 
TCGA-60-2713 TCGA-60-2722 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-A5MB 
       56.91        29.85        23.57        11.77        52.67       102.67 
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-70-6723 TCGA-77-6843 TCGA-77-7138 TCGA-77-7338 TCGA-77-7465 
       14.73        12.33        73.12        11.18         0.16        32.55 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8136 TCGA-77-8148 TCGA-85-7696 TCGA-85-7697 
        6.51        55.73        39.09        66.51        36.53        34.95 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       32.91         1.38         1.15        26.79        30.64        34.52 
TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8354 TCGA-85-8664 
       10.09        13.22        22.45        16.77        32.71        18.08 
TCGA-85-A4CL TCGA-85-A4JC TCGA-85-A512 TCGA-90-A4EE TCGA-92-8064 TCGA-92-8065 
       30.28        19.86        15.29        22.62         5.26         2.30 
TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-98-8023 TCGA-LA-A446 TCGA-LA-A7SW 
       26.63        17.69        71.01        21.34        13.18        13.41 
TCGA-MF-A522 TCGA-O2-A52N TCGA-O2-A52S TCGA-XC-AA0X 
       11.84        33.07        12.72         0.20 

$`DEL PEAK  4(2Q22.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
        4.47       123.19         4.80         6.18        27.19        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 
       14.93        48.82        60.66        64.93       129.01       133.74 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 
        1.55        19.76        31.50        28.96        31.27        17.88 
TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 TCGA-43-8118 TCGA-43-A56V TCGA-56-7221 
       22.49        18.38        78.18         2.93        12.03        19.99 
TCGA-56-8201 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 
       13.05        17.00        16.77        17.85        21.04         3.58 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
       41.42         9.01        32.32         8.02        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       30.81         9.50        14.07        21.04         0.16        18.38 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH 
       57.07        19.36         2.76         5.69        21.21        19.10 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A7XE TCGA-O2-A52W 
        0.07        76.80        39.85        65.65         0.43         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       75.75       117.57        23.54        92.42        86.96         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 
      154.32        49.94       119.54        46.88        99.16        60.89 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5784 
       15.58        31.73       122.43         9.34        43.23        41.69 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
        4.31        64.21         1.74        14.10        27.02        20.48 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
        0.56        38.17        34.75        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 
       11.77        63.55         0.79        86.30        71.34        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-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN 
      173.82       103.53       151.27        14.07        63.35         4.70 
TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
        0.30       110.99        44.19         2.63        61.61        32.88 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       81.24        74.66         9.07        60.30        50.66        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       44.75        39.32         4.96         1.12        38.79         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
       26.43        33.90         0.43         0.39         7.96         7.46 
TCGA-37-4133 TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        7.82        21.70       126.58       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       36.39        71.18        17.06        40.21        38.66        39.12 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 
       33.11        27.91        22.98        24.89         5.46         3.81 
TCGA-43-7656 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       19.59         9.73        14.20        13.32        12.16        13.02 
TCGA-46-3769 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 
        4.44        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        12.43        18.25        21.90 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       18.48        31.27        30.41        19.76         6.51         0.10 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 
       33.24        14.96         4.93        14.07         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BW 
       13.81        10.36         9.93        20.25        20.94        19.23 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       13.32        18.74         0.26         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 
       29.95        34.78        85.12        56.65        29.92        21.11 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       12.23        96.82        37.94        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       49.48        66.54        50.33        48.49        42.64         3.19 
TCGA-60-2723 TCGA-60-2725 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       35.90        26.83        70.13        70.42        68.15        55.30 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       70.62        58.65        45.57        14.99        11.34        25.28 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
       78.28        16.37        36.16        16.96        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-66-2759 TCGA-66-2765 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
       25.05         2.01         7.07        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2788 
       19.00        12.03        12.00        24.95         1.97        22.98 
TCGA-66-2789 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 
        4.04        30.02        54.08         4.01         2.73         6.64 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-70-6722 TCGA-77-6842 TCGA-77-6844 
        6.94        13.35        16.18        12.07        29.56        75.09 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       23.28       140.09         0.49        73.22        70.13       106.95 
TCGA-77-7463 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
       46.78        86.76        37.81       156.66        12.59        53.92 
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-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
       54.41        65.49        60.53        36.36       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH 
      150.25        22.29         5.92        61.94        27.62        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7698 TCGA-85-7844 
        9.67        41.39        40.24         6.41        31.30        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8287 
       18.94        25.15        19.04        24.13        31.56         0.76 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 
        5.29         3.09         2.01        15.39         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA 
       38.14        12.59        22.59        34.13        30.97        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       30.48        19.73        27.16        16.21        15.85        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 
       29.92        12.39         3.65        24.92         2.93        11.77 
TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-94-8035 
       20.22        10.59         2.70         3.48         4.01         4.01 
TCGA-94-8490 TCGA-94-A4VJ TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
        5.03        14.14        18.31        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       30.81        30.67        27.16        18.15         2.01        27.02 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HF 
       20.32        18.58        20.71        12.89        16.11         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
       64.54         1.22        57.30        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
       49.28        43.92        25.32        14.73        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB 
        3.65         3.72        43.89        11.18 

  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                         0.13                          0.03 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       133.25                        173.82 
  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE 
                       22.255                        21.325 
[1] "0.1 - 133.2 (22.3)" "0.0 - 173.8 (21.3)"
[1] "hr=" "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        26
  DEL PEAK  4(2Q22.1) WILD-TYPE       1       64      124        2        39
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(2Q22.1) MUTATED          26         1         18          4
  DEL PEAK  4(2Q22.1) WILD-TYPE        69         2         45         15
                               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                            64
  STAGE IB                            28                           124
  STAGE II                             0                             2
  STAGE IIA                           26                            39
  STAGE IIB                           26                            69
  STAGE III                            1                             2
  STAGE IIIA                          18                            45
  STAGE IIIB                           4                            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  4(2Q22.1) MUTATED    32  77  18   4
  DEL PEAK  4(2Q22.1) WILD-TYPE  80 217  53  20
D34V4, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  T1                          32                            80
  T2                          77                           217
  T3                          18                            53
  T4                           4                            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  4(2Q22.1) MUTATED    72  46  11   2
  DEL PEAK  4(2Q22.1) WILD-TYPE 245  87  29   3
D34V5, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  N0                          72                           245
  N1                          46                            87
  N2                          11                            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"
D34V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED   105   1
  DEL PEAK  4(2Q22.1) WILD-TYPE 306   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED    105    1
  DEL PEAK  4(2Q22.1) WILD-TYPE  306    6
   clus
vv  DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  0                         105                           306
  1                           1                             6
[1] 2 2
[1] FALSE
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED    27 104
  DEL PEAK  4(2Q22.1) WILD-TYPE 103 267
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     27  104
  DEL PEAK  4(2Q22.1) WILD-TYPE  103  267
        clus
vv       DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  FEMALE                          27                           103
  MALE                           104                           267
[1] 2 2
[1] FALSE
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q22.1) MUTATED    95  12
  DEL PEAK  4(2Q22.1) WILD-TYPE 289  41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED     95   12
  DEL PEAK  4(2Q22.1) WILD-TYPE  289   41
     clus
vv    DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  NO                           95                           289
  YES                          12                            41
[1] 2 2
[1] FALSE
D34V9, 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 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                                                           126
  DEL PEAK  4(2Q22.1) WILD-TYPE                                                         353
D34V10, multiclass
                                                             clus
vv                                                            DEL PEAK  4(2Q22.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         126
                                                             clus
vv                                                            DEL PEAK  4(2Q22.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           353
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous
D34V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(2Q22.1) MUTATED   106   3   0   9
  DEL PEAK  4(2Q22.1) WILD-TYPE 293   9   4  14
D34V13, multiclass
    clus
vv   DEL PEAK  4(2Q22.1) MUTATED DEL PEAK  4(2Q22.1) WILD-TYPE
  R0                         106                           293
  R1                           3                             9
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q22.1) MUTATED       1                        10    89
  DEL PEAK  4(2Q22.1) WILD-TYPE     8                        21   260
D34V14, multiclass
                           clus
vv                          DEL PEAK  4(2Q22.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              89
                           clus
vv                          DEL PEAK  4(2Q22.1) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               260
[1] 3 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  85
  DEL PEAK  4(2Q22.1) WILD-TYPE   7 232
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q22.1) MUTATED      1   85
  DEL PEAK  4(2Q22.1) WILD-TYPE    7  232
                        clus
vv                       DEL PEAK  4(2Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          85
                        clus
vv                       DEL PEAK  4(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           232
[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    90  66
  DEL PEAK  5(2Q37.1) WILD-TYPE 190 148
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                          156                           338 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                           66                           148 
$`DEL PEAK  5(2Q37.1) MUTATED`
TCGA-18-4083 TCGA-33-4532 TCGA-33-4533 TCGA-34-2605 TCGA-43-2578 TCGA-43-7657 
        6.18       129.01       133.74        28.96        22.49         7.76 
TCGA-43-8118 TCGA-56-8201 TCGA-56-8305 TCGA-56-8504 TCGA-56-A4BY TCGA-60-2696 
        2.93        13.05         3.45        16.77        17.85         3.58 
TCGA-60-2711 TCGA-60-2712 TCGA-63-A5MH TCGA-68-8250 TCGA-94-A5I4 TCGA-96-7545 
       41.42         9.01        66.61         8.02        16.14        57.07 
TCGA-96-A4JK TCGA-98-8020 TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HR TCGA-18-3415 
       19.36         2.76        19.10        76.80        40.90        92.15 
TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-21-1070 TCGA-21-1075 TCGA-21-1083 
       36.07        86.96         2.79       119.54        70.16        43.23 
TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 
       33.93        21.99         7.33         1.74        14.10        27.02 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4613 TCGA-22-5474 TCGA-22-5477 
       34.75        13.12        32.02        11.77        14.63        44.25 
TCGA-22-5481 TCGA-22-5482 TCGA-22-5491 TCGA-33-4538 TCGA-33-4582 TCGA-33-AAS8 
       79.20        11.74        56.32        97.94       103.53        36.62 
TCGA-33-AASJ TCGA-34-5231 TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-7107 
      118.36        65.23         9.07        50.66        16.93         1.12 
TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5029 TCGA-39-5035 TCGA-39-5036 
        0.39        37.58        21.70        24.33        68.38        71.18 
TCGA-39-5037 TCGA-43-3394 TCGA-43-6143 TCGA-43-8115 TCGA-43-A56U TCGA-46-3765 
       55.56        39.12        22.98        13.38        14.20        13.32 
TCGA-51-4081 TCGA-52-7810 TCGA-52-7811 TCGA-56-7579 TCGA-56-7582 TCGA-56-7823 
       29.95        30.35         8.75        31.27        19.76        33.24 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T 
        3.48        26.89        15.81        20.94        18.74        14.47 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L TCGA-60-2713 TCGA-60-2722 
       16.47        34.78        34.36        56.65        56.91        29.85 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MP TCGA-63-A5MR 
       55.30       102.67        58.65        59.97        25.28        89.29 
TCGA-63-A5MY TCGA-66-2727 TCGA-66-2755 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 
       34.59        16.96         0.92        21.01         0.99         1.02 
TCGA-66-2767 TCGA-66-2769 TCGA-66-2777 TCGA-66-2787 TCGA-66-2792 TCGA-66-2793 
        2.01         7.07         2.01        40.01        30.02        10.06 
TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J TCGA-70-6723 TCGA-77-6845 TCGA-77-7141 
       49.05         2.73        14.73        12.33        23.28         0.49 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8136 
       73.22       106.95        32.55         6.51        55.73        39.09 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-85-6798 
       66.51        54.41        65.49        60.53        36.36         6.41 
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-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8352 TCGA-85-8479 
       30.64        34.52        10.09        13.22         5.29        15.39 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A511 TCGA-85-A53L 
       18.08        22.59        34.13        19.73        14.96        12.39 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
        2.93        11.77        22.62         2.70         3.48         5.26 
TCGA-92-8065 TCGA-94-8491 TCGA-96-7544 TCGA-98-A53B TCGA-L3-A524 TCGA-LA-A446 
        2.30        26.63        71.01         2.01        16.11        13.18 
TCGA-NC-A5HG TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NK-A5CR TCGA-O2-A52Q TCGA-O2-A5IB 
       64.54        49.28        43.92        83.57         3.72        11.18 

$`DEL PEAK  5(2Q37.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 
       12.20         4.47       123.19         4.80        31.99        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 
        1.55        19.76        31.50        31.27        17.88        18.38 
TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8308 TCGA-56-A4ZJ 
       78.18        11.61        12.03        19.99        17.00        21.04 
TCGA-56-A5DR TCGA-60-2715 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
        0.13        35.34        32.32        20.78        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-98-A539 
        9.50        14.07        21.04         0.16        18.38         5.69 
TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE 
       21.21         0.07        39.85        65.65        16.80         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3419 
        8.58        75.75       117.57        11.34        23.54        92.42 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 
      154.32        49.94        46.88        99.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 
       15.58        31.73       122.43         9.34       119.80        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-1002 TCGA-22-1005 TCGA-22-4591 
       88.11        41.69        10.82         4.31        64.21        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4607 
       35.08        48.33        24.13         0.56        38.17        19.30 
TCGA-22-4609 TCGA-22-5473 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5483 
        9.57        63.55         0.79        86.30        71.34        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 
       30.12        62.86        16.64        79.53       173.82       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB 
       14.07        54.44        63.35         4.70         0.30         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
      110.99        44.19        27.16         2.63        61.61        32.88 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       81.24        74.66        60.30        44.75        39.32         4.96 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       38.79         4.04        26.43        33.90         4.01         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.39         7.96         8.12         7.46         7.82         6.81 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        3.39       133.25       126.58       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       82.52       102.18         1.71         1.94        60.53        36.39 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 
       17.06        40.21        38.66        33.11        27.91        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8116 TCGA-43-A475 
       21.47         5.46         3.81        19.59        11.77         9.73 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       12.16        13.02         9.83         4.44        10.65        13.91 
TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 TCGA-52-7809 TCGA-52-7812 TCGA-56-1622 
        0.39         0.39        28.34         5.46        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 
       12.43        18.25        21.90        18.48        14.53        30.41 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 TCGA-56-8083 TCGA-56-8309 
        6.51         0.10        17.49        14.96         4.93        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        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 
       20.25        19.23        13.32         0.26         0.03        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46M TCGA-58-A46N 
       13.55        29.95        71.24        85.12        35.24        29.92 
TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
       21.11        12.23        10.22        96.82        37.94        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2714 TCGA-60-2716 
       21.93        80.45        49.48        66.54        50.33        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       42.64         3.19        35.90        23.57        26.83        11.77 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5ML 
       52.67        70.13        70.42        68.15        70.62        45.57 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       14.99        11.34        78.28        16.37        36.16        53.88 
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-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2768 TCGA-66-2770 
        0.99        43.99        25.05         2.01         2.01        23.01 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
       19.00         3.02        19.00        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
       24.95         1.97        25.97        22.98         4.04        22.98 
TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
        5.03        54.08         4.01         6.64         6.94        13.35 
TCGA-68-A59I TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 
       16.18        12.07        29.56        73.12        75.09        11.18 
TCGA-77-7139 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-8008 TCGA-77-8128 
      140.09        70.13         0.16        46.78        86.76        37.81 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
      156.66        12.59        53.92        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       26.40        27.39         6.97       126.18       132.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       22.29         5.92        61.94        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
       41.39        40.24        29.95        18.94        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 
       24.13        31.56        26.79         0.76        22.45        16.77 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
        3.09        32.71         2.01         7.76        36.59        38.14 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       12.59        30.28        30.97        19.86        24.36        30.48 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 
       27.16        16.21        15.85        15.29        29.92         3.65 
TCGA-90-6837 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-8063 TCGA-94-8035 TCGA-94-8490 
       24.92        20.22        10.59         4.01         4.01         5.03 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       14.14        17.69        18.31        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C 
       30.81        30.67        21.34        27.16        18.15        27.02 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 
       20.32        18.58        20.71        12.89        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54         1.22        57.30        13.74         4.21         2.89 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52S 
       25.32        14.73        26.43         3.65        33.07        12.72 
TCGA-O2-A52V TCGA-XC-AA0X 
       43.89         0.20 

  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                         0.39                          0.03 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                       133.74                        173.82 
  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE 
                        22.80                         21.16 
[1] "0.4 - 133.7 (22.8)" "0.0 - 173.8 (21.2)"
[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        24
  DEL PEAK  5(2Q37.1) WILD-TYPE       2       62      105        1        41
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q37.1) MUTATED          30         2         20          6
  DEL PEAK  5(2Q37.1) WILD-TYPE        65         1         43         13
                               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                            62
  STAGE IB                            47                           105
  STAGE II                             1                             1
  STAGE IIA                           24                            41
  STAGE IIB                           30                            65
  STAGE III                            2                             1
  STAGE IIIA                          20                            43
  STAGE IIIB                           6                            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
  DEL PEAK  5(2Q37.1) MUTATED    35  96  21   7
  DEL PEAK  5(2Q37.1) WILD-TYPE  77 198  50  17
D35V4, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  T1                          35                            77
  T2                          96                           198
  T3                          21                            50
  T4                           7                            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    96  52  10   1
  DEL PEAK  5(2Q37.1) WILD-TYPE 221  81  30   4
D35V5, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  N0                          96                           221
  N1                          52                            81
  N2                          10                            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   128   1
  DEL PEAK  5(2Q37.1) WILD-TYPE 283   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED    128    1
  DEL PEAK  5(2Q37.1) WILD-TYPE  283    6
   clus
vv  DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  0                         128                           283
  1                           1                             6
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED    45 114
  DEL PEAK  5(2Q37.1) WILD-TYPE  85 257
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED     45  114
  DEL PEAK  5(2Q37.1) WILD-TYPE   85  257
        clus
vv       DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  FEMALE                          45                            85
  MALE                           114                           257
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.1) MUTATED   123  14
  DEL PEAK  5(2Q37.1) WILD-TYPE 261  39
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED    123   14
  DEL PEAK  5(2Q37.1) WILD-TYPE  261   39
     clus
vv    DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  NO                          123                           261
  YES                          14                            39
[1] 2 2
[1] FALSE
D35V9, 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 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                                                           151
  DEL PEAK  5(2Q37.1) WILD-TYPE                                                         328
D35V10, multiclass
                                                             clus
vv                                                            DEL PEAK  5(2Q37.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         151
                                                             clus
vv                                                            DEL PEAK  5(2Q37.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
D35V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q37.1) MUTATED   124   4   0   9
  DEL PEAK  5(2Q37.1) WILD-TYPE 275   8   4  14
D35V13, multiclass
    clus
vv   DEL PEAK  5(2Q37.1) MUTATED DEL PEAK  5(2Q37.1) WILD-TYPE
  R0                         124                           275
  R1                           4                             8
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.1) MUTATED       2                        10   112
  DEL PEAK  5(2Q37.1) WILD-TYPE     7                        21   237
D35V14, multiclass
                           clus
vv                          DEL PEAK  5(2Q37.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                             112
                           clus
vv                          DEL PEAK  5(2Q37.1) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               237
[1] 3 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     3 100
  DEL PEAK  5(2Q37.1) WILD-TYPE   5 217
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.1) MUTATED      3  100
  DEL PEAK  5(2Q37.1) WILD-TYPE    5  217
                        clus
vv                       DEL PEAK  5(2Q37.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         100
                        clus
vv                       DEL PEAK  5(2Q37.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           217
[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   222 170
  DEL PEAK  6(3P25.3) WILD-TYPE  58  44
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                          392                           102 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                          170                            44 
$`DEL PEAK  6(3P25.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 
       32.19        14.93        60.66        64.93        22.06       129.01 
TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
        1.55        31.50        28.96         7.76        78.18         2.93 
TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 
       11.61        12.03        19.99        13.05         3.45        17.00 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 
       16.77        17.85        21.04         3.58        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA TCGA-77-A5GB 
       35.34        32.32        66.61         8.02        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
        9.50        14.07        21.04         0.16        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE 
       57.07        19.36         5.69        19.10         0.07        76.80 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       39.85        40.90        16.80         8.58        75.75       117.57 
TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       11.34        92.15        36.07         2.79       154.32        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 
      119.54        46.88        70.16        34.78        31.73       122.43 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
       43.23        31.63        88.11        33.93        10.82        21.99 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 
        7.33         4.31        14.10        27.02        20.48        48.33 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 
       24.13        38.17        34.75        13.12        32.02         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 
       11.77        63.55        44.25         0.79        86.30        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-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 
       97.94       103.53       151.27        14.07        54.44        63.35 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ 
        4.70         0.30        36.62         6.94       110.99       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       27.16         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
        9.07        60.30        16.93        44.75        39.32         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        1.12        38.79         4.04        26.43        33.90         4.01 
TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 
        0.43         7.96         8.12         7.46         7.82         6.81 
TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        0.39        37.58        21.70       133.25       126.58       111.35 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
       68.58        55.20        82.52       102.18         1.71         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 
       60.53        36.39        68.38        71.18        55.56        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 
       38.66        39.12        33.11        22.98        21.47        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6026 
       13.38        11.77        12.16        13.02         9.83        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-56-7222 TCGA-56-7223 TCGA-56-7579 
       28.96        12.43        18.25        18.48        14.53        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       30.41        19.76         6.51         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       14.96         4.93         3.48        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.81        13.81         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       19.23        13.32        18.74         0.26        14.47         0.03 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K 
       13.55        29.95        71.24        16.47        34.78        34.36 
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-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 
       80.45        49.48        66.54        56.91        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 
       29.85        35.90        23.57        26.83        11.77        70.13 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ 
       70.42        68.15        55.30       102.67        58.65        59.97 
TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       45.57        25.28        89.29        78.28        16.37        36.16 
TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2754 
       53.88        16.96        43.10         2.01        21.07         2.01 
TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 
        0.92         0.99        43.99        21.01         0.99         2.01 
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-66-2783 
        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-68-8251 TCGA-68-A59I TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 
        6.94        13.35        16.18        12.07        12.33        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       140.09         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
       73.22        70.13       106.95         0.16        46.78        32.55 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
       86.76        55.73        37.81       156.66        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-77-8154 TCGA-77-8156 TCGA-77-A5G1 
       66.51        54.41        65.49        60.53        36.36       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH 
      150.25        22.29         5.92        61.94        27.62        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 
        9.67        41.39        40.24         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        26.79        30.64        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 
       36.59        18.08        22.59        30.28        34.13        30.97 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       19.86        30.48        19.73        16.21        15.85        14.96 
TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE 
       15.29        12.39         3.65         2.93        20.22        22.62 
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-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
        5.03        17.69        71.01        18.31        17.46        27.68 
TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I 
       30.81        30.67        27.16        18.15         2.01        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF 
       20.71        12.89        13.18        13.41        11.84         4.54 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       64.54        57.30        13.74        49.28        43.92        25.32 
TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       14.73        83.57         3.65         3.72        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

$`DEL PEAK  6(3P25.3) WILD-TYPE`
TCGA-18-5595 TCGA-22-1017 TCGA-33-4533 TCGA-33-6737 TCGA-34-2609 TCGA-39-5039 
       27.19        48.82       133.74        19.76        31.27        17.88 
TCGA-43-2578 TCGA-43-5668 TCGA-56-A5DR TCGA-77-7140 TCGA-98-8020 TCGA-98-A53D 
       22.49        18.38         0.13        20.78         2.76        21.21 
TCGA-NK-A5CT TCGA-NK-A7XE TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-21-1072 
       65.65         0.43        23.54        92.42        86.96        99.16 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1081 TCGA-21-1082 TCGA-21-5784 TCGA-22-1005 
       60.89        15.58         9.34       119.80        41.69        64.21 
TCGA-22-1011 TCGA-22-4593 TCGA-22-4596 TCGA-22-4607 TCGA-22-5474 TCGA-22-5489 
        1.74        35.08         0.56        19.30        14.63        62.86 
TCGA-33-4547 TCGA-33-4566 TCGA-33-AASI TCGA-34-5234 TCGA-34-5240 TCGA-37-3792 
       79.53       173.82        44.19        74.66        50.66         0.39 
TCGA-37-5819 TCGA-39-5029 TCGA-39-5040 TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 
        3.39        24.33        17.06        27.91        24.89         5.46 
TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3769 TCGA-46-6025 
        3.81         9.73        14.20        13.32         4.44        10.65 
TCGA-52-7810 TCGA-52-7812 TCGA-56-6545 TCGA-56-8623 TCGA-56-8625 TCGA-58-8387 
       30.35        27.45        21.90        22.75        10.36        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-63-6202 TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MY 
       48.49        52.67        70.62        14.99        11.34        34.59 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2759 TCGA-66-2766 TCGA-66-2789 TCGA-66-2794 
        0.99         1.02        25.05         1.02         4.04        54.08 
TCGA-68-A59J TCGA-77-8007 TCGA-77-8131 TCGA-77-A5FZ TCGA-85-7696 TCGA-85-7843 
       14.73         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        15.39        38.14        12.59 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-92-7340 
       24.36        27.16        29.92        24.92        11.77         2.70 
TCGA-94-8491 TCGA-94-A4VJ TCGA-98-7454 TCGA-98-8023 TCGA-98-A53C TCGA-98-A53H 
       26.63        14.14        21.44        21.34        27.02        20.32 
TCGA-L3-A524 TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HT TCGA-O2-A52N 
       16.11         1.22         4.21         2.89        26.43        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 
                       156.66                        173.82 
  DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE 
                       21.815                        21.670 
[1] "0.0 - 156.7 (21.8)" "0.1 - 173.8 (21.7)"
[1] "hr=" "1"  
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(3P25.3) MUTATED         1       70      126        2        51
  DEL PEAK  6(3P25.3) WILD-TYPE       1       19       26        0        14
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(3P25.3) MUTATED          71         3         51         15
  DEL PEAK  6(3P25.3) WILD-TYPE        24         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                            70                            19
  STAGE IB                           126                            26
  STAGE II                             2                             0
  STAGE IIA                           51                            14
  STAGE IIB                           71                            24
  STAGE III                            3                             0
  STAGE IIIA                          51                            12
  STAGE IIIB                          15                             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    89 230  60  19
  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                          89                            23
  T2                         230                            64
  T3                          60                            11
  T4                          19                             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   256 106  28   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                         256                            61
  N1                         106                            27
  N2                          28                            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   323   6
  DEL PEAK  6(3P25.3) WILD-TYPE  88   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED    323    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                         323                            88
  1                           6                             1
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P25.3) MUTATED   102 296
  DEL PEAK  6(3P25.3) WILD-TYPE  28  75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED    102  296
  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                         102                            28
  MALE                           296                            75
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P25.3) MUTATED   305  43
  DEL PEAK  6(3P25.3) WILD-TYPE  79  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED    305   43
  DEL PEAK  6(3P25.3) WILD-TYPE   79   10
     clus
vv    DEL PEAK  6(3P25.3) MUTATED DEL PEAK  6(3P25.3) WILD-TYPE
  NO                          305                            79
  YES                          43                            10
[1] 2 2
[1] FALSE
D36V9, 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 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                                                           384
  DEL PEAK  6(3P25.3) WILD-TYPE                                                          95
D36V10, multiclass
                                                             clus
vv                                                            DEL PEAK  6(3P25.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         384
                                                             clus
vv                                                            DEL PEAK  6(3P25.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
D36V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(3P25.3) MUTATED   317   8   4  18
  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                         317                            82
  R1                           8                             4
  R2                           4                             0
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P25.3) MUTATED       6                        26   271
  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                                             271
                           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     6 249
  DEL PEAK  6(3P25.3) WILD-TYPE   2  68
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P25.3) MUTATED      6  249
  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                         249
                        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   242 186
  DEL PEAK  7(3P13) WILD-TYPE  38  28
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                        428                          66 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                        186                          28 
$`DEL PEAK  7(3P13) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
      129.01       133.74         1.55        31.50        28.96        31.27 
TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
       22.49         7.76        78.18         2.93        11.61        12.03 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY 
       19.99        13.05         3.45        17.00        16.77        17.85 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 
       21.04         0.13         3.58        41.42         9.01        32.32 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 
       66.61         8.02        42.08        30.81         9.50        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       21.04         0.16        18.38        16.14        57.07        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        2.76         5.69        19.10         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       40.90        65.65        16.80         8.58        75.75       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        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 
        2.79       154.32        49.94       119.54        46.88        70.16 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       34.78        31.73       122.43       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       88.11        33.93        10.82        21.99         7.33         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-22-4607 TCGA-22-4609 TCGA-22-4613 
       34.75        13.12        32.02        19.30         9.57        11.77 
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        86.30        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-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       16.64        97.94        79.53       103.53       151.27        14.07 
TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       54.44        63.35         4.70         0.30        36.62         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-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 
       32.88        65.23        81.24         9.07        60.30        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       44.75        39.32         4.96         1.12        38.79         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 
       26.43        33.90         4.01         0.43         7.96         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
        7.46         7.82         6.81         0.39         3.39        37.58 
TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
       21.70       133.25       126.58       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       36.39        68.38        71.18        40.21        38.66        39.12 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-8115 
       33.11        27.91        22.98        21.47        19.59        13.38 
TCGA-43-8116 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 
       11.77        13.32        12.16        13.02         9.83        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        12.43        18.25 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
       21.90        18.48        14.53        31.27        30.41        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
        6.51         0.10        17.49        33.24        14.96         4.93 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8624 TCGA-56-8625 
        3.48        26.89        14.07         1.35        13.81        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-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       18.74         0.26        14.47         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-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
       35.24        21.11        10.22        96.82        37.94        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 
       21.93        80.45        49.48        66.54        56.91        42.64 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
       29.85        35.90        23.57        26.83        11.77        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MI 
       70.13        70.42        68.15        55.30       102.67        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-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 
       16.37        36.16        34.59        16.96        43.10        21.07 
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-66-2765 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-66-2780 TCGA-66-2781 
       19.00         3.02         2.01        19.00        12.03         3.98 
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-66-2790 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-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
        4.01         2.73         6.64         6.94        13.35        16.18 
TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       14.73        12.07        12.33        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       140.09         0.49        73.22        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        32.55        86.76        55.73 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       37.81       156.66        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        66.51        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 
       65.49        60.53        36.36       132.36       150.25        22.29 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
        5.92        61.94        27.62        38.86         9.67        41.39 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       40.24         6.41        36.53        34.95        31.30        32.91 
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-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       31.56        26.79        30.64        34.52        10.09         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       13.22        22.45        16.77         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       15.39         7.76        36.59        18.08        22.59        30.28 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z 
       34.13        30.97        19.86        30.48        19.73        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 
       15.85        14.96        15.29        12.39         3.65         2.93 
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-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        2.30         4.01         5.03        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       71.01        18.31        17.46        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       27.16        18.15         2.01        18.58        20.71        12.89 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       13.18        13.41        11.84         4.54        64.54        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       13.74         4.21         2.89        49.28        43.92        25.32 
TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       14.73        83.57         3.65         3.72        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

$`DEL PEAK  7(3P13) WILD-TYPE`
TCGA-18-5595 TCGA-33-6737 TCGA-39-5039 TCGA-43-5668 TCGA-60-2715 TCGA-77-7140 
       27.19        19.76        17.88        18.38        35.34        20.78 
TCGA-98-A53D TCGA-NK-A7XE TCGA-21-1072 TCGA-21-1076 TCGA-21-1078 TCGA-21-1081 
       21.21         0.43        99.16        60.89        15.58         9.34 
TCGA-21-5784 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 TCGA-22-4596 TCGA-33-4566 
       41.69        64.21         1.74        35.08         0.56       173.82 
TCGA-34-5234 TCGA-34-5240 TCGA-37-3792 TCGA-39-5037 TCGA-39-5040 TCGA-43-6647 
       74.66        50.66         0.39        55.56        17.06        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U TCGA-46-3769 TCGA-56-8622 
        5.46         3.81         9.73        14.20         4.44         1.81 
TCGA-56-8623 TCGA-58-A46J TCGA-58-A46N TCGA-60-2697 TCGA-60-2714 TCGA-60-2716 
       22.75        85.12        29.92        12.23        50.33        48.49 
TCGA-60-2720 TCGA-63-A5MG TCGA-63-A5MN TCGA-63-A5MW TCGA-66-2737 TCGA-66-2744 
        3.19        70.62        11.34        53.88         2.01         0.99 
TCGA-66-2753 TCGA-66-2763 TCGA-66-2800 TCGA-77-8007 TCGA-77-8131 TCGA-77-A5FZ 
        1.02         0.99        49.05         6.51        12.59       126.18 
TCGA-85-8048 TCGA-85-8352 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4PA TCGA-85-A50M 
       25.15         5.29        38.14        12.59        24.36        27.16 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-92-7340 TCGA-96-A4JL TCGA-98-7454 
       29.92        24.92        11.77         2.70        27.68        21.44 
TCGA-98-A53C TCGA-98-A53H TCGA-L3-A524 TCGA-NC-A5HH TCGA-NC-A5HT TCGA-O2-A52N 
       27.02        20.32        16.11         1.22        26.43        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 
                     156.66                      173.82 
  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE 
                     21.960                      20.995 
[1] "0.0 - 156.7 (22.0)" "0.4 - 173.8 (21.0)"
[1] "hr=" "1.1"
D37V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(3P13) MUTATED         1       79      131        2        55
  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          78         3         59         16
  DEL PEAK  7(3P13) WILD-TYPE        17         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                          79                          10
  STAGE IB                         131                          21
  STAGE II                           2                           0
  STAGE IIA                         55                          10
  STAGE IIB                         78                          17
  STAGE III                          3                           0
  STAGE IIIA                        59                           4
  STAGE IIIB                        16                           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    99 251  64  20
  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                        99                          13
  T2                       251                          43
  T3                        64                           7
  T4                        20                           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   275 114  36   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                       275                          42
  N1                       114                          19
  N2                        36                           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   354   7
  DEL PEAK  7(3P13) WILD-TYPE  57   0
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3P13) MUTATED    354    7
  DEL PEAK  7(3P13) WILD-TYPE   57    0
   clus
vv  DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  0                       354                          57
  1                         7                           0
[1] 2 2
[1] FALSE
D37V7, binary
                             cls
clus                            0   1
  DEL PEAK  7(3P13) MUTATED   111 323
  DEL PEAK  7(3P13) WILD-TYPE  19  48
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3P13) MUTATED    111  323
  DEL PEAK  7(3P13) WILD-TYPE   19   48
        clus
vv       DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  FEMALE                       111                          19
  MALE                         323                          48
[1] 2 2
[1] FALSE
D37V8, binary
                             cls
clus                            0   1
  DEL PEAK  7(3P13) MUTATED   335  47
  DEL PEAK  7(3P13) WILD-TYPE  49   6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3P13) MUTATED    335   47
  DEL PEAK  7(3P13) WILD-TYPE   49    6
     clus
vv    DEL PEAK  7(3P13) MUTATED DEL PEAK  7(3P13) WILD-TYPE
  NO                        335                          49
  YES                        47                           6
[1] 2 2
[1] FALSE
D37V9, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK  7(3P13) MUTATED                                      12
  DEL PEAK  7(3P13) WILD-TYPE                                     3
                             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                                                           418
  DEL PEAK  7(3P13) WILD-TYPE                                                          61
D37V10, multiclass
                                                             clus
vv                                                            DEL PEAK  7(3P13) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                              12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       418
                                                             clus
vv                                                            DEL PEAK  7(3P13) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous
D37V12, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  7(3P13) MUTATED   347   8   4  19
  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                       347                          52
  R1                         8                           4
  R2                         4                           0
  RX                        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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P13) MUTATED       6                        30   299
  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                                           299
                           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     8 272
  DEL PEAK  7(3P13) WILD-TYPE   0  45
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3P13) MUTATED      8  272
  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                       272                          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   240 181
  DEL PEAK  8(3P12.3) WILD-TYPE  40  33
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          421                            73 
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                          181                            33 
$`DEL PEAK  8(3P12.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
      129.01       133.74         1.55        31.50        28.96        31.27 
TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
       22.49         7.76        78.18         2.93        11.61        12.03 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY 
       19.99        13.05         3.45        17.00        16.77        17.85 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 
       21.04         0.13         3.58        41.42         9.01        32.32 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 
       66.61         8.02        42.08        30.81         9.50        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       21.04         0.16        18.38        16.14        57.07        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        2.76         5.69        19.10         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       40.90        65.65        16.80         8.58        75.75       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        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 
        2.79       154.32        49.94       119.54        46.88        70.16 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       31.73       122.43       119.80        43.23        31.63        88.11 
TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 
       33.93        21.99         7.33         4.31        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-22-5473 
       13.12        32.02        19.30         9.57        11.77        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        86.30        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-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       97.94        79.53       103.53       151.27        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       63.35         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-34-2608 
       44.19       118.36        27.16         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 
       65.23        81.24         9.07        60.30        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       39.32         4.96         1.12        38.79         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       33.90         4.01         0.43         7.96         8.12         7.46 
TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        7.82         0.39         3.39        37.58        21.70       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
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        68.38        71.18 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       40.21        38.66        39.12        33.11        27.91        22.98 
TCGA-43-6770 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-46-3765 TCGA-46-3766 
       21.47        19.59        13.38        11.77        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
       13.02         9.83        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-56-7222 TCGA-56-7223 
       28.96        12.43        18.25        21.90        18.48        14.53 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
       31.27        30.41        19.76         6.51         0.10        17.49 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
       33.24        14.96         4.93         3.48        26.89        14.07 
TCGA-56-8503 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
        1.35        13.81        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       20.94        19.23        13.32        18.74         0.26        14.47 
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-60-2698 TCGA-60-2703 
       34.36        56.65        35.24        21.11        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-60-2713 TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       56.91        42.64        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       11.77        52.67        70.13        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MP 
      102.67        58.65        59.97        45.57        14.99        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 
       89.29        78.28        16.37        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-66-2766 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-66-2771 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-66-2782 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-66-2790 TCGA-66-2791 TCGA-66-2792 
       40.01        22.98         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-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 
        6.94        13.35        16.18        14.73        12.07        12.33 
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       140.09 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        0.49        73.22        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 
       32.55        86.76        55.73       156.66        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        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 
       54.41        65.49        60.53        36.36       132.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       22.29         5.92        61.94        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       41.39        40.24         6.41        36.53        34.95        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
       32.91         1.38         1.15        29.95        18.94        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       24.13        31.56        26.79        30.64        34.52        10.09 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 
        0.76        13.22        22.45        16.77         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 
        2.01        15.39         7.76        36.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR 
       30.28        34.13        30.97        19.86        30.48        19.73 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 
       16.21        15.85        15.29        12.39         3.65         2.93 
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-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        2.30         4.01         5.03        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       71.01        18.31        17.46        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       27.16        18.15         2.01        18.58        20.71        12.89 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       13.18        13.41        11.84         4.54        64.54        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       13.74         4.21         2.89        49.28        43.92        25.32 
TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       14.73         3.65         3.72        12.72        43.89        11.18 
TCGA-XC-AA0X 
        0.20 

$`DEL PEAK  8(3P12.3) WILD-TYPE`
TCGA-18-5595 TCGA-33-6737 TCGA-39-5039 TCGA-43-5668 TCGA-60-2715 TCGA-77-7140 
       27.19        19.76        17.88        18.38        35.34        20.78 
TCGA-98-A53D TCGA-NK-A7XE TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       21.21         0.43        99.16        60.89        34.78        15.58 
TCGA-21-1081 TCGA-21-5784 TCGA-21-5787 TCGA-22-1005 TCGA-22-1011 TCGA-22-4596 
        9.34        41.69        10.82        64.21         1.74         0.56 
TCGA-33-4566 TCGA-34-5234 TCGA-34-5240 TCGA-37-3792 TCGA-37-4135 TCGA-39-5031 
      173.82        74.66        50.66         0.39         6.81        60.53 
TCGA-39-5037 TCGA-39-5040 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-A475 
       55.56        17.06        24.89         5.46         3.81         9.73 
TCGA-43-A56U TCGA-46-3769 TCGA-56-8622 TCGA-56-8623 TCGA-58-8393 TCGA-58-A46J 
       14.20         4.44         1.81        22.75        34.78        85.12 
TCGA-58-A46N TCGA-60-2697 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-63-A5MG 
       29.92        12.23        50.33        48.49         3.19        70.62 
TCGA-63-A5MN TCGA-63-A5MW TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2763 
       11.34        53.88         2.01         0.99         1.02         0.99 
TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 TCGA-77-8143 TCGA-77-A5FZ TCGA-85-8048 
        6.51        37.81        12.59        26.40       126.18        25.15 
TCGA-85-8352 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A511 
        5.29        38.14        12.59        24.36        27.16        14.96 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 TCGA-92-7340 TCGA-96-A4JL TCGA-98-7454 
       29.92        24.92        11.77         2.70        27.68        21.44 
TCGA-98-A53C TCGA-98-A53H TCGA-L3-A524 TCGA-NC-A5HH TCGA-NC-A5HT TCGA-NK-A5CR 
       27.02        20.32        16.11         1.22        26.43        83.57 
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 
                       156.66                        173.82 
  DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE 
                        21.93                         21.21 
[1] "0.0 - 156.7 (21.9)" "0.4 - 173.8 (21.2)"
[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       78      128        2        56
  DEL PEAK  8(3P12.3) WILD-TYPE       1       11       24        0         9
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P12.3) MUTATED          76         3         56         17
  DEL PEAK  8(3P12.3) WILD-TYPE        19         0          7          2
                               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                            78                            11
  STAGE IB                           128                            24
  STAGE II                             2                             0
  STAGE IIA                           56                             9
  STAGE IIB                           76                            19
  STAGE III                            3                             0
  STAGE IIIA                          56                             7
  STAGE IIIB                          17                             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  8(3P12.3) MUTATED    98 244  64  21
  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                          98                            14
  T2                         244                            50
  T3                          64                             7
  T4                          21                             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   273 112  33   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                         273                            44
  N1                         112                            21
  N2                          33                             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   348   7
  DEL PEAK  8(3P12.3) WILD-TYPE  63   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.3) MUTATED    348    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                         348                            63
  1                           7                             0
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.3) MUTATED   109 318
  DEL PEAK  8(3P12.3) WILD-TYPE  21  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.3) MUTATED    109  318
  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                         109                            21
  MALE                           318                            53
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P12.3) MUTATED   331  45
  DEL PEAK  8(3P12.3) WILD-TYPE  53   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.3) MUTATED    331   45
  DEL PEAK  8(3P12.3) WILD-TYPE   53    8
     clus
vv    DEL PEAK  8(3P12.3) MUTATED DEL PEAK  8(3P12.3) WILD-TYPE
  NO                          331                            53
  YES                          45                             8
[1] 2 2
[1] FALSE
D38V9, 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 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                                                           411
  DEL PEAK  8(3P12.3) WILD-TYPE                                                          68
D38V10, multiclass
                                                             clus
vv                                                            DEL PEAK  8(3P12.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         411
                                                             clus
vv                                                            DEL PEAK  8(3P12.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
D38V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(3P12.3) MUTATED   341   8   4  19
  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                         341                            58
  R1                           8                             4
  R2                           4                             0
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P12.3) MUTATED       6                        29   296
  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                                             296
                           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     8 266
  DEL PEAK  8(3P12.3) WILD-TYPE   0  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P12.3) MUTATED      8  266
  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                         266
                        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   235 180
  DEL PEAK  9(3P12.3) WILD-TYPE  45  34
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                          415                            79 
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                          180                            34 
$`DEL PEAK  9(3P12.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
      129.01       133.74         1.55        31.50        28.96        31.27 
TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
       22.49         7.76        78.18         2.93        11.61        12.03 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY 
       19.99        13.05         3.45        17.00        16.77        17.85 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 
       21.04         0.13         3.58        41.42         9.01        32.32 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 
       66.61         8.02        42.08        30.81         9.50        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       21.04         0.16        18.38        16.14        57.07        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        2.76         5.69        19.10         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 
       40.90        65.65        16.80         8.58        75.75       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        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 
        2.79       154.32        49.94       119.54        46.88        70.16 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       31.73       122.43       119.80        43.23        31.63        88.11 
TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 
       33.93        21.99         7.33         4.31        14.10        27.02 
TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       20.48        48.33        24.13        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       32.02        19.30         9.57        11.77        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        86.30        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 
       18.84        30.12        62.86        56.32        16.64        97.94 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 
       79.53       103.53       151.27        14.07        54.44        63.35 
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-34-2608 TCGA-34-5231 
      118.36        27.16         2.63        61.61        32.88        65.23 
TCGA-34-5232 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       81.24         9.07        60.30        16.93        44.75        39.32 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
        4.96         1.12        38.79         4.04        26.43        33.90 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        4.01         0.43         7.96         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        6.81         0.39         3.39        37.58        21.70       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 
      126.58       111.35        68.58        55.20       102.18         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        68.38        71.18        40.21 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 
       38.66        39.12        33.11        27.91        22.98        21.47 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       19.59        13.38        11.77        13.32        12.16        13.02 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        9.83        10.65        13.91         0.39         0.39        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-56-7222 TCGA-56-7223 TCGA-56-7579 
       12.43        18.25        21.90        18.48        14.53        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       30.41        19.76         6.51         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       14.96         4.93         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 
       13.81        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       19.23        13.32        18.74         0.26        14.47         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-60-2698 TCGA-60-2703 TCGA-60-2704 
       56.65        35.24        21.11        10.22        96.82        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       92.71        21.93        80.45        49.48        66.54        56.91 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 
       42.64        29.85        35.90        23.57        26.83        11.77 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB 
       52.67        70.13        70.42        68.15        55.30       102.67 
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-A5MV TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       78.28        16.37        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-66-2767 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-66-2773 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-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
       24.95        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-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
        2.73         6.64         6.94        13.35        16.18        14.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       12.07        12.33        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       140.09         0.49        73.22        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        32.55        86.76        55.73       156.66 
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        66.51        54.41        65.49        60.53        36.36 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      132.36       150.25        22.29         5.92        61.94        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       38.86         9.67        41.39        40.24         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-85-8071 TCGA-85-8072 TCGA-85-8276 
       18.94        19.04        24.13        26.79        30.64        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        15.39         7.76        36.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ 
       22.59        30.28        34.13        30.97        19.86        30.48 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 
       19.73        16.21        15.85        15.29        12.39         3.65 
TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 
        2.93        20.22        22.62        10.59         3.48         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        5.26         2.30         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-8021 TCGA-98-8022 
       17.69        71.01        18.31        17.46        30.81        30.67 
TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       21.34        18.15         2.01        18.58        20.71        12.89 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       13.18        13.41        11.84         4.54        64.54        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       13.74         4.21         2.89        49.28        43.92        25.32 
TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       14.73         3.65         3.72        12.72        43.89        11.18 
TCGA-XC-AA0X 
        0.20 

$`DEL PEAK  9(3P12.3) WILD-TYPE`
TCGA-18-5595 TCGA-33-6737 TCGA-39-5039 TCGA-43-5668 TCGA-60-2715 TCGA-77-7140 
       27.19        19.76        17.88        18.38        35.34        20.78 
TCGA-98-A53D TCGA-NK-A7XE TCGA-21-1072 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
       21.21         0.43        99.16        60.89        34.78        15.58 
TCGA-21-1081 TCGA-21-5784 TCGA-21-5787 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 
        9.34        41.69        10.82        64.21         1.74        35.08 
TCGA-22-4596 TCGA-33-4566 TCGA-34-5234 TCGA-34-5240 TCGA-37-3792 TCGA-39-5024 
        0.56       173.82        74.66        50.66         0.39        82.52 
TCGA-39-5031 TCGA-39-5037 TCGA-39-5040 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 
       60.53        55.56        17.06        24.89         5.46         3.81 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3769 TCGA-56-8622 TCGA-56-8623 TCGA-58-8393 
        9.73        14.20         4.44         1.81        22.75        34.78 
TCGA-58-A46J TCGA-58-A46N TCGA-60-2697 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 
       85.12        29.92        12.23        50.33        48.49         3.19 
TCGA-63-A5MG TCGA-63-A5MN TCGA-63-A5MW TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 
       70.62        11.34        53.88         2.01         0.99         1.02 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2781 TCGA-66-2785 TCGA-77-8007 TCGA-77-8128 
        0.99         1.02         3.98         1.97         6.51        37.81 
TCGA-77-8131 TCGA-77-8143 TCGA-77-A5FZ TCGA-85-8048 TCGA-85-8070 TCGA-85-8352 
       12.59        26.40       126.18        25.15        31.56         5.29 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A511 TCGA-85-A513 
       38.14        12.59        24.36        27.16        14.96        29.92 
TCGA-90-6837 TCGA-90-7769 TCGA-92-7340 TCGA-96-A4JL TCGA-98-7454 TCGA-98-A538 
       24.92        11.77         2.70        27.68        21.44        27.16 
TCGA-98-A53C TCGA-98-A53H TCGA-L3-A524 TCGA-NC-A5HH TCGA-NC-A5HT TCGA-NK-A5CR 
       27.02        20.32        16.11         1.22        26.43        83.57 
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 
                       156.66                        173.82 
  DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE 
                        21.90                         21.44 
[1] "0.0 - 156.7 (21.9)" "0.4 - 173.8 (21.4)"
[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       78      126        2        55
  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          75         3         54         17
  DEL PEAK  9(3P12.3) WILD-TYPE        20         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                            78                            11
  STAGE IB                           126                            26
  STAGE II                             2                             0
  STAGE IIA                           55                            10
  STAGE IIB                           75                            20
  STAGE III                            3                             0
  STAGE IIIA                          54                             9
  STAGE IIIB                          17                             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    98 239  63  21
  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                          98                            14
  T2                         239                            55
  T3                          63                             8
  T4                          21                             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   269 112  31   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                         269                            48
  N1                         112                            21
  N2                          31                             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   342   7
  DEL PEAK  9(3P12.3) WILD-TYPE  69   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.3) MUTATED    342    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                         342                            69
  1                           7                             0
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P12.3) MUTATED   108 313
  DEL PEAK  9(3P12.3) WILD-TYPE  22  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.3) MUTATED    108  313
  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                         108                            22
  MALE                           313                            58
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(3P12.3) MUTATED   327  45
  DEL PEAK  9(3P12.3) WILD-TYPE  57   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.3) MUTATED    327   45
  DEL PEAK  9(3P12.3) WILD-TYPE   57    8
     clus
vv    DEL PEAK  9(3P12.3) MUTATED DEL PEAK  9(3P12.3) WILD-TYPE
  NO                          327                            57
  YES                          45                             8
[1] 2 2
[1] FALSE
D39V9, 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 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                                                           405
  DEL PEAK  9(3P12.3) WILD-TYPE                                                          74
D39V10, multiclass
                                                             clus
vv                                                            DEL PEAK  9(3P12.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         405
                                                             clus
vv                                                            DEL PEAK  9(3P12.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
D39V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(3P12.3) MUTATED   335   8   4  19
  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                         335                            64
  R1                           8                             4
  R2                           4                             0
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3P12.3) MUTATED       6                        29   293
  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                                             293
                           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     8 264
  DEL PEAK  9(3P12.3) WILD-TYPE   0  53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(3P12.3) MUTATED      8  264
  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                         264
                        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  27
  DEL PEAK 10(3Q11.1) WILD-TYPE 230 187
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                           77                           417 
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                           27                           187 
$`DEL PEAK 10(3Q11.1) MUTATED`
TCGA-22-1017 TCGA-33-4533 TCGA-33-4589 TCGA-43-A474 TCGA-56-8308 TCGA-56-8504 
       48.82       133.74         1.55        11.61        17.00        16.77 
TCGA-60-2711 TCGA-63-A5MH TCGA-77-A5GB TCGA-94-A5I4 TCGA-96-7545 TCGA-NK-A5CT 
       41.42        66.61        30.81        16.14        57.07        65.65 
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-22-4594 TCGA-33-4583 TCGA-33-6738 
      119.80        21.99        27.02        48.33       151.27        63.35 
TCGA-33-AASJ TCGA-34-5232 TCGA-37-4129 TCGA-37-4132 TCGA-37-5819 TCGA-39-5019 
      118.36        81.24         7.96         7.46         3.39       111.35 
TCGA-43-8115 TCGA-46-3767 TCGA-46-6025 TCGA-46-6026 TCGA-52-7811 TCGA-52-7812 
       13.38        13.02        10.65        13.91         8.75        27.45 
TCGA-56-1622 TCGA-56-7579 TCGA-56-A4BX TCGA-56-A5DS TCGA-60-2719 TCGA-63-A5MP 
       28.96        31.27        13.32         0.26        42.64        25.28 
TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2754 TCGA-66-2767 TCGA-66-2781 TCGA-66-2794 
       16.37        34.59         2.01         2.01         3.98        54.08 
TCGA-66-2800 TCGA-68-7755 TCGA-68-8251 TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 
       49.05         2.73        13.35        14.73        12.33        29.56 
TCGA-77-8130 TCGA-77-8138 TCGA-77-A5G1 TCGA-77-A5GH TCGA-85-6175 TCGA-85-7697 
      156.66        17.72       132.36        38.86         9.67        34.95 
TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8354 TCGA-85-8481 TCGA-85-8666 
       19.04        26.79        30.64        32.71         7.76        22.59 
TCGA-85-A4CN TCGA-90-A4ED TCGA-92-7341 TCGA-98-8022 TCGA-98-8023 TCGA-LA-A7SW 
       34.13        20.22         3.48        30.67        21.34        13.41 
TCGA-NC-A5HF TCGA-NC-A5HO TCGA-NK-A5CR TCGA-O2-A52S TCGA-O2-A52V 
        4.54        43.92        83.57        12.72        43.89 

$`DEL PEAK 10(3Q11.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       27.19        32.19        14.93        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 
      129.01        19.76        31.50        28.96        31.27        17.88 
TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A56V 
       22.49        18.38         7.76        78.18         2.93        12.03 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
       19.99        13.05         3.45        17.85        21.04         0.13 
TCGA-60-2696 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 
        3.58         9.01        35.34        32.32         8.02        20.78 
TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       42.08         9.50        14.07        21.04         0.16        18.38 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       19.36         2.76         5.69        21.21        19.10         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W 
       76.80        39.85        40.90        16.80         0.43         8.58 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       23.54        92.15        92.42        86.96         2.79       154.32 
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-21-1080 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 
       15.58       122.43         9.34        43.23        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
       41.69        33.93        10.82         7.33         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 
        1.74        14.10        20.48        35.08        24.13         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-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       11.77        63.55        14.63        44.25         0.79        86.30 
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-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
       56.32        16.64        97.94        79.53       173.82       103.53 
TCGA-33-4586 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       14.07        54.44         4.70         0.30        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
      110.99        44.19        27.16         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       65.23        74.66         9.07        60.30        50.66        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       44.75        39.32         4.96         1.12        38.79         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 
       26.43        33.90         4.01         0.43         0.39         8.12 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        7.82         6.81         0.39        37.58        21.70       133.25 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      126.58        68.58        55.20        82.52       102.18         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       24.33         1.94        60.53        36.39        68.38        71.18 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       55.56        17.06        40.21        38.66        39.12        33.11 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       27.91        22.98        24.89        21.47         5.46         3.81 
TCGA-43-7656 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       19.59        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3768 TCGA-46-3769 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        9.83         4.44         0.39         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 
        5.46        30.35        12.43        18.25        21.90        18.48 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 
       14.53        30.41        19.76         6.51         0.10        17.49 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
       33.24        14.96         4.93         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        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A62T 
       20.25        15.81        20.94        19.23        18.74        14.47 
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-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-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
       21.11        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-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       48.49         3.19        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       11.77        52.67        70.13        70.42        68.15        55.30 
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-A5MV TCGA-63-A5MW TCGA-66-2727 
       11.34        89.29        78.28        36.16        53.88        16.96 
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-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        0.99        43.99        21.01        25.05         0.99         2.01 
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-66-2782 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-66-2793 TCGA-66-2795 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I 
       30.02        10.06         4.01         6.64         6.94        16.18 
TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 
       12.07        73.12        75.09        23.28        11.18       140.09 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
        0.49        73.22        70.13       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 
       32.55         6.51        86.76        55.73        37.81        12.59 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       53.92        39.09       104.09        11.54        26.40        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        6.97        66.51        54.41        65.49        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      126.18       150.25        22.29         5.92        61.94        27.62 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 
       41.39        40.24         6.41        36.53        31.30        32.91 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 
        1.38         1.15        29.95        18.94        25.15        24.13 
TCGA-85-8070 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       31.56        34.52        10.09         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 
       16.77         5.29         3.09         2.01        15.39        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC 
       38.14        12.59        18.08        30.28        30.97        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       24.36        30.48        19.73        27.16        16.21        15.85 
TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       14.96        15.29        29.92        12.39         3.65        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
        2.93        11.77        22.62        10.59         2.70         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        5.26         2.30         4.01         5.03        26.63        14.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       17.69        71.01        18.31        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       30.81        27.16        18.15         2.01        27.02        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
       18.58        20.71        12.89        16.11        13.18        11.84 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
       64.54         1.22        57.30        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52N 
       49.28        25.32        14.73        26.43         3.65        33.07 
TCGA-O2-A52Q TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        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 
                       156.66                        173.82 
  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE 
                        27.02                         21.11 
[1] "0.3 - 156.7 (27.0)" "0.0 - 173.8 (21.1)"
[1] "hr=" "1.5"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(3Q11.1) MUTATED         0       10       25        1         9
  DEL PEAK 10(3Q11.1) WILD-TYPE       2       79      127        1        56
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(3Q11.1) MUTATED          15         1         11          4
  DEL PEAK 10(3Q11.1) WILD-TYPE        80         2         52         15
                               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                            79
  STAGE IB                            25                           127
  STAGE II                             1                             1
  STAGE IIA                            9                            56
  STAGE IIB                           15                            80
  STAGE III                            1                             2
  STAGE IIIA                          11                            52
  STAGE IIIB                           4                            15
  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  44  15   4
  DEL PEAK 10(3Q11.1) WILD-TYPE  96 250  56  20
D40V4, multiclass
    clus
vv   DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  T1                          16                            96
  T2                          44                           250
  T3                          15                            56
  T4                           4                            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 10(3Q11.1) MUTATED    48  21   8   1
  DEL PEAK 10(3Q11.1) WILD-TYPE 269 112  32   4
D40V5, multiclass
    clus
vv   DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  N0                          48                           269
  N1                          21                           112
  N2                           8                            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"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(3Q11.1) MUTATED    60   2
  DEL PEAK 10(3Q11.1) WILD-TYPE 351   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3Q11.1) MUTATED     60    2
  DEL PEAK 10(3Q11.1) WILD-TYPE  351    5
   clus
vv  DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  0                          60                           351
  1                           2                             5
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(3Q11.1) MUTATED    20  59
  DEL PEAK 10(3Q11.1) WILD-TYPE 110 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3Q11.1) MUTATED     20   59
  DEL PEAK 10(3Q11.1) WILD-TYPE  110  312
        clus
vv       DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  FEMALE                          20                           110
  MALE                            59                           312
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(3Q11.1) MUTATED    58  13
  DEL PEAK 10(3Q11.1) WILD-TYPE 326  40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3Q11.1) MUTATED     58   13
  DEL PEAK 10(3Q11.1) WILD-TYPE  326   40
     clus
vv    DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  NO                           58                           326
  YES                          13                            40
[1] 2 2
[1] FALSE
D40V9, 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 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                                                            77
  DEL PEAK 10(3Q11.1) WILD-TYPE                                                         402
D40V10, multiclass
                                                             clus
vv                                                            DEL PEAK 10(3Q11.1) MUTATED
  LUNG BASALOID 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)                          77
                                                             clus
vv                                                            DEL PEAK 10(3Q11.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  15
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           402
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
D40V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(3Q11.1) MUTATED    62   1   1   3
  DEL PEAK 10(3Q11.1) WILD-TYPE 337  11   3  20
D40V13, multiclass
    clus
vv   DEL PEAK 10(3Q11.1) MUTATED DEL PEAK 10(3Q11.1) WILD-TYPE
  R0                          62                           337
  R1                           1                            11
  R2                           1                             3
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(3Q11.1) MUTATED       1                         5    52
  DEL PEAK 10(3Q11.1) WILD-TYPE     8                        26   297
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                                               297
[1] 3 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   4 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(3Q11.1) MUTATED      4   51
  DEL PEAK 10(3Q11.1) WILD-TYPE    4  266
                        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                           266
[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   177 135
  DEL PEAK 11(4P15.2) WILD-TYPE 103  79
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          312                           182 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                          135                            79 
$`DEL PEAK 11(4P15.2) MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 
        4.47        31.99        14.93        60.66        64.93       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-43-2578 TCGA-43-7657 
      133.74         1.55        19.76        28.96        22.49         7.76 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 
        2.93        11.61        12.03        19.99        13.05        17.00 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH 
        0.13         3.58        41.42         9.01        32.32        66.61 
TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7557 TCGA-94-7943 
       42.08        30.81         9.50        14.07         0.16        18.38 
TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HE 
       16.14        19.36         2.76         5.69         0.07        76.80 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 
       39.85        40.90        65.65         8.58       117.57        11.34 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 
       92.15        36.07        86.96         2.79        49.94       119.54 
TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       46.88        60.89        34.78        31.73       122.43         9.34 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 
      119.80        43.23        31.63        33.93        10.82        21.99 
TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 
        7.33         1.74        14.10        35.08        48.33        24.13 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       38.17        13.12        32.02        19.30         9.57        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 
       63.55        14.63        44.25        86.30        11.74        18.84 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
       30.12        62.86        56.32        97.94        79.53       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 
      151.27        14.07        54.44        63.35         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-34-5231 TCGA-34-5232 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       65.23        81.24         9.07        16.93        44.75        39.32 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 
        4.96         1.12        26.43         4.01         0.43         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 
        6.81         0.39         3.39        37.58        21.70       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5031 TCGA-39-5035 TCGA-39-5037 
      111.35        68.58       102.18        60.53        68.38        55.56 
TCGA-39-5040 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6771 TCGA-43-6773 
       17.06        39.12        27.91        22.98         5.46         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-A56U TCGA-46-3765 TCGA-46-3767 TCGA-46-3768 
       19.59        13.38        14.20        13.32        13.02         9.83 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
       10.65        13.91        29.95         5.46        30.35         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 
       27.45        28.96        18.25        21.90        18.48        14.53 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 
       31.27        19.76         6.51        33.24         4.93         3.48 
TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A62T 
       10.36        20.94        19.23        13.32        18.74        14.47 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
        0.03        13.25        16.47        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 
       56.65        35.24        21.11        10.22        96.82        92.71 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 
       21.93        80.45        49.48        66.54        56.91        42.64 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 
        3.19        29.85        35.90        23.57        11.77        70.13 
TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MR 
       70.42        55.30       102.67        59.97        45.57        89.29 
TCGA-63-A5MS TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       78.28        34.59        16.96        43.10         2.01        21.07 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 TCGA-66-2766 
        1.02         2.01        21.01        25.05         2.01         1.02 
TCGA-66-2767 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        2.01        19.00         3.02         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 TCGA-66-2786 TCGA-66-2791 TCGA-66-2792 
        3.98        24.95         1.97        25.97         5.03        30.02 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59J 
       54.08         4.01        49.05         2.73         6.64        14.73 
TCGA-70-6723 TCGA-77-6845 TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       12.33        23.28       140.09        73.22        70.13       106.95 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 
       46.78        32.55        55.73        37.81       156.66        53.92 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       17.72       104.09        27.39         6.97        66.51        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
       65.49        60.53       150.25         5.92        61.94        27.62 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       38.86        41.39        40.24        36.53        34.95        31.30 
TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
       32.91         1.15        25.15        19.04        24.13        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
       30.64        34.52        10.09        13.22        22.45        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 
        5.29         3.09        32.71         7.76        36.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A510 TCGA-85-A511 
       22.59        30.28        34.13        19.73        15.85        14.96 
TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       15.29        12.39         3.65        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 
        2.70         3.48         4.01         5.26         2.30         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-98-7454 TCGA-98-8021 TCGA-98-A538 
        5.03        26.63        17.69        21.44        30.81        27.16 
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-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ 
       13.41        11.84         4.54        64.54        57.30        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
        4.21         2.89        49.28        43.92        25.32        14.73 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       83.57         3.65        12.72        43.89        11.18         0.20 

$`DEL PEAK 11(4P15.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
       12.20       123.19         4.80         6.18        27.19        32.19 
TCGA-22-1017 TCGA-22-A5C4 TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 
       48.82        22.06        31.50        31.27        17.88        18.38 
TCGA-43-7658 TCGA-56-8305 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2715 
       78.18         3.45        16.77        17.85        21.04        35.34 
TCGA-68-8250 TCGA-77-7140 TCGA-94-7033 TCGA-96-7545 TCGA-98-A53D TCGA-J1-A4AH 
        8.02        20.78        21.04        57.07        21.21        19.10 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3414 TCGA-18-3419 TCGA-18-4721 
       16.80         0.43        75.75        23.54        92.42       154.32 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 TCGA-21-5783 TCGA-21-5784 TCGA-22-1002 
       99.16        70.16        15.58        88.11        41.69         4.31 
TCGA-22-1005 TCGA-22-1016 TCGA-22-4591 TCGA-22-4596 TCGA-22-4601 TCGA-22-5478 
       64.21        27.02        20.48         0.56        34.75         0.79 
TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 TCGA-33-4566 TCGA-33-A5GW TCGA-34-2596 
       71.34        79.20        16.64       173.82         0.30         2.63 
TCGA-34-2608 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 TCGA-34-8455 
       32.88        74.66        60.30        50.66        38.79         4.04 
TCGA-34-A5IX TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-39-5011 
       33.90         0.39         7.96         8.12         7.46       133.25 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 
       55.20        82.52         1.71        24.33         1.94        36.39 
TCGA-39-5036 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 
       71.18        40.21        38.66        33.11        24.89        21.47 
TCGA-43-8116 TCGA-43-A475 TCGA-46-3766 TCGA-46-3769 TCGA-51-4079 TCGA-51-4080 
       11.77         9.73        12.16         4.44         0.39         0.39 
TCGA-52-7622 TCGA-56-5897 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 
       28.34        12.43        30.41         0.10        17.49        14.96 
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        13.81 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A5DS TCGA-58-8388 TCGA-58-8390 
        9.93        20.25        15.81         0.26        13.55        29.95 
TCGA-58-8391 TCGA-58-A46N TCGA-60-2697 TCGA-60-2704 TCGA-60-2714 TCGA-60-2716 
       71.24        29.92        12.23        37.94        50.33        48.49 
TCGA-60-2725 TCGA-63-6202 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM 
       26.83        52.67        68.15        70.62        58.65        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2744 
       11.34        25.28        16.37        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-68-8251 TCGA-68-A59I TCGA-70-6722 TCGA-77-6842 
       10.06         6.94        13.35        16.18        12.07        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7141 TCGA-77-7338 TCGA-77-8007 
       73.12        75.09        11.18         0.49         0.16         6.51 
TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8140 TCGA-77-8143 TCGA-77-8156 
       86.76        12.59        39.09        11.54        26.40        36.36 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-85-6175 TCGA-85-6798 TCGA-85-7710 
      126.18       132.36        22.29         9.67         6.41         1.38 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8070 TCGA-85-8287 TCGA-85-8355 TCGA-85-8479 
       29.95        18.94        31.56         0.76         2.01        15.39 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ 
       38.14        12.59        30.97        19.86        24.36        30.48 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A513 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 
       27.16        16.21        29.92        24.92         2.93        11.77 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8022 
       14.14        71.01        18.31        17.46        27.68        30.67 
TCGA-98-8023 TCGA-98-A53C TCGA-98-A53H TCGA-LA-A446 TCGA-NC-A5HH TCGA-NC-A5HT 
       21.34        27.02        20.32        13.18         1.22        26.43 
TCGA-O2-A52N TCGA-O2-A52Q 
       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 
                       156.66                        173.82 
  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE 
                       22.220                        21.125 
[1] "0.0 - 156.7 (22.2)" "0.1 - 173.8 (21.1)"
[1] "hr=" "1.1"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(4P15.2) MUTATED         1       48      104        2        45
  DEL PEAK 11(4P15.2) WILD-TYPE       1       41       48        0        20
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4P15.2) MUTATED          54         2         41         12
  DEL PEAK 11(4P15.2) WILD-TYPE        41         1         22          7
                               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                            48                            41
  STAGE IB                           104                            48
  STAGE II                             2                             0
  STAGE IIA                           45                            20
  STAGE IIB                           54                            41
  STAGE III                            2                             1
  STAGE IIIA                          41                            22
  STAGE IIIB                          12                             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
  DEL PEAK 11(4P15.2) MUTATED    64 194  46  12
  DEL PEAK 11(4P15.2) WILD-TYPE  48 100  25  12
D41V4, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  T1                          64                            48
  T2                         194                           100
  T3                          46                            25
  T4                          12                            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   195  85  28   4
  DEL PEAK 11(4P15.2) WILD-TYPE 122  48  12   1
D41V5, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  N0                         195                           122
  N1                          85                            48
  N2                          28                            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   259   4
  DEL PEAK 11(4P15.2) WILD-TYPE 152   3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED    259    4
  DEL PEAK 11(4P15.2) WILD-TYPE  152    3
   clus
vv  DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  0                         259                           152
  1                           4                             3
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P15.2) MUTATED    76 240
  DEL PEAK 11(4P15.2) WILD-TYPE  54 131
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED     76  240
  DEL PEAK 11(4P15.2) WILD-TYPE   54  131
        clus
vv       DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  FEMALE                          76                            54
  MALE                           240                           131
[1] 2 2
[1] FALSE
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(4P15.2) MUTATED   240  40
  DEL PEAK 11(4P15.2) WILD-TYPE 144  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED    240   40
  DEL PEAK 11(4P15.2) WILD-TYPE  144   13
     clus
vv    DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  NO                          240                           144
  YES                          40                            13
[1] 2 2
[1] FALSE
D41V9, 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 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                                                           305
  DEL PEAK 11(4P15.2) WILD-TYPE                                                         174
D41V10, multiclass
                                                             clus
vv                                                            DEL PEAK 11(4P15.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         305
                                                             clus
vv                                                            DEL PEAK 11(4P15.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           174
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
D41V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4P15.2) MUTATED   250   7   4  15
  DEL PEAK 11(4P15.2) WILD-TYPE 149   5   0   8
D41V13, multiclass
    clus
vv   DEL PEAK 11(4P15.2) MUTATED DEL PEAK 11(4P15.2) WILD-TYPE
  R0                         250                           149
  R1                           7                             5
  R2                           4                             0
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4P15.2) MUTATED       3                        23   221
  DEL PEAK 11(4P15.2) WILD-TYPE     6                         8   128
D41V14, multiclass
                           clus
vv                          DEL PEAK 11(4P15.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          23
  WHITE                                             221
                           clus
vv                          DEL PEAK 11(4P15.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               128
[1] 3 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     5 194
  DEL PEAK 11(4P15.2) WILD-TYPE   3 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4P15.2) MUTATED      5  194
  DEL PEAK 11(4P15.2) WILD-TYPE    3  123
                        clus
vv                       DEL PEAK 11(4P15.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         194
                        clus
vv                       DEL PEAK 11(4P15.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           123
[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   159 123
  DEL PEAK 12(4Q22.1) WILD-TYPE 121  91
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          282                           212 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                          123                            91 
$`DEL PEAK 12(4Q22.1) MUTATED`
TCGA-18-3407 TCGA-18-4083 TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 
        4.47         6.18        14.93        60.66        64.93       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 
      133.74         1.55        19.76        28.96        31.27        22.49 
TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 
        7.76        78.18        11.61        12.03        19.99        13.05 
TCGA-56-8308 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2712 TCGA-77-A5GA 
       17.00        21.04         0.13         3.58         9.01        42.08 
TCGA-77-A5GB TCGA-90-7964 TCGA-94-7557 TCGA-94-7943 TCGA-96-A4JK TCGA-98-8020 
       30.81        14.07         0.16        18.38        19.36         2.76 
TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT 
        5.69        19.10         0.07        39.85        40.90        65.65 
TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-4086 
       16.80         8.58       117.57        11.34        92.15         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-22-1011 TCGA-22-1012 TCGA-22-4594 
       33.93        10.82         7.33         1.74        14.10        48.33 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
       24.13        38.17        13.12        32.02        19.30        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       63.55        14.63        86.30        11.74        18.84        30.12 
TCGA-22-5489 TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       62.86        97.94       173.82       103.53       151.27        14.07 
TCGA-33-4587 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 
       54.44         4.70        36.62       118.36        27.16         2.63 
TCGA-34-2600 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       61.61         9.07        16.93        44.75        39.32         4.96 
TCGA-34-7107 TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        1.12         4.01         0.43         7.82         6.81         0.39 
TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 
        3.39        37.58        21.70       111.35        68.58       102.18 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 
       60.53        36.39        68.38        71.18        17.06        40.21 
TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
       39.12        33.11        22.98        21.47         5.46        19.59 
TCGA-43-8115 TCGA-43-A56U TCGA-46-3765 TCGA-46-3768 TCGA-46-6026 TCGA-51-4079 
       13.38        14.20        13.32         9.83        13.91         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-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 
       21.90        18.48        14.53        19.76         6.51        33.24 
TCGA-56-8304 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A62T TCGA-58-8390 
        3.48        10.36        20.94        13.32        14.47        29.95 
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-60-2695 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       21.11        92.71        21.93        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 
       56.91        50.33        42.64         3.19        35.90        23.57 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MB 
       11.77        52.67        70.13        70.42        55.30       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-70-6722 TCGA-70-6723 TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       12.07        12.33        73.12       140.09         0.49        73.22 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 
       70.13       106.95        46.78        32.55         6.51        55.73 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8144 
       37.81       156.66        53.92        39.09        17.72        27.39 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G6 TCGA-77-A5G7 
       66.51        54.41        65.49        60.53        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 
       61.94        27.62        38.86        41.39         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        15.39        36.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 
       18.08        22.59        34.13        30.48        19.73        15.85 
TCGA-85-A512 TCGA-85-A53L TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       15.29        12.39        11.77        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 
        2.70         3.48         4.01         5.26         2.30         4.01 
TCGA-94-A5I6 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53B 
       17.69        21.44        30.81        30.67        27.16         2.01 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF 
       18.58        20.71        16.11        13.41        11.84         4.54 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
       57.30         4.21         2.89        25.32        14.73        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       83.57         3.65         3.72        12.72        43.89         0.20 

$`DEL PEAK 12(4Q22.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI 
       12.20       123.19         4.80        31.99        27.19        32.19 
TCGA-22-1017 TCGA-22-A5C4 TCGA-34-2604 TCGA-39-5039 TCGA-43-5668 TCGA-43-8118 
       48.82        22.06        31.50        17.88        18.38         2.93 
TCGA-56-8305 TCGA-56-8504 TCGA-56-A4BY TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 
        3.45        16.77        17.85        41.42        35.34        32.32 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-90-7766 TCGA-94-7033 TCGA-94-A5I4 
       66.61         8.02        20.78         9.50        21.04        16.14 
TCGA-96-7545 TCGA-98-A53D TCGA-NC-A5HE TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3414 
       57.07        21.21        76.80         0.43        75.75        23.54 
TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-21-1078 TCGA-21-1081 TCGA-21-5782 
       36.07        92.42        86.96        15.58         9.34        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 
       88.11        41.69        21.99         4.31        64.21        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-4609 TCGA-22-5477 
       20.48        35.08         0.56        34.75         9.57        44.25 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 
        0.79        71.34        79.20        56.32        16.64        79.53 
TCGA-33-6738 TCGA-33-A5GW TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-34-2608 
       63.35         0.30         6.94       110.99        44.19        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 
       65.23        81.24        74.66        60.30        50.66        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
        4.04        26.43        33.90         0.39         7.96         8.12 
TCGA-37-4132 TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
        7.46       133.25       126.58        55.20        82.52         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5037 TCGA-43-2581 TCGA-43-5670 TCGA-43-6647 
       24.33         1.94        55.56        38.66        27.91        24.89 
TCGA-43-6773 TCGA-43-8116 TCGA-43-A475 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 
        3.81        11.77         9.73        12.16        13.02         4.44 
TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7812 TCGA-56-5897 TCGA-56-7579 
       10.65         0.39        28.34        27.45        12.43        31.27 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 TCGA-56-8083 TCGA-56-8307 
       30.41         0.10        17.49        14.96         4.93        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 
       14.07         1.35         1.81        22.75        13.81         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 
       20.25        15.81        19.23        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-60-2716 TCGA-60-2722 TCGA-60-2725 TCGA-63-7022 
       96.82        37.94        48.49        29.85        26.83        68.15 
TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MV TCGA-63-A5MY 
       58.65        14.99        11.34        25.28        36.16        34.59 
TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2759 TCGA-66-2766 TCGA-66-2767 
        0.99         0.92         0.99        25.05         1.02         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2782 TCGA-66-2783 TCGA-66-2788 
        2.01         7.07        23.01        12.00        24.95        22.98 
TCGA-66-2789 TCGA-66-2790 TCGA-66-2794 TCGA-68-8251 TCGA-77-6842 TCGA-77-6844 
        4.04        22.98        54.08        13.35        29.56        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7338 TCGA-77-8008 TCGA-77-8131 TCGA-77-8139 
       23.28        11.18         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        36.36       126.18       132.36 
TCGA-77-A5G3 TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 
      150.25         9.67        40.24        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        26.79        30.64 
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        38.14 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50M 
       12.59        30.28        30.97        19.86        24.36        27.16 
TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 
       16.21        14.96        29.92         3.65        24.92         2.93 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
        5.03        26.63        14.14        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-8023 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 
       27.68        21.34        18.15        27.02        20.32        12.89 
TCGA-LA-A446 TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HN TCGA-NC-A5HO 
       13.18        64.54         1.22        13.74        49.28        43.92 
TCGA-O2-A52N TCGA-O2-A5IB 
       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 
                       173.82                        150.25 
  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE 
                       21.275                        22.865 
[1] "0.1 - 173.8 (21.3)" "0.0 - 150.2 (22.9)"
[1] "hr=" "1.1"
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(4Q22.1) MUTATED         1       43      103        2        34
  DEL PEAK 12(4Q22.1) WILD-TYPE       1       46       49        0        31
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q22.1) MUTATED          47         2         40          9
  DEL PEAK 12(4Q22.1) WILD-TYPE        48         1         23         10
                               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                            46
  STAGE IB                           103                            49
  STAGE II                             2                             0
  STAGE IIA                           34                            31
  STAGE IIB                           47                            48
  STAGE III                            2                             1
  STAGE IIIA                          40                            23
  STAGE IIIB                           9                            10
  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    54 178  42  11
  DEL PEAK 12(4Q22.1) WILD-TYPE  58 116  29  13
D42V4, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  T1                          54                            58
  T2                         178                           116
  T3                          42                            29
  T4                          11                            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   186  71  24   2
  DEL PEAK 12(4Q22.1) WILD-TYPE 131  62  16   3
D42V5, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  N0                         186                           131
  N1                          71                            62
  N2                          24                            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   233   2
  DEL PEAK 12(4Q22.1) WILD-TYPE 178   5
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED    233    2
  DEL PEAK 12(4Q22.1) WILD-TYPE  178    5
   clus
vv  DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  0                         233                           178
  1                           2                             5
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED    79 206
  DEL PEAK 12(4Q22.1) WILD-TYPE  51 165
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED     79  206
  DEL PEAK 12(4Q22.1) WILD-TYPE   51  165
        clus
vv       DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  FEMALE                          79                            51
  MALE                           206                           165
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q22.1) MUTATED   215  33
  DEL PEAK 12(4Q22.1) WILD-TYPE 169  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED    215   33
  DEL PEAK 12(4Q22.1) WILD-TYPE  169   20
     clus
vv    DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  NO                          215                           169
  YES                          33                            20
[1] 2 2
[1] FALSE
D42V9, 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 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                                                           275
  DEL PEAK 12(4Q22.1) WILD-TYPE                                                         204
D42V10, multiclass
                                                             clus
vv                                                            DEL PEAK 12(4Q22.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         275
                                                             clus
vv                                                            DEL PEAK 12(4Q22.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
D42V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(4Q22.1) MUTATED   226   5   3  15
  DEL PEAK 12(4Q22.1) WILD-TYPE 173   7   1   8
D42V13, multiclass
    clus
vv   DEL PEAK 12(4Q22.1) MUTATED DEL PEAK 12(4Q22.1) WILD-TYPE
  R0                         226                           173
  R1                           5                             7
  R2                           3                             1
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(4Q22.1) MUTATED       4                        22   193
  DEL PEAK 12(4Q22.1) WILD-TYPE     5                         9   156
D42V14, multiclass
                           clus
vv                          DEL PEAK 12(4Q22.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          22
  WHITE                                             193
                           clus
vv                          DEL PEAK 12(4Q22.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                               156
[1] 3 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     4 177
  DEL PEAK 12(4Q22.1) WILD-TYPE   4 140
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q22.1) MUTATED      4  177
  DEL PEAK 12(4Q22.1) WILD-TYPE    4  140
                        clus
vv                       DEL PEAK 12(4Q22.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         177
                        clus
vv                       DEL PEAK 12(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           140
[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   185 139
  DEL PEAK 13(4Q32.3) WILD-TYPE  95  75
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                          324                           170 
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                          139                            75 
$`DEL PEAK 13(4Q32.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-4083 TCGA-22-1000 TCGA-22-5472 TCGA-22-A5C4 
       12.20         4.47         6.18        14.93        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 
      129.01       133.74         1.55        19.76        31.50        28.96 
TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
       22.49         7.76        78.18         2.93        11.61        12.03 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4ZJ TCGA-56-A5DR 
       19.99        13.05         3.45        17.00        21.04         0.13 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 
        3.58        41.42         9.01        32.32        66.61         8.02 
TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       20.78        42.08        30.81        14.07        21.04         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 
       18.38        16.14        57.07        19.36         2.76         5.69 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-O2-A52W 
        0.07        76.80        39.85        40.90        65.65         8.58 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-4086 TCGA-18-5592 
      117.57        11.34        92.15        36.07         2.79        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-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 
       31.73       122.43       119.80        43.23        31.63        33.93 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 
       10.82         7.33         1.74        14.10        27.02        48.33 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
       24.13        38.17        13.12        32.02        19.30        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       63.55        14.63        86.30        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       62.86        56.32        97.94       173.82       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       14.07        54.44         4.70         0.30        36.62         6.94 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-5236 TCGA-34-5241 
      118.36        27.16         2.63        61.61         9.07        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-A5IX TCGA-37-4129 
       44.75        39.32         4.96         1.12        33.90         7.96 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
        8.12         7.82         6.81         0.39         3.39        37.58 
TCGA-37-A5EN TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5034 
       21.70       133.25       111.35        68.58       102.18        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 
       68.38        71.18        55.56        17.06        40.21        39.12 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-8116 
       33.11        22.98         5.46         3.81        13.38        11.77 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       14.20        13.32        12.16         9.83        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-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 
       28.96        18.25        21.90        18.48        14.53        19.76 
TCGA-56-7730 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8503 
        6.51        33.24        14.96         4.93         3.48         1.35 
TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-58-8390 
       10.36        15.81        20.94        13.32        18.74        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-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 
       35.24        21.11        10.22        96.82        37.94        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
       80.45        49.48        56.91        50.33        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-63-7020 TCGA-63-7023 TCGA-63-A5MB 
       29.85        35.90        23.57        70.13        55.30       102.67 
TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       70.62        59.97        45.57        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
       16.37        53.88        34.59        16.96        43.10         2.01 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
       21.07         1.02         2.01         0.99        43.99        21.01 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 
        0.99         2.01         1.02        19.00         3.02         2.01 
TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 
       19.00        12.03         3.98         1.97        25.97        40.01 
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-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
        2.73         6.64         6.94        16.18        14.73        12.07 
TCGA-70-6723 TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
       12.33        73.12       140.09         0.49        73.22         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
       46.78        32.55         6.51        86.76        55.73        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 
      156.66        53.92        39.09        17.72        11.54        27.39 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 
       66.51        54.41        65.49        60.53        36.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
       22.29         5.92        61.94        27.62        38.86        41.39 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-8048 TCGA-85-8049 
       40.24         6.41        36.53        32.91        25.15        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 
       24.13        31.56        30.64        10.09         0.76        22.45 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 
        5.29         3.09        15.39        36.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z 
       30.28        34.13        30.97        30.48        19.73        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
       15.85        14.96        12.39         2.93        11.77        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-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-98-7454 
        4.01         5.03        14.14        17.69        71.01        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I 
       30.81        30.67        27.16        18.15         2.01        18.58 
TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF 
       20.71        16.11        13.18        13.41        11.84         4.54 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP 
       57.30         4.21         2.89        49.28        43.92        25.32 
TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       14.73        83.57         3.65        12.72        43.89         0.20 

$`DEL PEAK 13(4Q32.3) WILD-TYPE`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1017 
      123.19         4.80        31.99        27.19        32.19        48.82 
TCGA-22-5471 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-56-8504 TCGA-56-A4BY 
       60.66        31.27        17.88        18.38        16.77        17.85 
TCGA-60-2715 TCGA-90-7766 TCGA-98-A53D TCGA-J1-A4AH TCGA-NK-A5D1 TCGA-NK-A7XE 
       35.34         9.50        21.21        19.10        16.80         0.43 
TCGA-18-3408 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 TCGA-21-1078 
       75.75        23.54        92.42        86.96       154.32        15.58 
TCGA-21-1081 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 
        9.34        88.11        41.69        21.99         4.31        64.21 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 TCGA-22-4609 TCGA-22-5477 
       20.48        35.08         0.56        34.75         9.57        44.25 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 TCGA-33-4547 TCGA-33-6738 
        0.79        71.34        79.20        16.64        79.53        63.35 
TCGA-33-AASD TCGA-33-AASI TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
      110.99        44.19        32.88        65.23        81.24        74.66 
TCGA-34-5239 TCGA-34-5240 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 
       60.30        50.66        38.79         4.04        26.43         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4132 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 
        0.43         0.39         7.46       126.58        55.20        82.52 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-43-2581 TCGA-43-5670 
        1.71        24.33         1.94        60.53        38.66        27.91 
TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-A475 TCGA-46-3767 TCGA-46-3769 
       24.89        21.47        19.59         9.73        13.02         4.44 
TCGA-51-4080 TCGA-52-7812 TCGA-56-5897 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 
        0.39        27.45        12.43        31.27        30.41         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        13.81 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
        9.93        20.25        19.23         0.26        14.47         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-A46N TCGA-60-2697 TCGA-60-2706 TCGA-60-2710 
       13.25        13.55        29.92        12.23        92.71        66.54 
TCGA-60-2716 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 
       48.49        26.83        11.77        52.67        70.42        68.15 
TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MV TCGA-66-2744 TCGA-66-2755 
       58.65        14.99        11.34        36.16         0.99         0.92 
TCGA-66-2759 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2782 
       25.05         2.01         2.01         7.07        23.01        12.00 
TCGA-66-2783 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-68-8251 TCGA-77-6842 
       24.95        22.98         4.04        22.98        13.35        29.56 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7335 TCGA-77-7337 TCGA-77-8131 
       75.09        23.28        11.18        70.13       106.95        12.59 
TCGA-77-8139 TCGA-77-8143 TCGA-77-8145 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-85-6175 
      104.09        26.40         6.97       126.18       132.36         9.67 
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-85-8071 TCGA-85-8276 TCGA-85-8288 TCGA-85-8351 TCGA-85-8354 TCGA-85-8355 
       26.79        34.52        13.22        16.77        32.71         2.01 
TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A50M 
        7.76        38.14        12.59        19.86        24.36        27.16 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-92-7341 TCGA-94-8491 
       15.29        29.92         3.65        24.92         3.48        26.63 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8023 TCGA-98-A53C TCGA-98-A53H 
       18.31        17.46        27.68        21.34        27.02        20.32 
TCGA-L3-A4E7 TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HT TCGA-O2-A52N 
       12.89        64.54         1.22        13.74        26.43        33.07 
TCGA-O2-A52Q TCGA-O2-A5IB 
        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 
                       173.82                        154.32 
  DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE 
                        21.09                         22.98 
[1] "0.1 - 173.8 (21.1)" "0.0 - 154.3 (23.0)"
[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       55      115        2        34
  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          65         1         41         10
  DEL PEAK 13(4Q32.3) WILD-TYPE        30         2         22          9
                               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                            55                            34
  STAGE IB                           115                            37
  STAGE II                             2                             0
  STAGE IIA                           34                            31
  STAGE IIB                           65                            30
  STAGE III                            1                             2
  STAGE IIIA                          41                            22
  STAGE IIIB                          10                             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 13(4Q32.3) MUTATED    65 208  44  12
  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                          65                            47
  T2                         208                            86
  T3                          44                            27
  T4                          12                            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   215  84  25   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                         215                           102
  N1                          84                            49
  N2                          25                            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   270   3
  DEL PEAK 13(4Q32.3) WILD-TYPE 141   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q32.3) MUTATED    270    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                         270                           141
  1                           3                             4
[1] 2 2
[1] FALSE
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q32.3) MUTATED    90 239
  DEL PEAK 13(4Q32.3) WILD-TYPE  40 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q32.3) MUTATED     90  239
  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                          90                            40
  MALE                           239                           132
[1] 2 2
[1] FALSE
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q32.3) MUTATED   251  36
  DEL PEAK 13(4Q32.3) WILD-TYPE 133  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q32.3) MUTATED    251   36
  DEL PEAK 13(4Q32.3) WILD-TYPE  133   17
     clus
vv    DEL PEAK 13(4Q32.3) MUTATED DEL PEAK 13(4Q32.3) WILD-TYPE
  NO                          251                           133
  YES                          36                            17
[1] 2 2
[1] FALSE
D43V9, 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 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                                                           320
  DEL PEAK 13(4Q32.3) WILD-TYPE                                                         159
D43V10, multiclass
                                                             clus
vv                                                            DEL PEAK 13(4Q32.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         320
                                                             clus
vv                                                            DEL PEAK 13(4Q32.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous
D43V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(4Q32.3) MUTATED   265   6   2  16
  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                         265                           134
  R1                           6                             6
  R2                           2                             2
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(4Q32.3) MUTATED       4                        22   227
  DEL PEAK 13(4Q32.3) WILD-TYPE     5                         9   122
D43V14, multiclass
                           clus
vv                          DEL PEAK 13(4Q32.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          22
  WHITE                                             227
                           clus
vv                          DEL PEAK 13(4Q32.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             9
  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"
D43V15, binary
                               cls
clus                              0   1
  DEL PEAK 13(4Q32.3) MUTATED     5 206
  DEL PEAK 13(4Q32.3) WILD-TYPE   3 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(4Q32.3) MUTATED      5  206
  DEL PEAK 13(4Q32.3) WILD-TYPE    3  111
                        clus
vv                       DEL PEAK 13(4Q32.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         206
                        clus
vv                       DEL PEAK 13(4Q32.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           111
[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   181 146
  DEL PEAK 14(4Q35.2) WILD-TYPE  99  68
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          327                           167 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                          146                            68 
$`DEL PEAK 14(4Q35.2) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3416 TCGA-18-4083 TCGA-22-1000 TCGA-22-5472 
       12.20         4.47        31.99         6.18        14.93        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 
       22.06       129.01       133.74         1.55        19.76        31.50 
TCGA-34-2605 TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 
       28.96        22.49         7.76        78.18         2.93        11.61 
TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4ZJ 
       12.03        19.99        13.05         3.45        17.00        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2712 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 
        0.13         3.58         9.01        66.61         8.02        20.78 
TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       42.08        30.81        14.07        21.04         0.16        18.38 
TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HE 
       16.14        57.07        19.36         5.69         0.07        76.80 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-O2-A52W TCGA-18-3411 TCGA-18-3415 
       39.85        40.90        65.65         8.58       117.57        92.15 
TCGA-18-3417 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
       36.07         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-22-1011 
       43.23        31.63        33.93        10.82         7.33         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 
       14.10        27.02        48.33        24.13        38.17        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 
       32.02        19.30        11.77        63.55        14.63        86.30 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 
       11.74        18.84        30.12        62.86        56.32        97.94 
TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       79.53       173.82       103.53       151.27        14.07        54.44 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ 
        4.70         0.30        36.62         6.94        44.19       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5236 TCGA-34-5241 
       27.16         2.63        61.61        32.88         9.07        16.93 
TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 
       44.75         4.96         1.12        33.90         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        7.96         8.12         7.82         6.81         0.39         3.39 
TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 
       37.58        21.70       133.25       111.35        68.58       102.18 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
       36.39        68.38        71.18        55.56        17.06        40.21 
TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 
       39.12        33.11        22.98        24.89        21.47         5.46 
TCGA-43-6773 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 
        3.81        13.38        11.77         9.73        14.20        13.32 
TCGA-46-3766 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 
       12.16        10.65        13.91         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-7222 
        5.46        30.35         8.75        28.96        18.25        18.48 
TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
       14.53        19.76         6.51        33.24        14.96         4.93 
TCGA-56-8304 TCGA-56-8503 TCGA-56-8622 TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D 
        3.48         1.35         1.81        10.36        15.81        20.94 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       13.32        18.74        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2695 TCGA-60-2698 
       85.12        34.36        56.65        35.24        21.11        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2713 
       96.82        37.94        21.93        80.45        49.48        56.91 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       50.33        42.64         3.19        29.85        35.90        23.57 
TCGA-60-2726 TCGA-63-7020 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5ML 
       11.77        70.13        55.30       102.67        70.62        45.57 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY 
       25.28        89.29        78.28        16.37        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-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
        0.99        43.99        21.01         0.99         2.01         1.02 
TCGA-66-2769 TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        7.07         3.02         2.01        19.00        12.03         3.98 
TCGA-66-2785 TCGA-66-2787 TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 
        1.97        40.01         4.04         5.03        30.02        10.06 
TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
       54.08         4.01        49.05         2.73         6.64         6.94 
TCGA-68-A59I TCGA-68-A59J TCGA-70-6723 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 
       16.18        14.73        12.33        73.12        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
      140.09         0.49        73.22         0.16        46.78        32.55 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 
        6.51        86.76        55.73        37.81       156.66        53.92 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 
       39.09        17.72       104.09        11.54        27.39        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5G7 
       54.41        65.49        60.53        36.36        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       61.94        27.62        41.39        40.24         6.41        36.53 
TCGA-85-7698 TCGA-85-7699 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       31.30        32.91        25.15        19.04        24.13        31.56 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8352 
       30.64        34.52        10.09         0.76        22.45         5.29 
TCGA-85-8353 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 
        3.09        15.39         7.76        36.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       30.28        34.13        30.97        30.48        19.73        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-90-7769 TCGA-90-A4ED 
       16.21        15.85        14.96        12.39        11.77        20.22 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 
       22.62        10.59         4.01         2.30         4.01         5.03 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       14.14        17.69        71.01        21.44        30.81        30.67 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 
       27.16        18.15         2.01        18.58        20.71        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HI TCGA-NC-A5HK 
       13.18        13.41        11.84         4.54        57.30         4.21 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CX 
        2.89        49.28        43.92        25.32        14.73         3.65 
TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       12.72        43.89         0.20 

$`DEL PEAK 14(4Q35.2) WILD-TYPE`
TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1017 TCGA-22-5471 
      123.19         4.80        27.19        32.19        48.82        60.66 
TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-56-8504 TCGA-56-A4BY TCGA-60-2711 
       31.27        17.88        18.38        16.77        17.85        41.42 
TCGA-60-2715 TCGA-60-2721 TCGA-90-7766 TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH 
       35.34        32.32         9.50         2.76        21.21        19.10 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 TCGA-18-3419 
       16.80         0.43        75.75        11.34        23.54        92.42 
TCGA-18-3421 TCGA-18-4721 TCGA-21-1078 TCGA-21-1081 TCGA-21-5783 TCGA-21-5784 
       86.96       154.32        15.58         9.34        88.11        41.69 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 
       21.99         4.31        64.21        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-22-5492 TCGA-33-6738 TCGA-33-AASD TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       16.64        63.35       110.99        65.23        81.24        74.66 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       60.30        50.66        39.32        38.79         4.04        26.43 
TCGA-37-3783 TCGA-37-4132 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
        4.01         7.46       126.58        55.20        82.52         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-43-2581 TCGA-43-5670 TCGA-43-7656 
       24.33         1.94        60.53        38.66        27.91        19.59 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-51-4080 TCGA-52-7812 TCGA-56-5897 
       13.02         9.83         4.44         0.39        27.45        12.43 
TCGA-56-6545 TCGA-56-7579 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8307 
       21.90        31.27        30.41         0.10        17.49        26.89 
TCGA-56-8309 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW 
       14.07        22.75        13.81         9.93        20.25        19.23 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-A46N 
        0.26        14.47         0.03        13.25        13.55        29.92 
TCGA-60-2697 TCGA-60-2706 TCGA-60-2710 TCGA-60-2716 TCGA-60-2725 TCGA-63-6202 
       12.23        92.71        66.54        48.49        26.83        52.67 
TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN 
       70.42        68.15        58.65        59.97        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-66-2770 TCGA-66-2771 TCGA-66-2782 TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 
       23.01        19.00        12.00        24.95        25.97        22.98 
TCGA-66-2790 TCGA-68-8251 TCGA-70-6722 TCGA-77-6842 TCGA-77-6844 TCGA-77-7335 
       22.98        13.35        12.07        29.56        75.09        70.13 
TCGA-77-7337 TCGA-77-8131 TCGA-77-8143 TCGA-77-8145 TCGA-77-A5FZ TCGA-77-A5G1 
      106.95        12.59        26.40         6.97       126.18       132.36 
TCGA-77-A5G3 TCGA-77-A5GH TCGA-85-6175 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 
      150.25        38.86         9.67        34.95         1.38         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8071 TCGA-85-8288 TCGA-85-8351 TCGA-85-8354 
       29.95        18.94        26.79        13.22        16.77        32.71 
TCGA-85-8355 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A512 
        2.01        38.14        12.59        19.86        24.36        15.29 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-92-7340 TCGA-92-7341 
       29.92         3.65        24.92         2.93         2.70         3.48 
TCGA-92-8064 TCGA-94-8491 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8023 
        5.26        26.63        18.31        17.46        27.68        21.34 
TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HJ 
       27.02        20.32        12.89        64.54         1.22        13.74 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A5IB 
       26.43        83.57        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 
                       173.82                        154.32 
  DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE 
                        21.11                         22.98 
[1] "0.1 - 173.8 (21.1)" "0.0 - 154.3 (23.0)"
[1] "hr=" "1.1"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(4Q35.2) MUTATED         1       55      116        2        36
  DEL PEAK 14(4Q35.2) WILD-TYPE       1       34       36        0        29
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(4Q35.2) MUTATED          66         1         38         12
  DEL PEAK 14(4Q35.2) WILD-TYPE        29         2         25          7
                               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                            55                            34
  STAGE IB                           116                            36
  STAGE II                             2                             0
  STAGE IIA                           36                            29
  STAGE IIB                           66                            29
  STAGE III                            1                             2
  STAGE IIIA                          38                            25
  STAGE IIIB                          12                             7
  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    67 205  46  13
  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                          67                            45
  T2                         205                            89
  T3                          46                            25
  T4                          13                            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   221  80  24   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                         221                            96
  N1                          80                            53
  N2                          24                            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   272   3
  DEL PEAK 14(4Q35.2) WILD-TYPE 139   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED    272    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                         272                           139
  1                           3                             4
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q35.2) MUTATED    88 243
  DEL PEAK 14(4Q35.2) WILD-TYPE  42 128
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED     88  243
  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                          88                            42
  MALE                           243                           128
[1] 2 2
[1] FALSE
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(4Q35.2) MUTATED   249  36
  DEL PEAK 14(4Q35.2) WILD-TYPE 135  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED    249   36
  DEL PEAK 14(4Q35.2) WILD-TYPE  135   17
     clus
vv    DEL PEAK 14(4Q35.2) MUTATED DEL PEAK 14(4Q35.2) WILD-TYPE
  NO                          249                           135
  YES                          36                            17
[1] 2 2
[1] FALSE
D44V9, 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 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                                                           321
  DEL PEAK 14(4Q35.2) WILD-TYPE                                                         158
D44V10, multiclass
                                                             clus
vv                                                            DEL PEAK 14(4Q35.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         321
                                                             clus
vv                                                            DEL PEAK 14(4Q35.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
D44V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(4Q35.2) MUTATED   267   7   2  17
  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                         267                           132
  R1                           7                             5
  R2                           2                             2
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(4Q35.2) MUTATED       4                        23   230
  DEL PEAK 14(4Q35.2) WILD-TYPE     5                         8   119
D44V14, multiclass
                           clus
vv                          DEL PEAK 14(4Q35.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          23
  WHITE                                             230
                           clus
vv                          DEL PEAK 14(4Q35.2) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               119
[1] 3 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     5 209
  DEL PEAK 14(4Q35.2) WILD-TYPE   3 108
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(4Q35.2) MUTATED      5  209
  DEL PEAK 14(4Q35.2) WILD-TYPE    3  108
                        clus
vv                       DEL PEAK 14(4Q35.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         209
                        clus
vv                       DEL PEAK 14(4Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           108
[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   208 155
  DEL PEAK 15(5Q12.1) WILD-TYPE  72  59
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          363                           131 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                          155                            59 
$`DEL PEAK 15(5Q12.1) MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI TCGA-22-5471 
      123.19         4.80        31.99         6.18        32.19        60.66 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-34-2604 TCGA-34-2605 
       64.93        22.06       129.01       133.74        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       31.27        17.88        22.49        18.38         7.76        78.18 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 TCGA-56-8308 
        2.93        11.61        12.03        19.99         3.45        17.00 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-63-A5MH 
       17.85        21.04         0.13         3.58        41.42        66.61 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
        8.02        20.78        42.08         9.50        14.07        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
        0.16        18.38        16.14        57.07        19.36         2.76 
TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 
        5.69         0.07        39.85        40.90        65.65        16.80 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-4086 
        8.58        75.75        23.54        92.15        36.07         2.79 
TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1079 
      154.32        49.94       119.54        99.16        70.16        31.73 
TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
      122.43       119.80        43.23        31.63        41.69        33.93 
TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 
       10.82        21.99         7.33         4.31         1.74        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
       27.02        20.48        35.08        24.13        38.17        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       13.12        32.02        19.30         9.57        11.77        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        86.30        11.74        18.84 
TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 
       30.12        56.32        16.64        97.94        79.53       103.53 
TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB 
       14.07        63.35         4.70         0.30        36.62         6.94 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 
      110.99        44.19       118.36         2.63        61.61        32.88 
TCGA-34-5231 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 
       65.23         9.07        60.30        16.93        44.75         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        33.90         0.43         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
        7.46         7.82         6.81         0.39         3.39        37.58 
TCGA-37-A5EN TCGA-39-5016 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 
       21.70       126.58        68.58        82.52       102.18        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 
        1.94        60.53        71.18        55.56        40.21        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 
       39.12        33.11        27.91        24.89        21.47         3.81 
TCGA-43-7656 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       19.59        11.77        14.20        13.32        12.16        13.02 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
        9.83         4.44        10.65        13.91         0.39         0.39 
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-56-5897 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       12.43        21.90        18.48        14.53        31.27        30.41 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       19.76         6.51         0.10        17.49        33.24        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8625 
        4.93         3.48        14.07         1.35         1.81        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-A4ZK TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
       18.74         0.26         0.03        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       71.24        16.47        85.12        34.36        56.65        35.24 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       21.11        10.22        96.82        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
       49.48        66.54        56.91        50.33        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-7020 TCGA-63-7022 
       29.85        35.90        23.57        26.83        70.13        68.15 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MP 
       55.30       102.67        58.65        59.97        45.57        25.28 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 
       78.28        16.37        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-68-8251 TCGA-68-A59I TCGA-70-6723 TCGA-77-6842 TCGA-77-6844 
        6.94        13.35        16.18        12.33        29.56        75.09 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 
       23.28       140.09         0.49        73.22       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
       46.78        32.55         6.51        86.76        55.73        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
      156.66        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        66.51        54.41        65.49        60.53 
TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 
       36.36       150.25         5.92        27.62        38.86        41.39 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       40.24         6.41        36.53        34.95        31.30        32.91 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
        1.15        29.95        24.13        31.56        26.79        30.64 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
       34.52         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-85-8666 
       32.71         2.01        15.39         7.76        36.59        22.59 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       34.13        30.97        19.86        30.48        19.73        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7767 
       16.21        15.85        14.96        15.29         3.65         2.93 
TCGA-90-7769 TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8064 TCGA-94-8035 
       11.77        10.59         2.70         4.01         5.26         4.01 
TCGA-94-8490 TCGA-96-7544 TCGA-96-8169 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
        5.03        71.01        18.31        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 
       27.16        18.15         2.01        18.58        12.89        16.11 
TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       13.18        13.41        11.84         4.54        64.54        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HT 
       13.74         4.21         2.89        49.28        25.32        26.43 
TCGA-NK-A5CR TCGA-O2-A52S TCGA-XC-AA0X 
       83.57        12.72         0.20 

$`DEL PEAK 15(5Q12.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-33-4589 
       12.20         4.47        27.19        14.93        48.82         1.55 
TCGA-33-6737 TCGA-56-8201 TCGA-56-8504 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 
       19.76        13.05        16.77         9.01        35.34        32.32 
TCGA-77-A5GB TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NK-A7XE TCGA-18-3411 
       30.81        21.21        19.10        76.80         0.43       117.57 
TCGA-18-3412 TCGA-18-3419 TCGA-18-3421 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 
       11.34        92.42        86.96        46.88        60.89        34.78 
TCGA-21-1078 TCGA-21-1081 TCGA-21-5783 TCGA-22-1005 TCGA-22-4594 TCGA-22-4596 
       15.58         9.34        88.11        64.21        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       173.82       151.27        54.44 
TCGA-33-AASL TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 TCGA-34-5928 TCGA-34-8454 
       27.16        81.24        74.66        50.66        39.32        38.79 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-39-5011 TCGA-39-5019 TCGA-39-5022 
        4.01         0.39         7.96       133.25       111.35        55.20 
TCGA-39-5028 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-6143 TCGA-43-6771 
        1.71        36.39        68.38        17.06        22.98         5.46 
TCGA-43-8115 TCGA-43-A475 TCGA-52-7812 TCGA-56-5898 TCGA-56-8307 TCGA-56-8623 
       13.38         9.73        27.45        18.25        26.89        22.75 
TCGA-56-8624 TCGA-56-A62T TCGA-58-8393 TCGA-58-A46N TCGA-60-2697 TCGA-60-2704 
       13.81        14.47        34.78        29.92        12.23        37.94 
TCGA-60-2716 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-A5MG TCGA-63-A5MM 
       48.49        11.77        52.67        70.42        70.62        14.99 
TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MY TCGA-66-2744 TCGA-66-2765 TCGA-66-2767 
       11.34        89.29        34.59         0.99         2.01         2.01 
TCGA-66-2770 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2795 
       23.01        19.00        12.03        12.00        24.95         4.01 
TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 TCGA-77-7138 TCGA-77-7335 TCGA-77-8131 
       14.73        12.07        73.12        11.18        70.13        12.59 
TCGA-77-8144 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-6175 
       27.39       126.18       132.36        22.29        61.94         9.67 
TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8277 TCGA-85-8352 
        1.38        18.94        25.15        19.04        10.09         5.29 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A513 
       38.14        12.59        18.08        30.28        24.36        29.92 
TCGA-85-A53L TCGA-90-6837 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8065 
       12.39        24.92        20.22        22.62         3.48         2.30 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
       26.63        14.14        17.69        17.46        27.68        21.44 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-NC-A5HH TCGA-NC-A5HO TCGA-NC-A5HQ 
       27.02        20.32        20.71         1.22        43.92        14.73 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB 
        3.65        33.07         3.72        43.89        11.18 

  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                         0.03                          0.39 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                       156.66                        173.82 
  DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE 
                        21.47                         22.62 
[1] "0.0 - 156.7 (21.5)" "0.4 - 173.8 (22.6)"
[1] "hr=" "1"  
D45V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(5Q12.1) MUTATED         1       65      113        1        50
  DEL PEAK 15(5Q12.1) WILD-TYPE       1       24       39        1        15
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(5Q12.1) MUTATED          68         1         48         12
  DEL PEAK 15(5Q12.1) WILD-TYPE        27         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                            65                            24
  STAGE IB                           113                            39
  STAGE II                             1                             1
  STAGE IIA                           50                            15
  STAGE IIB                           68                            27
  STAGE III                            1                             2
  STAGE IIIA                          48                            15
  STAGE IIIB                          12                             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    84 221  45  19
  DEL PEAK 15(5Q12.1) WILD-TYPE  28  73  26   5
D45V4, multiclass
    clus
vv   DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  T1                          84                            28
  T2                         221                            73
  T3                          45                            26
  T4                          19                             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   236  99  29   2
  DEL PEAK 15(5Q12.1) WILD-TYPE  81  34  11   3
D45V5, multiclass
    clus
vv   DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  N0                         236                            81
  N1                          99                            34
  N2                          29                            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   300   7
  DEL PEAK 15(5Q12.1) WILD-TYPE 111   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED    300    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                         300                           111
  1                           7                             0
[1] 2 2
[1] FALSE
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED    88 281
  DEL PEAK 15(5Q12.1) WILD-TYPE  42  90
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED     88  281
  DEL PEAK 15(5Q12.1) WILD-TYPE   42   90
        clus
vv       DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  FEMALE                          88                            42
  MALE                           281                            90
[1] 2 2
[1] FALSE
D45V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q12.1) MUTATED   281  39
  DEL PEAK 15(5Q12.1) WILD-TYPE 103  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED    281   39
  DEL PEAK 15(5Q12.1) WILD-TYPE  103   14
     clus
vv    DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  NO                          281                           103
  YES                          39                            14
[1] 2 2
[1] FALSE
D45V9, 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 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                                                           355
  DEL PEAK 15(5Q12.1) WILD-TYPE                                                         124
D45V10, multiclass
                                                             clus
vv                                                            DEL PEAK 15(5Q12.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         355
                                                             clus
vv                                                            DEL PEAK 15(5Q12.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           124
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
D45V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(5Q12.1) MUTATED   298   9   2  15
  DEL PEAK 15(5Q12.1) WILD-TYPE 101   3   2   8
D45V13, multiclass
    clus
vv   DEL PEAK 15(5Q12.1) MUTATED DEL PEAK 15(5Q12.1) WILD-TYPE
  R0                         298                           101
  R1                           9                             3
  R2                           2                             2
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(5Q12.1) MUTATED       4                        26   257
  DEL PEAK 15(5Q12.1) WILD-TYPE     5                         5    92
D45V14, multiclass
                           clus
vv                          DEL PEAK 15(5Q12.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          26
  WHITE                                             257
                           clus
vv                          DEL PEAK 15(5Q12.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                92
[1] 3 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     6 229
  DEL PEAK 15(5Q12.1) WILD-TYPE   2  88
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q12.1) MUTATED      6  229
  DEL PEAK 15(5Q12.1) WILD-TYPE    2   88
                        clus
vv                       DEL PEAK 15(5Q12.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         229
                        clus
vv                       DEL PEAK 15(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            88
[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   219 160
  DEL PEAK 16(5Q31.1) WILD-TYPE  61  54
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                          379                           115 
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                          160                            54 
$`DEL PEAK 16(5Q31.1) MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI TCGA-22-5471 
      123.19         4.80        31.99         6.18        32.19        60.66 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-34-2604 
       64.93        22.06       129.01       133.74        19.76        31.50 
TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 
       28.96        31.27        17.88        22.49        18.38         7.76 
TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 
       78.18         2.93        11.61        12.03        19.99         3.45 
TCGA-56-8308 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       17.00        17.85        21.04         0.13         3.58        41.42 
TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-90-7766 TCGA-90-7964 
       32.32        66.61         8.02        20.78         9.50        14.07 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
        0.16        18.38        16.14        57.07        19.36         2.76 
TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT 
        5.69        19.10         0.07        39.85        40.90        65.65 
TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       16.80         8.58        75.75       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       92.15        36.07         2.79       154.32        49.94       119.54 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1082 TCGA-21-5782 
       99.16        70.16        60.89        31.73       119.80        31.63 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 
       41.69        33.93        10.82        21.99         7.33         4.31 
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-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       24.13        38.17        34.75        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
        9.57        11.77        63.55        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 
       86.30        11.74        18.84        30.12        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 
       97.94        79.53       103.53        14.07        54.44        63.35 
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-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5234 
      118.36         2.63        61.61        32.88        65.23        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 
        9.07        60.30        16.93        44.75         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4130 TCGA-37-4132 
       38.79         4.04        26.43        33.90         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN 
        7.82         6.81         0.39         3.39        37.58        21.70 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 
      133.25       126.58        68.58        82.52       102.18        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 
        1.94        60.53        71.18        55.56        40.21        38.66 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 
       39.12        33.11        27.91        24.89        21.47         3.81 
TCGA-43-7656 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3768 
       19.59        11.77        14.20        13.32        12.16         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 
        4.44        10.65        13.91         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
        5.46        30.35         8.75        28.96        12.43        18.25 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       18.48        31.27        30.41        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
       17.49        33.24        14.96         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
       14.07         1.35         1.81        10.36         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
       15.81        20.94        19.23        13.32        18.74         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-60-2703 
       85.12        34.36        56.65        35.24        21.11        96.82 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       92.71        21.93        80.45        49.48        66.54        56.91 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       50.33        42.64         3.19        29.85        35.90        23.57 
TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB 
       26.83        52.67        70.13        68.15        55.30       102.67 
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-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-66-2742 TCGA-66-2753 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 
       21.07         1.02         0.92         0.99        43.99        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
        0.99         2.01         1.02         2.01         7.07        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        3.02         2.01        19.00        12.03         3.98        12.00 
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-66-2800 TCGA-68-7755 
        5.03        30.02        10.06        54.08        49.05         2.73 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-70-6723 TCGA-77-6842 TCGA-77-6844 
        6.64         6.94        13.35        12.33        29.56        75.09 
TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 
       23.28       140.09         0.49        73.22       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 
       46.78        32.55         6.51        86.76        37.81       156.66 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       53.92        39.09        17.72       104.09        11.54        26.40 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        6.97        66.51        54.41        65.49        60.53        36.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH 
      150.25        22.29         5.92        61.94        27.62        38.86 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       41.39        40.24         6.41        36.53        34.95        31.30 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 
       32.91         1.38         1.15        18.94        24.13        31.56 
TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
       26.79        30.64        34.52        10.09         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-85-8664 TCGA-85-8666 
       15.39         7.76        36.59        38.14        18.08        22.59 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       34.13        30.97        19.86        30.48        19.73        27.16 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
       15.85        14.96        15.29         3.65         2.93        11.77 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       22.62        10.59         2.70         3.48         4.01         5.26 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        4.01         5.03        26.63        14.14        71.01        18.31 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B 
       30.81        30.67        21.34        27.16        18.15         2.01 
TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       18.58        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54        64.54        57.30        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52S 
       49.28        25.32        26.43        83.57         3.65        12.72 
TCGA-XC-AA0X 
        0.20 

$`DEL PEAK 16(5Q31.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-33-4589 
       12.20         4.47        27.19        14.93        48.82         1.55 
TCGA-56-8201 TCGA-56-8504 TCGA-60-2712 TCGA-60-2715 TCGA-77-A5GA TCGA-77-A5GB 
       13.05        16.77         9.01        35.34        42.08        30.81 
TCGA-94-7033 TCGA-98-A53D TCGA-NC-A5HE TCGA-NK-A7XE TCGA-18-3419 TCGA-18-3421 
       21.04        21.21        76.80         0.43        92.42        86.96 
TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 
       46.88        34.78        15.58       122.43         9.34        43.23 
TCGA-21-5783 TCGA-22-1005 TCGA-22-4596 TCGA-22-5480 TCGA-22-5481 TCGA-22-5489 
       88.11        64.21         0.56        71.34        79.20        62.86 
TCGA-33-4566 TCGA-33-4583 TCGA-33-AASL TCGA-34-5232 TCGA-34-5240 TCGA-34-5928 
      173.82       151.27        27.16        81.24        50.66        39.32 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-39-5019 TCGA-39-5022 
        4.01         0.43         0.39         7.96       111.35        55.20 
TCGA-39-5028 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-6143 TCGA-43-6771 
        1.71        36.39        68.38        17.06        22.98         5.46 
TCGA-43-8115 TCGA-43-A475 TCGA-46-3767 TCGA-51-4080 TCGA-52-7812 TCGA-56-6545 
       13.38         9.73        13.02         0.39        27.45        21.90 
TCGA-56-7223 TCGA-56-8623 TCGA-56-8624 TCGA-56-A62T TCGA-58-8393 TCGA-58-A46N 
       14.53        22.75        13.81        14.47        34.78        29.92 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2716 TCGA-60-2726 TCGA-63-7021 
       12.23        10.22        37.94        48.49        11.77        70.42 
TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-66-2744 TCGA-66-2754 
       70.62        14.99        11.34        89.29         0.99         2.01 
TCGA-66-2758 TCGA-66-2767 TCGA-66-2770 TCGA-66-2783 TCGA-66-2795 TCGA-68-A59I 
       21.01         2.01        23.01        24.95         4.01        16.18 
TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 TCGA-77-7138 TCGA-77-7335 TCGA-77-8009 
       14.73        12.07        73.12        11.18        70.13        55.73 
TCGA-77-8131 TCGA-77-8144 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-85-6175 TCGA-85-7844 
       12.59        27.39       126.18       132.36         9.67        29.95 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A50Z 
       25.15        19.04        12.59        30.28        24.36        16.21 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-A4ED TCGA-92-8065 TCGA-94-A5I6 
       29.92        12.39        24.92        20.22         2.30        17.69 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J 
       17.46        27.68        21.44        27.02        20.32        20.71 
TCGA-NC-A5HH TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V 
        1.22        43.92        14.73        33.07         3.72        43.89 
TCGA-O2-A5IB 
       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 
                       156.66                        173.82 
  DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE 
                        21.93                         21.44 
[1] "0.0 - 156.7 (21.9)" "0.4 - 173.8 (21.4)"
[1] "hr=" "1"  
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(5Q31.1) MUTATED         1       70      114        1        54
  DEL PEAK 16(5Q31.1) WILD-TYPE       1       19       38        1        11
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(5Q31.1) MUTATED          70         1         53         12
  DEL PEAK 16(5Q31.1) WILD-TYPE        25         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                            70                            19
  STAGE IB                           114                            38
  STAGE II                             1                             1
  STAGE IIA                           54                            11
  STAGE IIB                           70                            25
  STAGE III                            1                             2
  STAGE IIIA                          53                            10
  STAGE IIIB                          12                             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    89 228  51  18
  DEL PEAK 16(5Q31.1) WILD-TYPE  23  66  20   6
D46V4, multiclass
    clus
vv   DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  T1                          89                            23
  T2                         228                            66
  T3                          51                            20
  T4                          18                             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   247 101  32   3
  DEL PEAK 16(5Q31.1) WILD-TYPE  70  32   8   2
D46V5, multiclass
    clus
vv   DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  N0                         247                            70
  N1                         101                            32
  N2                          32                             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   316   7
  DEL PEAK 16(5Q31.1) WILD-TYPE  95   0
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q31.1) MUTATED    316    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                         316                            95
  1                           7                             0
[1] 2 2
[1] FALSE
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(5Q31.1) MUTATED    97 289
  DEL PEAK 16(5Q31.1) WILD-TYPE  33  82
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q31.1) MUTATED     97  289
  DEL PEAK 16(5Q31.1) WILD-TYPE   33   82
        clus
vv       DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  FEMALE                          97                            33
  MALE                           289                            82
[1] 2 2
[1] FALSE
D46V8, binary
                               cls
clus                              0   1
  DEL PEAK 16(5Q31.1) MUTATED   296  40
  DEL PEAK 16(5Q31.1) WILD-TYPE  88  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q31.1) MUTATED    296   40
  DEL PEAK 16(5Q31.1) WILD-TYPE   88   13
     clus
vv    DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  NO                          296                            88
  YES                          40                            13
[1] 2 2
[1] FALSE
D46V9, 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 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                                                           372
  DEL PEAK 16(5Q31.1) WILD-TYPE                                                         107
D46V10, multiclass
                                                             clus
vv                                                            DEL PEAK 16(5Q31.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         372
                                                             clus
vv                                                            DEL PEAK 16(5Q31.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
D46V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(5Q31.1) MUTATED   309   9   3  15
  DEL PEAK 16(5Q31.1) WILD-TYPE  90   3   1   8
D46V13, multiclass
    clus
vv   DEL PEAK 16(5Q31.1) MUTATED DEL PEAK 16(5Q31.1) WILD-TYPE
  R0                         309                            90
  R1                           9                             3
  R2                           3                             1
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(5Q31.1) MUTATED       4                        24   269
  DEL PEAK 16(5Q31.1) WILD-TYPE     5                         7    80
D46V14, multiclass
                           clus
vv                          DEL PEAK 16(5Q31.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          24
  WHITE                                             269
                           clus
vv                          DEL PEAK 16(5Q31.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                80
[1] 3 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     6 239
  DEL PEAK 16(5Q31.1) WILD-TYPE   2  78
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(5Q31.1) MUTATED      6  239
  DEL PEAK 16(5Q31.1) WILD-TYPE    2   78
                        clus
vv                       DEL PEAK 16(5Q31.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         239
                        clus
vv                       DEL PEAK 16(5Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            78
[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    67  66
  DEL PEAK 17(6P25.3) WILD-TYPE 213 148
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                          133                           361 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                           66                           148 
$`DEL PEAK 17(6P25.3) MUTATED`
TCGA-18-3406 TCGA-18-3416 TCGA-18-4083 TCGA-33-4589 TCGA-34-2604 TCGA-39-5039 
       12.20        31.99         6.18         1.55        31.50        17.88 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-77-7140 TCGA-94-A5I4 TCGA-96-A4JK 
        2.93        11.61        12.03        20.78        16.14        19.36 
TCGA-98-8020 TCGA-J1-A4AH TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 
        2.76        19.10        16.80        75.75       117.57        11.34 
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        86.30        11.74        18.84        56.32 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 TCGA-33-AASD TCGA-33-AASL TCGA-34-2596 
       79.53       103.53       151.27       110.99        27.16         2.63 
TCGA-34-5232 TCGA-34-7107 TCGA-34-8455 TCGA-37-3789 TCGA-37-5819 TCGA-37-A5EL 
       81.24         1.12         4.04         0.43         3.39        37.58 
TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5027 TCGA-39-5029 TCGA-39-5035 
       21.70       133.25       126.58       102.18        24.33        68.38 
TCGA-39-5037 TCGA-43-6143 TCGA-43-A475 TCGA-46-3768 TCGA-46-3769 TCGA-51-4081 
       55.56        22.98         9.73         9.83         4.44        29.95 
TCGA-52-7622 TCGA-56-7579 TCGA-56-7582 TCGA-56-7822 TCGA-56-8309 TCGA-56-8624 
       28.34        31.27        19.76        17.49        14.07        13.81 
TCGA-56-8626 TCGA-56-A4ZK TCGA-58-8386 TCGA-58-8391 TCGA-58-A46M TCGA-60-2698 
        9.93        18.74         0.03        71.24        35.24        10.22 
TCGA-60-2707 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-A5MB 
       21.93        26.83        11.77        70.13        70.42       102.67 
TCGA-63-A5MJ TCGA-63-A5MP TCGA-63-A5MR TCGA-66-2782 TCGA-66-2786 TCGA-66-2788 
       59.97        25.28        89.29        12.00        25.97        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-68-7755 TCGA-68-7756 
        4.04         5.03        30.02        54.08         2.73         6.64 
TCGA-68-A59I TCGA-70-6723 TCGA-77-7141 TCGA-77-7337 TCGA-77-7338 TCGA-77-8128 
       16.18        12.33         0.49       106.95         0.16        37.81 
TCGA-77-8131 TCGA-77-8138 TCGA-77-8150 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-85-7696 
       12.59        17.72        54.41       150.25        61.94        36.53 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7843 TCGA-85-7950 TCGA-85-8049 TCGA-85-8070 
       34.95        31.30         1.15        18.94        19.04        31.56 
TCGA-85-8277 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QQ 
       10.09        22.59        30.28        34.13        19.86        30.48 
TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 
       15.29         3.65         2.93        10.59         3.48         4.01 
TCGA-92-8064 TCGA-92-8065 TCGA-94-8491 TCGA-96-7544 TCGA-98-A53I TCGA-98-A53J 
        5.26         2.30        26.63        71.01        18.58        20.71 
TCGA-LA-A7SW TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-O2-A52V 
       13.41         2.89        25.32        14.73        83.57        43.89 
TCGA-XC-AA0X 
        0.20 

$`DEL PEAK 17(6P25.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
        4.47       123.19         4.80        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
       48.82        60.66        64.93        22.06       129.01       133.74 
TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 
       19.76        28.96        31.27        22.49        18.38         7.76 
TCGA-43-7658 TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
       78.18        19.99        13.05         3.45        17.00        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 
       17.85        21.04         0.13         3.58        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA TCGA-77-A5GB 
       35.34        32.32        66.61         8.02        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-96-7545 
        9.50        14.07        21.04         0.16        18.38        57.07 
TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR 
        5.69        21.21         0.07        76.80        39.85        40.90 
TCGA-NK-A5CT TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
       65.65         0.43         8.58        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
       92.42        86.96        49.94       119.54        46.88        99.16 
TCGA-21-1075 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 
       70.16        34.78        15.58        31.73       122.43         9.34 
TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
      119.80        43.23        31.63        41.69        33.93        10.82 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 
        7.33         4.31        64.21         1.74        27.02        20.48 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 
       48.33        24.13        34.75        32.02        19.30        11.77 
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-33-4538 TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
       97.94       173.82        14.07        54.44        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-34-2600 
        0.30        36.62         6.94        44.19       118.36        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       32.88        65.23        74.66         9.07        60.30        50.66 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 
       16.93        44.75        39.32         4.96        38.79        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
       33.90         4.01         0.39         7.96         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       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
       82.52         1.71         1.94        60.53        36.39        71.18 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       17.06        40.21        38.66        39.12        33.11        27.91 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       24.89        21.47         5.46         3.81        19.59        13.38 
TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-6025 
       11.77        14.20        13.32        12.16        13.02        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
       13.91         0.39         0.39         5.46        30.35         8.75 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 
       27.45        28.96        12.43        18.25        21.90        18.48 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 
       14.53        30.41         6.51         0.10        33.24        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
        4.93         3.48        26.89         1.35         1.81        22.75 
TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
       10.36        20.25        15.81        20.94        19.23        13.32 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 
        0.26        14.47        13.25        13.55        29.95        16.47 
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-60-2703 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-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       66.54        56.91        50.33        48.49        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 TCGA-63-7022 TCGA-63-7023 
       29.85        35.90        23.57        52.67        68.15        55.30 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MS 
       70.62        58.65        45.57        14.99        11.34        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-66-2744 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-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        0.99        43.99        21.01        25.05         0.99         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-66-2773 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-66-2787 TCGA-66-2790 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 
        1.97        40.01        22.98        10.06         4.01        49.05 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 
        6.94        13.35        14.73        12.07        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7142 TCGA-77-7335 
       75.09        23.28        11.18       140.09        73.22        70.13 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 
       46.78        32.55         6.51        86.76        55.73       156.66 
TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       53.92        39.09       104.09        11.54        26.40        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
        6.97        66.51        65.49        60.53        36.36       126.18 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
      132.36        22.29         5.92        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 
       41.39        40.24         6.41        32.91         1.38        29.95 
TCGA-85-8048 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 
       25.15        24.13        26.79        30.64        34.52         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
       13.22        22.45        16.77         5.29         3.09        32.71 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        2.01        15.39         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       18.08        30.97        24.36        19.73        27.16        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 
       15.85        14.96        29.92        12.39        24.92        11.77 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ 
       20.22        22.62         2.70         4.01         5.03        14.14 
TCGA-94-A5I6 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       17.69        18.31        17.46        27.68        21.44        30.81 
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-A53H TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HF 
       20.32        12.89        16.11        13.18        11.84         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN 
       64.54         1.22        57.30        13.74         4.21        49.28 
TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       43.92        26.43         3.65        33.07         3.72        12.72 
TCGA-O2-A5IB 
       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                        173.82 
  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE 
                        19.86                         22.45 
[1] "0.0 - 154.3 (19.9)" "0.1 - 173.8 (22.4)"
[1] "hr=" "1.2"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(6P25.3) MUTATED         0       23       35        2        23
  DEL PEAK 17(6P25.3) WILD-TYPE       2       66      117        0        42
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6P25.3) MUTATED          24         0         17          4
  DEL PEAK 17(6P25.3) WILD-TYPE        71         3         46         15
                               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                            66
  STAGE IB                            35                           117
  STAGE II                             2                             0
  STAGE IIA                           23                            42
  STAGE IIB                           24                            71
  STAGE III                            0                             3
  STAGE IIIA                          17                            46
  STAGE IIIB                           4                            15
  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  19   5
  DEL PEAK 17(6P25.3) WILD-TYPE  80 216  52  19
D47V4, multiclass
    clus
vv   DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  T1                          32                            80
  T2                          78                           216
  T3                          19                            52
  T4                           5                            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    78  41  11   2
  DEL PEAK 17(6P25.3) WILD-TYPE 239  92  29   3
D47V5, multiclass
    clus
vv   DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  N0                          78                           239
  N1                          41                            92
  N2                          11                            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   112   3
  DEL PEAK 17(6P25.3) WILD-TYPE 299   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED    112    3
  DEL PEAK 17(6P25.3) WILD-TYPE  299    4
   clus
vv  DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  0                         112                           299
  1                           3                             4
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 17(6P25.3) MUTATED    28 106
  DEL PEAK 17(6P25.3) WILD-TYPE 102 265
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED     28  106
  DEL PEAK 17(6P25.3) WILD-TYPE  102  265
        clus
vv       DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  FEMALE                          28                           102
  MALE                           106                           265
[1] 2 2
[1] FALSE
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(6P25.3) MUTATED   100  19
  DEL PEAK 17(6P25.3) WILD-TYPE 284  34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED    100   19
  DEL PEAK 17(6P25.3) WILD-TYPE  284   34
     clus
vv    DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  NO                          100                           284
  YES                          19                            34
[1] 2 2
[1] FALSE
D47V9, 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 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                                                           130
  DEL PEAK 17(6P25.3) WILD-TYPE                                                         349
D47V10, multiclass
                                                             clus
vv                                                            DEL PEAK 17(6P25.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         130
                                                             clus
vv                                                            DEL PEAK 17(6P25.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           349
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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 294   7   4  14
D47V13, multiclass
    clus
vv   DEL PEAK 17(6P25.3) MUTATED DEL PEAK 17(6P25.3) WILD-TYPE
  R0                         105                           294
  R1                           5                             7
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(6P25.3) MUTATED       1                        10    96
  DEL PEAK 17(6P25.3) WILD-TYPE     8                        21   253
D47V14, multiclass
                           clus
vv                          DEL PEAK 17(6P25.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              96
                           clus
vv                          DEL PEAK 17(6P25.3) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               253
[1] 3 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  84
  DEL PEAK 17(6P25.3) WILD-TYPE   4 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(6P25.3) MUTATED      4   84
  DEL PEAK 17(6P25.3) WILD-TYPE    4  233
                        clus
vv                       DEL PEAK 17(6P25.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          84
                        clus
vv                       DEL PEAK 17(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           233
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 18(6Q26) MUTATION ANALYSIS
D48V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 18(6Q26) MUTATED    67  64
  DEL PEAK 18(6Q26) WILD-TYPE 213 150
  DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE 
                        131                         363 
  DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE 
                         64                         150 
$`DEL PEAK 18(6Q26) MUTATED`
TCGA-18-4083 TCGA-22-5471 TCGA-33-6737 TCGA-34-2604 TCGA-39-5039 TCGA-43-5668 
        6.18        60.66        19.76        31.50        17.88        18.38 
TCGA-43-8118 TCGA-56-A4BY TCGA-94-7557 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HR 
        2.93        17.85         0.16        19.10         0.07        40.90 
TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3411 TCGA-18-3415 TCGA-18-3419 TCGA-18-5592 
       16.80        75.75       117.57        92.15        92.42        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-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5489 TCGA-22-5492 TCGA-33-4582 
        0.79        86.30        79.20        62.86        16.64       103.53 
TCGA-33-4583 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2608 
      151.27         6.94        44.19        27.16         2.63        32.88 
TCGA-34-5231 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-8455 TCGA-37-4133 
       65.23        44.75        39.32         4.96         4.04         7.82 
TCGA-37-A5EL TCGA-39-5016 TCGA-39-5021 TCGA-39-5027 TCGA-39-5028 TCGA-39-5034 
       37.58       126.58        68.58       102.18         1.71        36.39 
TCGA-39-5037 TCGA-43-2581 TCGA-43-6143 TCGA-43-6770 TCGA-46-3765 TCGA-46-6025 
       55.56        38.66        22.98        21.47        13.32        10.65 
TCGA-51-4081 TCGA-52-7812 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 
       29.95        27.45        21.90        18.48        14.53        19.76 
TCGA-56-7730 TCGA-56-8624 TCGA-56-8625 TCGA-56-A4ZK TCGA-58-8393 TCGA-58-A46K 
        6.51        13.81        10.36        18.74        34.78        34.36 
TCGA-58-A46M TCGA-60-2707 TCGA-60-2722 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 
       35.24        21.93        29.85        11.77        52.67        70.13 
TCGA-63-A5MB TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MY TCGA-66-2727 TCGA-66-2758 
      102.67        45.57        89.29        34.59        16.96        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
       25.05         0.99         3.02        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2791 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
       24.95         5.03         4.01         2.73         6.64         6.94 
TCGA-70-6723 TCGA-77-7141 TCGA-77-8007 TCGA-77-8009 TCGA-77-8144 TCGA-77-8150 
       12.33         0.49         6.51        55.73        27.39        54.41 
TCGA-77-A5G3 TCGA-77-A5G8 TCGA-85-7696 TCGA-85-7698 TCGA-85-7710 TCGA-85-8052 
      150.25        61.94        36.53        31.30         1.38        24.13 
TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8354 TCGA-85-8479 TCGA-85-A4CL 
       31.56        30.64        10.09        32.71        15.39        30.28 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       19.86        30.48        19.73        27.16        16.21        15.85 
TCGA-85-A5B5 TCGA-92-7341 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53I TCGA-L3-A524 
        3.65         3.48        27.16         2.01        18.58        16.11 
TCGA-LA-A446 TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HQ 
       13.18         1.22         4.21        49.28        14.73 

$`DEL PEAK 18(6Q26) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 
       12.20         4.47       123.19         4.80        31.99        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 
       32.19        14.93        48.82        64.93        22.06       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 TCGA-43-7657 
      133.74         1.55        28.96        31.27        22.49         7.76 
TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 
       78.18        11.61        12.03        19.99        13.05         3.45 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       17.00        16.77        21.04         0.13         3.58        41.42 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 
        9.01        35.34        32.32        66.61         8.02        20.78 
TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 
       42.08        30.81         9.50        14.07        21.04        18.38 
TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D 
       16.14        57.07        19.36         2.76         5.69        21.21 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3412 
       76.80        39.85        65.65         0.43         8.58        11.34 
TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 
       23.54        36.07        86.96         2.79       154.32       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-22-0944 
      122.43         9.34       119.80        31.63        41.69         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
        4.31        64.21        14.10        27.02        20.48        35.08 
TCGA-22-4594 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       48.33        13.12        32.02         9.57        11.77        63.55 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       14.63        44.25        71.34        11.74        18.84        30.12 
TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4586 TCGA-33-4587 
       56.32        97.94        79.53       173.82        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ 
       63.35         4.70         0.30        36.62       110.99       118.36 
TCGA-34-2600 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       61.61        81.24        74.66         9.07        60.30        50.66 
TCGA-34-5241 TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
       16.93         1.12        38.79        26.43        33.90         4.01 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 
        0.43         0.39         7.96         8.12         7.46         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5019 TCGA-39-5022 
        0.39         3.39        21.70       133.25       111.35        55.20 
TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5035 TCGA-39-5036 
       82.52        24.33         1.94        60.53        68.38        71.18 
TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 
       17.06        40.21        39.12        33.11        27.91        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
        5.46         3.81        19.59        13.38        11.77         9.73 
TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6026 
       14.20        12.16        13.02         9.83         4.44        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-56-7579 TCGA-56-7580 TCGA-56-7731 
       28.96        12.43        18.25        31.27        30.41         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
       17.49        33.24        14.96         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8626 TCGA-56-8628 
       14.07         1.35         1.81        22.75         9.93        20.25 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS TCGA-56-A62T 
       15.81        20.94        19.23        13.32         0.26        14.47 
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-A46L TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 
       85.12        56.65        29.92        21.11        12.23        10.22 
TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
       96.82        37.94        92.71        80.45        49.48        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 
       56.91        50.33        48.49        42.64         3.19        35.90 
TCGA-60-2724 TCGA-60-2725 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG 
       23.57        26.83        70.42        68.15        55.30        70.62 
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-66-2785 TCGA-66-2786 TCGA-66-2787 
       19.00         2.01        19.00         1.97        25.97        40.01 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 
       22.98         4.04        22.98        30.02        10.06        54.08 
TCGA-66-2800 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 
       49.05        13.35        16.18        14.73        12.07        29.56 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7142 
       73.12        75.09        23.28        11.18       140.09        73.22 
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        32.55        86.76 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       37.81       156.66        12.59        53.92        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 
      104.09        11.54        26.40         6.97        66.51        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
       60.53        36.36       126.18       132.36        22.29         5.92 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
       27.62        38.86         9.67        41.39        40.24         6.41 
TCGA-85-7697 TCGA-85-7699 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
       34.95        32.91         1.15        29.95        18.94        25.15 
TCGA-85-8049 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       19.04        26.79        34.52         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 
       16.77         5.29         3.09         2.01         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB 
       38.14        12.59        18.08        22.59        34.13        30.97 
TCGA-85-A4PA TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       24.36        14.96        15.29        29.92        12.39        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
        2.93        11.77        20.22        22.62        10.59         2.70 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        4.01         5.26         2.30         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
       14.14        17.69        71.01        18.31        17.46        27.68 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53C 
       21.44        30.81        30.67        21.34        18.15        27.02 
TCGA-98-A53H TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF 
       20.32        20.71        12.89        13.41        11.84         4.54 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP 
       64.54        57.30        13.74         2.89        43.92        25.32 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       26.43        83.57         3.65        33.07         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

  DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE 
                       0.07                        0.03 
  DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE 
                     151.27                      173.82 
  DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE 
                      21.93                       21.44 
[1] "0.1 - 151.3 (21.9)" "0.0 - 173.8 (21.4)"
[1] "hr=" "1.2"
D48V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(6Q26) MUTATED         0       21       47        0        18
  DEL PEAK 18(6Q26) WILD-TYPE       2       68      105        2        47
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(6Q26) MUTATED          27         0         17          3
  DEL PEAK 18(6Q26) WILD-TYPE        68         3         46         16
                             vv
clus                          STAGE IV
  DEL PEAK 18(6Q26) MUTATED          1
  DEL PEAK 18(6Q26) WILD-TYPE        6
D48V3, multiclass
            clus
vv           DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE
  STAGE I                            0                           2
  STAGE IA                          21                          68
  STAGE IB                          47                         105
  STAGE II                           0                           2
  STAGE IIA                         18                          47
  STAGE IIB                         27                          68
  STAGE III                          0                           3
  STAGE IIIA                        17                          46
  STAGE IIIB                         3                          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 18(6Q26) MUTATED    26  84  19   6
  DEL PEAK 18(6Q26) WILD-TYPE  86 210  52  18
D48V4, multiclass
    clus
vv   DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE
  T1                        26                          86
  T2                        84                         210
  T3                        19                          52
  T4                         6                          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 18(6Q26) MUTATED    90  34   9   2
  DEL PEAK 18(6Q26) WILD-TYPE 227  99  31   3
D48V5, multiclass
    clus
vv   DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE
  N0                        90                         227
  N1                        34                          99
  N2                         9                          31
  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"
D48V6, binary
                             cls
clus                            0   1
  DEL PEAK 18(6Q26) MUTATED   119   1
  DEL PEAK 18(6Q26) WILD-TYPE 292   6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 18(6Q26) MUTATED    119    1
  DEL PEAK 18(6Q26) WILD-TYPE  292    6
   clus
vv  DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE
  0                       119                         292
  1                         1                           6
[1] 2 2
[1] FALSE
D48V7, binary
                             cls
clus                            0   1
  DEL PEAK 18(6Q26) MUTATED    33 102
  DEL PEAK 18(6Q26) WILD-TYPE  97 269
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 18(6Q26) MUTATED     33  102
  DEL PEAK 18(6Q26) WILD-TYPE   97  269
        clus
vv       DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE
  FEMALE                        33                          97
  MALE                         102                         269
[1] 2 2
[1] FALSE
D48V8, binary
                             cls
clus                            0   1
  DEL PEAK 18(6Q26) MUTATED   101  17
  DEL PEAK 18(6Q26) WILD-TYPE 283  36
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 18(6Q26) MUTATED    101   17
  DEL PEAK 18(6Q26) WILD-TYPE  283   36
     clus
vv    DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE
  NO                        101                         283
  YES                        17                          36
[1] 2 2
[1] FALSE
D48V9, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(6Q26) MUTATED                                       6
  DEL PEAK 18(6Q26) WILD-TYPE                                     9
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 18(6Q26) MUTATED                                        2
  DEL PEAK 18(6Q26) WILD-TYPE                                      4
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 18(6Q26) MUTATED                                         0
  DEL PEAK 18(6Q26) WILD-TYPE                                       1
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(6Q26) MUTATED                                                           127
  DEL PEAK 18(6Q26) WILD-TYPE                                                         352
D48V10, multiclass
                                                             clus
vv                                                            DEL PEAK 18(6Q26) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                              2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       127
                                                             clus
vv                                                            DEL PEAK 18(6Q26) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         352
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, continuous
D48V12, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 18(6Q26) MUTATED   106   3   2   9
  DEL PEAK 18(6Q26) WILD-TYPE 293   9   2  14
D48V13, multiclass
    clus
vv   DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE
  R0                       106                         293
  R1                         3                           9
  R2                         2                           2
  RX                         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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(6Q26) MUTATED       2                         7    93
  DEL PEAK 18(6Q26) WILD-TYPE     7                        24   256
D48V14, multiclass
                           clus
vv                          DEL PEAK 18(6Q26) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         7
  WHITE                                            93
                           clus
vv                          DEL PEAK 18(6Q26) WILD-TYPE
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          24
  WHITE                                             256
[1] 3 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(6Q26) MUTATED     2  80
  DEL PEAK 18(6Q26) WILD-TYPE   6 237
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 18(6Q26) MUTATED      2   80
  DEL PEAK 18(6Q26) WILD-TYPE    6  237
                        clus
vv                       DEL PEAK 18(6Q26) MUTATED DEL PEAK 18(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             2                           6
  NOT HISPANIC OR LATINO                        80                         237
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 19(7Q11.22) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(7Q11.22) MUTATED    30  16
  DEL PEAK 19(7Q11.22) WILD-TYPE 250 198
  DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE 
                            46                            448 
  DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE 
                            16                            198 
$`DEL PEAK 19(7Q11.22) MUTATED`
TCGA-43-2578 TCGA-56-8305 TCGA-63-A5MH TCGA-18-3421 TCGA-21-1082 TCGA-21-5787 
       22.49         3.45        66.61        86.96       119.80        10.82 
TCGA-22-1016 TCGA-22-5477 TCGA-22-5481 TCGA-33-AASI TCGA-37-5819 TCGA-43-2581 
       27.02        44.25        79.20        44.19         3.39        38.66 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-46-3765 TCGA-46-6026 TCGA-56-6545 
       21.47         5.46        19.59        13.32        13.91        21.90 
TCGA-56-7580 TCGA-56-8629 TCGA-56-A4BW TCGA-60-2695 TCGA-60-2703 TCGA-60-2719 
       30.41        15.81        19.23        21.11        96.82        42.64 
TCGA-63-A5MT TCGA-66-2727 TCGA-66-2754 TCGA-66-2773 TCGA-66-2788 TCGA-77-7465 
       16.37        16.96         2.01         3.02        22.98        32.55 
TCGA-77-8139 TCGA-77-8144 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-7843 
      104.09        27.39        38.86        41.39        32.91         1.15 
TCGA-85-8048 TCGA-85-8072 TCGA-85-8350 TCGA-85-8353 TCGA-85-A510 TCGA-98-A53B 
       25.15        30.64        22.45         3.09        15.85         2.01 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-O2-A52N TCGA-O2-A52S 
        4.21         2.89        33.07        12.72 

$`DEL PEAK 19(7Q11.22) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 
       27.19        32.19        14.93        48.82        60.66        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 
       22.06       129.01       133.74         1.55        19.76        31.50 
TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       28.96        31.27        17.88        18.38         7.76        78.18 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 
        2.93        11.61        12.03        19.99        13.05        17.00 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       16.77        17.85        21.04         0.13         3.58        41.42 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA 
        9.01        35.34        32.32         8.02        20.78        42.08 
TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       30.81         9.50        14.07        21.04         0.16        18.38 
TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D 
       16.14        57.07        19.36         2.76         5.69        21.21 
TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT 
       19.10         0.07        76.80        39.85        40.90        65.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 
       16.80         0.43         8.58        75.75       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 
       23.54        92.15        36.07        92.42         2.79       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
       49.94       119.54        46.88        99.16        70.16        60.89 
TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1083 
       34.78        15.58        31.73       122.43         9.34        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 TCGA-22-0944 
       31.63        88.11        41.69        33.93        21.99         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 
        4.31        64.21         1.74        14.10        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       48.33        24.13         0.56        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       32.02        19.30         9.57        11.77        63.55        14.63 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
        0.79        86.30        71.34        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       62.86        56.32        16.64        97.94        79.53       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
      103.53       151.27        14.07        54.44        63.35         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL 
        0.30        36.62         6.94       110.99       118.36        27.16 
TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
        2.63        61.61        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        9.07        60.30        50.66        16.93        44.75        39.32 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
        4.96         1.12        38.79         4.04        26.43        33.90 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
        4.01         0.43         0.39         7.96         8.12         7.46 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        7.82         6.81         0.39        37.58        21.70       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1.71        24.33         1.94        60.53        36.39        68.38 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 
       71.18        55.56        17.06        40.21        39.12        33.11 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6773 TCGA-43-8115 TCGA-43-8116 
       27.91        22.98        24.89         3.81        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
        9.73        14.20        12.16        13.02         9.83         4.44 
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-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       30.35         8.75        27.45        28.96        12.43        18.25 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       18.48        14.53        31.27        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
       17.49        33.24        14.96         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       14.07         1.35         1.81        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
        9.93        20.25        20.94        13.32        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
       14.47         0.03        13.25        13.55        29.95        71.24 
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-60-2697 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       29.92        12.23        10.22        37.94        92.71        21.93 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 
       80.45        49.48        66.54        56.91        50.33        48.49 
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-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB 
       52.67        70.13        70.42        68.15        55.30       102.67 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
       70.62        58.65        59.97        45.57        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       25.28        89.29        78.28        36.16        53.88        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-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 
        0.99        43.99        21.01        25.05         0.99         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-66-2780 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-66-2789 TCGA-66-2790 TCGA-66-2791 
        1.97        25.97        40.01         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-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
        6.64         6.94        13.35        16.18        14.73        12.07 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       12.33        29.56        73.12        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
      140.09         0.49        73.22        70.13       106.95         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        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 
       12.59        53.92        39.09        17.72        11.54        26.40 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
        6.97        66.51        54.41        65.49        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
      126.18       132.36       150.25        22.29         5.92        61.94 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       27.62         9.67        40.24         6.41        36.53        34.95 
TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 
       31.30         1.38        29.95        18.94        19.04        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
       31.56        26.79        34.52        10.09         0.76        13.22 
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        15.39         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       36.59        38.14        12.59        18.08        22.59        30.28 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       34.13        30.97        19.86        24.36        30.48        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L 
       27.16        16.21        14.96        15.29        29.92        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-92-8063 TCGA-92-8064 TCGA-92-8065 
       10.59         2.70         3.48         4.01         5.26         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        4.01         5.03        26.63        14.14        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       18.31        17.46        27.68        21.44        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       21.34        27.16        18.15        27.02        20.32        18.58 
TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       20.71        12.89        16.11        13.18        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HN 
        4.54        64.54         1.22        57.30        13.74        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
       43.92        25.32        14.73        26.43        83.57         3.65 
TCGA-O2-A52Q TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
        3.72        43.89        11.18         0.20 

  DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE 
                          1.15                           0.03 
  DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE 
                        119.80                         173.82 
  DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE 
                        22.175                         21.570 
[1] "1.1 - 119.8 (22.2)" "0.0 - 173.8 (21.6)"
[1] "hr=" "1.2"
D49V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(7Q11.22) MUTATED         1        8       16        0         7
  DEL PEAK 19(7Q11.22) WILD-TYPE       1       81      136        2        58
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(7Q11.22) MUTATED           9         1          6          0
  DEL PEAK 19(7Q11.22) WILD-TYPE        86         2         57         19
                                vv
clus                             STAGE IV
  DEL PEAK 19(7Q11.22) MUTATED          0
  DEL PEAK 19(7Q11.22) WILD-TYPE        7
D49V3, multiclass
            clus
vv           DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                              8                             81
  STAGE IB                             16                            136
  STAGE II                              0                              2
  STAGE IIA                             7                             58
  STAGE IIB                             9                             86
  STAGE III                             1                              2
  STAGE IIIA                            6                             57
  STAGE IIIB                            0                             19
  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 19(7Q11.22) MUTATED    10  31   5   2
  DEL PEAK 19(7Q11.22) WILD-TYPE 102 263  66  22
D49V4, multiclass
    clus
vv   DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE
  T1                           10                            102
  T2                           31                            263
  T3                            5                             66
  T4                            2                             22
[1] 4 2
[1] TRUE
[1] "dimension of 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(7Q11.22) MUTATED    32  12   4   0
  DEL PEAK 19(7Q11.22) WILD-TYPE 285 121  36   5
D49V5, multiclass
    clus
vv   DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE
  N0                           32                            285
  N1                           12                            121
  N2                            4                             36
  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"
D49V6, binary
                                cls
clus                               0   1
  DEL PEAK 19(7Q11.22) MUTATED    40   0
  DEL PEAK 19(7Q11.22) WILD-TYPE 371   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(7Q11.22) MUTATED     40    0
  DEL PEAK 19(7Q11.22) WILD-TYPE  371    7
   clus
vv  DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE
  0                           40                            371
  1                            0                              7
[1] 2 2
[1] FALSE
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(7Q11.22) MUTATED    14  34
  DEL PEAK 19(7Q11.22) WILD-TYPE 116 337
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(7Q11.22) MUTATED     14   34
  DEL PEAK 19(7Q11.22) WILD-TYPE  116  337
        clus
vv       DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE
  FEMALE                           14                            116
  MALE                             34                            337
[1] 2 2
[1] FALSE
D49V8, binary
                                cls
clus                               0   1
  DEL PEAK 19(7Q11.22) MUTATED    36   4
  DEL PEAK 19(7Q11.22) WILD-TYPE 348  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(7Q11.22) MUTATED     36    4
  DEL PEAK 19(7Q11.22) WILD-TYPE  348   49
     clus
vv    DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE
  NO                            36                            348
  YES                            4                             49
[1] 2 2
[1] FALSE
D49V9, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(7Q11.22) MUTATED                                       1
  DEL PEAK 19(7Q11.22) WILD-TYPE                                    14
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 19(7Q11.22) MUTATED                                        0
  DEL PEAK 19(7Q11.22) WILD-TYPE                                      6
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 19(7Q11.22) MUTATED                                         0
  DEL PEAK 19(7Q11.22) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(7Q11.22) MUTATED                                                            47
  DEL PEAK 19(7Q11.22) WILD-TYPE                                                         432
D49V10, multiclass
                                                             clus
vv                                                            DEL PEAK 19(7Q11.22) MUTATED
  LUNG BASALOID 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)                           47
                                                             clus
vv                                                            DEL PEAK 19(7Q11.22) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   14
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            432
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, continuous
D49V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 19(7Q11.22) MUTATED    39   0   1   4
  DEL PEAK 19(7Q11.22) WILD-TYPE 360  12   3  19
D49V13, multiclass
    clus
vv   DEL PEAK 19(7Q11.22) MUTATED DEL PEAK 19(7Q11.22) WILD-TYPE
  R0                           39                            360
  R1                            0                             12
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(7Q11.22) MUTATED       0                         3    35
  DEL PEAK 19(7Q11.22) WILD-TYPE     9                        28   314
D49V14, multiclass
                           clus
vv                          DEL PEAK 19(7Q11.22) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               35
                           clus
vv                          DEL PEAK 19(7Q11.22) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                             28
  WHITE                                                314
[1] 3 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(7Q11.22) MUTATED     0  31
  DEL PEAK 19(7Q11.22) WILD-TYPE   8 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(7Q11.22) MUTATED      0   31
  DEL PEAK 19(7Q11.22) WILD-TYPE    8  286
                        clus
vv                       DEL PEAK 19(7Q11.22) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           31
                        clus
vv                       DEL PEAK 19(7Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            286
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 20(7Q36.3) MUTATION ANALYSIS
D50V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 20(7Q36.3) MUTATED    56  46
  DEL PEAK 20(7Q36.3) WILD-TYPE 224 168
  DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE 
                          102                           392 
  DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE 
                           46                           168 
$`DEL PEAK 20(7Q36.3) MUTATED`
TCGA-18-3406 TCGA-18-5595 TCGA-22-1017 TCGA-33-4589 TCGA-43-2578 TCGA-43-5668 
       12.20        27.19        48.82         1.55        22.49        18.38 
TCGA-43-7658 TCGA-56-8305 TCGA-56-A4BY TCGA-60-2696 TCGA-60-2712 TCGA-63-A5MH 
       78.18         3.45        17.85         3.58         9.01        66.61 
TCGA-68-8250 TCGA-77-A5GB TCGA-94-A5I4 TCGA-NC-A5HM TCGA-18-3408 TCGA-18-3415 
        8.02        30.81        16.14        39.85        75.75        92.15 
TCGA-18-4721 TCGA-21-1072 TCGA-21-1082 TCGA-21-5786 TCGA-22-1002 TCGA-22-1011 
      154.32        99.16       119.80        33.93         4.31         1.74 
TCGA-22-1016 TCGA-22-4595 TCGA-22-4601 TCGA-22-5481 TCGA-22-5482 TCGA-33-A5GW 
       27.02        24.13        34.75        79.20        11.74         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        82.52 
TCGA-39-5031 TCGA-39-5034 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6771 
       60.53        36.39        38.66        33.11        27.91         5.46 
TCGA-43-A475 TCGA-46-3765 TCGA-46-6026 TCGA-52-7809 TCGA-56-1622 TCGA-56-6545 
        9.73        13.32        13.91         5.46        28.96        21.90 
TCGA-56-7580 TCGA-56-8083 TCGA-56-8503 TCGA-56-8626 TCGA-56-8629 TCGA-56-A49D 
       30.41         4.93         1.35         9.93        15.81        20.94 
TCGA-56-A4BW TCGA-58-A46L TCGA-60-2695 TCGA-60-2703 TCGA-60-2707 TCGA-60-2726 
       19.23        56.65        21.11        96.82        21.93        11.77 
TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW 
       68.15       102.67        89.29        78.28        36.16        53.88 
TCGA-63-A5MY TCGA-66-2753 TCGA-66-2773 TCGA-66-2788 TCGA-68-7755 TCGA-68-7757 
       34.59         1.02         3.02        22.98         2.73         6.94 
TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7337 TCGA-77-7465 TCGA-77-8131 
       73.12        75.09        11.18       106.95        32.55        12.59 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8144 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 
       39.09       104.09        27.39        38.86        41.39        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        30.97        30.48 
TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-7767 TCGA-92-8065 
       15.85        15.29        29.92        12.39         2.93         2.30 
TCGA-94-A4VJ TCGA-98-8022 TCGA-98-A53A TCGA-LA-A7SW TCGA-NC-A5HK TCGA-NC-A5HQ 
       14.14        30.67        18.15        13.41         4.21        14.73 

$`DEL PEAK 20(7Q36.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI 
        4.47       123.19         4.80        31.99         6.18        32.19 
TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 
       14.93        60.66        64.93        22.06       129.01       133.74 
TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-7657 
       19.76        31.50        28.96        31.27        17.88         7.76 
TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 
        2.93        11.61        12.03        19.99        13.05        17.00 
TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 
       16.77        21.04         0.13        41.42        35.34        32.32 
TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       20.78        42.08         9.50        14.07        21.04         0.16 
TCGA-94-7943 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D 
       18.38        57.07        19.36         2.76         5.69        21.21 
TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 
       19.10         0.07        76.80        40.90        65.65        16.80 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 
        0.43         8.58       117.57        11.34        23.54        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       92.42        86.96         2.79        49.94       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-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 
        9.34        43.23        31.63        88.11        41.69        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 
       21.99         7.33        64.21        14.10        20.48        35.08 
TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       48.33         0.56        38.17        13.12        32.02        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
        9.57        11.77        63.55        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       86.30        71.34        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       16.64        97.94        79.53       173.82       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB 
       14.07        54.44        63.35         4.70        36.62         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-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       32.88        65.23        81.24        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       50.66        44.75        39.32         4.96         1.12        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-4129 TCGA-37-4130 
        4.04        26.43        33.90         4.01         7.96         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        7.46         7.82         0.39        37.58        21.70       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 
      126.58       111.35        68.58        55.20       102.18         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
       24.33         1.94        68.38        71.18        55.56        17.06 
TCGA-43-2576 TCGA-43-3394 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 
       40.21        39.12        22.98        24.89        21.47         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 
       19.59        13.38        11.77        14.20        12.16        13.02 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        9.83         4.44        10.65         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 
       28.34        30.35         8.75        27.45        12.43        18.25 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       18.48        14.53        31.27        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
       17.49        33.24        14.96         3.48        26.89        14.07 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A4BX 
        1.81        22.75        13.81        10.36        20.25        13.32 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       18.74         0.26        14.47         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-60-2713 TCGA-60-2714 TCGA-60-2716 
       80.45        49.48        66.54        56.91        50.33        48.49 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       42.64         3.19        29.85        35.90        23.57        26.83 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI 
       52.67        70.13        70.42        55.30        70.62        58.65 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MT 
       59.97        45.57        14.99        11.34        25.28        16.37 
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-70-6722 TCGA-70-6723 
        6.64        13.35        16.18        14.73        12.07        12.33 
TCGA-77-6842 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       29.56        23.28       140.09         0.49        73.22        70.13 
TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 
        0.16        46.78         6.51        86.76        55.73        37.81 
TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 
      156.66        53.92        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 
       66.51        54.41        65.49        60.53        36.36       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      132.36       150.25        22.29         5.92        61.94        27.62 
TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
        9.67        40.24         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 
       26.79        30.64        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        15.39         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       36.59        38.14        12.59        18.08        22.59        30.28 
TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       34.13        19.86        24.36        19.73        27.16        16.21 
TCGA-85-A511 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE 
       14.96         3.65        24.92        11.77        20.22        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-8035 
       10.59         2.70         3.48         4.01         5.26         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
        5.03        26.63        17.69        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53B 
       27.68        21.44        30.81        21.34        27.16         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 
       27.02        20.32        18.58        20.71        12.89        16.11 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       13.18        11.84         4.54        64.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT 
       13.74         2.89        49.28        43.92        25.32        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       83.57         3.65        33.07         3.72        12.72        43.89 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

  DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE 
                         0.30                          0.03 
  DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE 
                       154.32                        173.82 
  DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE 
                       22.210                        21.455 
[1] "0.3 - 154.3 (22.2)" "0.0 - 173.8 (21.5)"
[1] "hr=" "1"  
D50V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(7Q36.3) MUTATED         0       19       40        0        15
  DEL PEAK 20(7Q36.3) WILD-TYPE       2       70      112        2        50
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(7Q36.3) MUTATED          18         0         12          0
  DEL PEAK 20(7Q36.3) WILD-TYPE        77         3         51         19
                               vv
clus                            STAGE IV
  DEL PEAK 20(7Q36.3) MUTATED          0
  DEL PEAK 20(7Q36.3) WILD-TYPE        7
D50V3, multiclass
            clus
vv           DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE
  STAGE I                              0                             2
  STAGE IA                            19                            70
  STAGE IB                            40                           112
  STAGE II                             0                             2
  STAGE IIA                           15                            50
  STAGE IIB                           18                            77
  STAGE III                            0                             3
  STAGE IIIA                          12                            51
  STAGE IIIB                           0                            19
  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(7Q36.3) MUTATED    25  64  13   2
  DEL PEAK 20(7Q36.3) WILD-TYPE  87 230  58  22
D50V4, multiclass
    clus
vv   DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE
  T1                          25                            87
  T2                          64                           230
  T3                          13                            58
  T4                           2                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2  N3
  DEL PEAK 20(7Q36.3) MUTATED    70  25   6   0
  DEL PEAK 20(7Q36.3) WILD-TYPE 247 108  34   5
D50V5, multiclass
    clus
vv   DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE
  N0                          70                           247
  N1                          25                           108
  N2                           6                            34
  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(7Q36.3) MUTATED    89   0
  DEL PEAK 20(7Q36.3) WILD-TYPE 322   7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q36.3) MUTATED     89    0
  DEL PEAK 20(7Q36.3) WILD-TYPE  322    7
   clus
vv  DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE
  0                          89                           322
  1                           0                             7
[1] 2 2
[1] FALSE
D50V7, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q36.3) MUTATED    27  77
  DEL PEAK 20(7Q36.3) WILD-TYPE 103 294
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q36.3) MUTATED     27   77
  DEL PEAK 20(7Q36.3) WILD-TYPE  103  294
        clus
vv       DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE
  FEMALE                          27                           103
  MALE                            77                           294
[1] 2 2
[1] FALSE
D50V8, binary
                               cls
clus                              0   1
  DEL PEAK 20(7Q36.3) MUTATED    81   7
  DEL PEAK 20(7Q36.3) WILD-TYPE 303  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q36.3) MUTATED     81    7
  DEL PEAK 20(7Q36.3) WILD-TYPE  303   46
     clus
vv    DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE
  NO                           81                           303
  YES                           7                            46
[1] 2 2
[1] FALSE
D50V9, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(7Q36.3) MUTATED                                       3
  DEL PEAK 20(7Q36.3) WILD-TYPE                                    12
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 20(7Q36.3) MUTATED                                        0
  DEL PEAK 20(7Q36.3) WILD-TYPE                                      6
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 20(7Q36.3) MUTATED                                         0
  DEL PEAK 20(7Q36.3) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(7Q36.3) MUTATED                                                           101
  DEL PEAK 20(7Q36.3) WILD-TYPE                                                         378
D50V10, multiclass
                                                             clus
vv                                                            DEL PEAK 20(7Q36.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         101
                                                             clus
vv                                                            DEL PEAK 20(7Q36.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           378
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
D50V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 20(7Q36.3) MUTATED    86   1   1   7
  DEL PEAK 20(7Q36.3) WILD-TYPE 313  11   3  16
D50V13, multiclass
    clus
vv   DEL PEAK 20(7Q36.3) MUTATED DEL PEAK 20(7Q36.3) WILD-TYPE
  R0                          86                           313
  R1                           1                            11
  R2                           1                             3
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(7Q36.3) MUTATED       2                         4    74
  DEL PEAK 20(7Q36.3) WILD-TYPE     7                        27   275
D50V14, multiclass
                           clus
vv                          DEL PEAK 20(7Q36.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              74
                           clus
vv                          DEL PEAK 20(7Q36.3) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            27
  WHITE                                               275
[1] 3 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(7Q36.3) MUTATED     2  64
  DEL PEAK 20(7Q36.3) WILD-TYPE   6 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 20(7Q36.3) MUTATED      2   64
  DEL PEAK 20(7Q36.3) WILD-TYPE    6  253
                        clus
vv                       DEL PEAK 20(7Q36.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          64
                        clus
vv                       DEL PEAK 20(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           253
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 21(8P23.2) MUTATION ANALYSIS
D51V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(8P23.2) MUTATED   186 150
  DEL PEAK 21(8P23.2) WILD-TYPE  94  64
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                          336                           158 
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                          150                            64 
$`DEL PEAK 21(8P23.2) MUTATED`
TCGA-18-3406 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 
       12.20        31.99         6.18        27.19        14.93        48.82 
TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 
       60.66        22.06       129.01         1.55        19.76        31.50 
TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 
       28.96        31.27        17.88        22.49        18.38         7.76 
TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 TCGA-56-8504 
       78.18         2.93        11.61        12.03        13.05        16.77 
TCGA-56-A4BY TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-68-8250 
       17.85         0.13        41.42         9.01        32.32         8.02 
TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
       20.78        42.08         9.50         0.16        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD 
       57.07        19.36         2.76         5.69        19.10         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 
       76.80        39.85        40.90         8.58       117.57        11.34 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       92.15        92.42         2.79       154.32        49.94       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-22-1002 
       43.23        31.63        88.11        33.93        10.82         4.31 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
       14.10        27.02        20.48        48.33         0.56        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
       34.75        13.12        32.02         9.57        11.77        63.55 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 
       44.25         0.79        71.34        79.20        18.84        30.12 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 
       56.32        16.64        79.53       173.82       103.53        14.07 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI 
       63.35         4.70         0.30        36.62       110.99        44.19 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-5231 TCGA-34-5236 TCGA-34-5241 
       27.16         2.63        61.61        65.23         9.07        16.93 
TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
       39.32        38.79         4.04         4.01         0.43         0.39 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 
        7.46         6.81         0.39        21.70       133.25       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
      111.35        68.58        82.52       102.18         1.71        24.33 
TCGA-39-5031 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
       60.53        55.56        17.06        40.21        38.66        39.12 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-8116 
       33.11        22.98        24.89        21.47         5.46        11.77 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-51-4080 
       13.32        12.16         9.83         4.44        10.65         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 
       29.95        28.34         5.46        30.35        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       12.43        18.25        18.48        14.53        31.27        30.41 
TCGA-56-7582 TCGA-56-8082 TCGA-56-8083 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
       19.76        14.96         4.93         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8387 
       20.94        19.23        13.32        18.74         0.26        13.25 
TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       29.95        16.47        34.78        34.36        56.65        35.24 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2710 
       10.22        96.82        37.94        92.71        80.45        66.54 
TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 
       56.91        50.33        42.64         3.19        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 
       26.83        11.77        52.67        70.13        70.42        55.30 
TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN 
      102.67        58.65        59.97        45.57        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       25.28        78.28        16.37        36.16        53.88        34.59 
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-66-2758 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-66-2780 TCGA-66-2781 TCGA-66-2782 
        1.02         2.01         7.07        12.03         3.98        12.00 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
       24.95         1.97        40.01         4.04        22.98         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-8251 
       30.02        10.06         4.01        49.05         2.73        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 
       16.18        14.73        12.07        12.33        29.56        73.12 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       75.09        23.28        11.18       140.09         0.49        73.22 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
      106.95         0.16        46.78        32.55         6.51        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       55.73        37.81       156.66        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 
       11.54        26.40        27.39         6.97        66.51        60.53 
TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       36.36        22.29        61.94        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       41.39        40.24         6.41        36.53        34.95        31.30 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 
        1.38         1.15        29.95        18.94        25.15        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 
       31.56        26.79        30.64        34.52        10.09        22.45 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 
        5.29         3.09        32.71         2.01         7.76        38.14 
TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ 
       12.59        18.08        34.13        30.97        19.86        30.48 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       19.73        27.16        16.21        14.96        29.92        12.39 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-94-8491 
        3.65         2.93        20.22         3.48         4.01        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-8021 
       14.14        17.69        71.01        18.31        17.46        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J 
       30.67        21.34        27.16        18.15         2.01        20.71 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       16.11        13.18        11.84        64.54         1.22        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
       13.74         2.89        49.28        25.32        14.73        26.43 
TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       83.57        33.07         3.72        12.72        43.89         0.20 

$`DEL PEAK 21(8P23.2) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-21-A5DI TCGA-22-5472 TCGA-33-4533 
        4.47       123.19         4.80        32.19        64.93       133.74 
TCGA-56-7221 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2715 
       19.99         3.45        17.00        21.04         3.58        35.34 
TCGA-63-A5MH TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-98-A53D TCGA-NK-A5CT 
       66.61        30.81        14.07        21.04        21.21        65.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
       16.80         0.43        75.75        23.54        36.07        86.96 
TCGA-21-1071 TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 TCGA-21-5784 TCGA-22-0940 
       46.88        15.58        31.73       119.80        41.69        21.99 
TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 TCGA-22-4595 TCGA-22-4607 
        7.33        64.21         1.74        35.08        24.13        19.30 
TCGA-22-5474 TCGA-22-5479 TCGA-22-5482 TCGA-22-5489 TCGA-33-4538 TCGA-33-4583 
       14.63        86.30        11.74        62.86        97.94       151.27 
TCGA-33-4587 TCGA-33-AASB TCGA-33-AASJ TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 
       54.44         6.94       118.36        32.88        81.24        74.66 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 
       60.30        50.66        44.75         4.96         1.12        26.43 
TCGA-34-A5IX TCGA-37-4129 TCGA-37-4130 TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EL 
       33.90         7.96         8.12         7.82         3.39        37.58 
TCGA-39-5022 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-43-5670 
       55.20         1.94        36.39        68.38        71.18        27.91 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U TCGA-46-3767 
        3.81        19.59        13.38         9.73        14.20        13.02 
TCGA-46-6026 TCGA-51-4079 TCGA-52-7811 TCGA-56-6545 TCGA-56-7730 TCGA-56-7731 
       13.91         0.39         8.75        21.90         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       17.49        33.24         3.48        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-A62T TCGA-58-8386 
        1.81        22.75        13.81        10.36        14.47         0.03 
TCGA-58-8388 TCGA-58-8391 TCGA-58-A46J TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 
       13.55        71.24        85.12        29.92        21.11        12.23 
TCGA-60-2707 TCGA-60-2709 TCGA-60-2716 TCGA-60-2722 TCGA-63-7022 TCGA-63-A5MG 
       21.93        49.48        48.49        29.85        68.15        70.62 
TCGA-63-A5MR TCGA-66-2742 TCGA-66-2765 TCGA-66-2767 TCGA-66-2770 TCGA-66-2771 
       89.29        21.07         2.01         2.01        23.01        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2786 TCGA-66-2788 TCGA-66-2794 
        3.02         2.01        19.00        25.97        22.98        54.08 
TCGA-68-7756 TCGA-68-7757 TCGA-77-7335 TCGA-77-8131 TCGA-77-8133 TCGA-77-8150 
        6.64         6.94        70.13        12.59        53.92        54.41 
TCGA-77-8153 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-85-7699 
       65.49       126.18       132.36       150.25         5.92        32.91 
TCGA-85-8049 TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8479 TCGA-85-8580 
       19.04         0.76        13.22        16.77        15.39        36.59 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A510 TCGA-85-A512 TCGA-90-6837 
       22.59        30.28        24.36        15.85        15.29        24.92 
TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 
       11.77        22.62        10.59         2.70         5.26         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53C TCGA-98-A53H 
        4.01         5.03        27.68        21.44        27.02        20.32 
TCGA-98-A53I TCGA-L3-A4E7 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HK TCGA-NC-A5HO 
       18.58        12.89        13.41         4.54         4.21        43.92 
TCGA-NK-A5CX TCGA-O2-A5IB 
        3.65        11.18 

  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                       173.82                        151.27 
  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE 
                       22.735                        21.055 
[1] "0.1 - 173.8 (22.7)" "0.0 - 151.3 (21.1)"
[1] "hr=" "1.1"
D51V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(8P23.2) MUTATED         2       61       98        1        42
  DEL PEAK 21(8P23.2) WILD-TYPE       0       28       54        1        23
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(8P23.2) MUTATED          69         2         48         12
  DEL PEAK 21(8P23.2) WILD-TYPE        26         1         15          7
                               vv
clus                            STAGE IV
  DEL PEAK 21(8P23.2) MUTATED          3
  DEL PEAK 21(8P23.2) WILD-TYPE        4
D51V3, multiclass
            clus
vv           DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                            61                            28
  STAGE IB                            98                            54
  STAGE II                             1                             1
  STAGE IIA                           42                            23
  STAGE IIB                           69                            26
  STAGE III                            2                             1
  STAGE IIIA                          48                            15
  STAGE IIIB                          12                             7
  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 21(8P23.2) MUTATED    78 202  47  14
  DEL PEAK 21(8P23.2) WILD-TYPE  34  92  24  10
D51V4, multiclass
    clus
vv   DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  T1                          78                            34
  T2                         202                            92
  T3                          47                            24
  T4                          14                            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 21(8P23.2) MUTATED   207  97  31   3
  DEL PEAK 21(8P23.2) WILD-TYPE 110  36   9   2
D51V5, multiclass
    clus
vv   DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  N0                         207                           110
  N1                          97                            36
  N2                          31                             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"
D51V6, binary
                               cls
clus                              0   1
  DEL PEAK 21(8P23.2) MUTATED   290   3
  DEL PEAK 21(8P23.2) WILD-TYPE 121   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8P23.2) MUTATED    290    3
  DEL PEAK 21(8P23.2) WILD-TYPE  121    4
   clus
vv  DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  0                         290                           121
  1                           3                             4
[1] 2 2
[1] FALSE
D51V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(8P23.2) MUTATED    84 257
  DEL PEAK 21(8P23.2) WILD-TYPE  46 114
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8P23.2) MUTATED     84  257
  DEL PEAK 21(8P23.2) WILD-TYPE   46  114
        clus
vv       DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  FEMALE                          84                            46
  MALE                           257                           114
[1] 2 2
[1] FALSE
D51V8, binary
                               cls
clus                              0   1
  DEL PEAK 21(8P23.2) MUTATED   257  39
  DEL PEAK 21(8P23.2) WILD-TYPE 127  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8P23.2) MUTATED    257   39
  DEL PEAK 21(8P23.2) WILD-TYPE  127   14
     clus
vv    DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  NO                          257                           127
  YES                          39                            14
[1] 2 2
[1] FALSE
D51V9, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(8P23.2) MUTATED                                       9
  DEL PEAK 21(8P23.2) WILD-TYPE                                     6
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 21(8P23.2) MUTATED                                        3
  DEL PEAK 21(8P23.2) WILD-TYPE                                      3
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 21(8P23.2) MUTATED                                         0
  DEL PEAK 21(8P23.2) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(8P23.2) MUTATED                                                           329
  DEL PEAK 21(8P23.2) WILD-TYPE                                                         150
D51V10, multiclass
                                                             clus
vv                                                            DEL PEAK 21(8P23.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         329
                                                             clus
vv                                                            DEL PEAK 21(8P23.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
D51V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(8P23.2) MUTATED   277   7   2  15
  DEL PEAK 21(8P23.2) WILD-TYPE 122   5   2   8
D51V13, multiclass
    clus
vv   DEL PEAK 21(8P23.2) MUTATED DEL PEAK 21(8P23.2) WILD-TYPE
  R0                         277                           122
  R1                           7                             5
  R2                           2                             2
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(8P23.2) MUTATED       5                        20   234
  DEL PEAK 21(8P23.2) WILD-TYPE     4                        11   115
D51V14, multiclass
                           clus
vv                          DEL PEAK 21(8P23.2) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                          20
  WHITE                                             234
                           clus
vv                          DEL PEAK 21(8P23.2) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               115
[1] 3 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(8P23.2) MUTATED     5 207
  DEL PEAK 21(8P23.2) WILD-TYPE   3 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8P23.2) MUTATED      5  207
  DEL PEAK 21(8P23.2) WILD-TYPE    3  110
                        clus
vv                       DEL PEAK 21(8P23.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         207
                        clus
vv                       DEL PEAK 21(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           110
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 22(9P23) MUTATION ANALYSIS
D52V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 22(9P23) MUTATED   187 140
  DEL PEAK 22(9P23) WILD-TYPE  93  74
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        327                         167 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                        140                          74 
$`DEL PEAK 22(9P23) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 
       12.20       123.19        32.19        14.93        60.66        64.93 
TCGA-22-A5C4 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 
       22.06        19.76        31.50        28.96        31.27        22.49 
TCGA-43-5668 TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
       18.38         7.76         2.93        11.61        12.03        19.99 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR 
       13.05         3.45        17.00        16.77        21.04         0.13 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2721 TCGA-63-A5MH TCGA-90-7766 TCGA-90-7964 
        3.58        41.42        32.32        66.61         9.50        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       21.04         0.16        18.38        16.14        57.07        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HD TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W 
        2.76         5.69         0.07        65.65        16.80         8.58 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
      117.57        11.34        23.54        92.15        36.07        92.42 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2.79       154.32        49.94        46.88        99.16        70.16 
TCGA-21-1077 TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5783 
       34.78        31.73       122.43       119.80        43.23        88.11 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       33.93        10.82        21.99        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
       27.02        20.48        35.08        48.33        24.13        38.17 
TCGA-22-4601 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5477 TCGA-22-5478 
       34.75        19.30         9.57        11.77        44.25         0.79 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 TCGA-33-4538 
       86.30        11.74        18.84        30.12        56.32        97.94 
TCGA-33-4547 TCGA-33-4582 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AAS8 TCGA-33-AASB 
       79.53       103.53        63.35         4.70        36.62         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-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 
       32.88        65.23        81.24        16.93        44.75         4.96 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       38.79         4.04        26.43        33.90         4.01         0.43 
TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN 
        8.12         6.81         0.39         3.39        37.58        21.70 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
      133.25       126.58       102.18         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5036 TCGA-39-5040 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       60.53        71.18        17.06        39.12        33.11        27.91 
TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-46-3765 
       21.47         5.46        19.59        13.38        11.77        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6026 TCGA-51-4079 
       12.16        13.02         9.83         4.44        13.91         0.39 
TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
       29.95         5.46        30.35        28.96        12.43        18.25 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
       21.90        18.48        14.53        31.27        30.41        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
        6.51         0.10        17.49        33.24        14.96         4.93 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 
       26.89        14.07         1.35         1.81        13.81        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-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 
        0.26         0.03        13.25        29.95        16.47        34.78 
TCGA-58-A46J TCGA-58-A46L TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 
       85.12        56.65        10.22        96.82        92.71        21.93 
TCGA-60-2708 TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-60-2720 TCGA-60-2724 
       80.45        66.54        56.91        42.64         3.19        23.57 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB 
       11.77        52.67        70.13        68.15        55.30       102.67 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       70.62        58.65        59.97        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       16.37        53.88        16.96        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2759 TCGA-66-2765 
        0.99         1.02         2.01         0.99        25.05         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        2.01         7.07        19.00         2.01        19.00        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 
        3.98        12.00         1.97        25.97        22.98         4.04 
TCGA-66-2790 TCGA-66-2793 TCGA-66-2800 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
       22.98        10.06        49.05         6.94        13.35        16.18 
TCGA-70-6723 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 
       12.33        73.12        75.09        23.28        11.18        73.22 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 
       70.13       106.95         0.16        32.55        86.76        55.73 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 
       37.81       156.66        53.92        17.72        11.54        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
       27.39         6.97        66.51        65.49        60.53        36.36 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 
      132.36        22.29         5.92        61.94        38.86         9.67 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       41.39        36.53        34.95        32.91         1.38         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 
       29.95        18.94        25.15        26.79        34.52         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 
       13.22        22.45        16.77         5.29        32.71        15.39 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
        7.76        36.59        18.08        22.59        30.28        34.13 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       30.97        19.86        30.48        19.73        27.16        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 
       15.85        14.96        29.92        12.39         3.65         2.93 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 
       10.59         2.70         3.48         4.01         2.30         4.01 
TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-96-A4JL TCGA-98-8021 
        5.03        14.14        17.69        18.31        27.68        30.81 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J 
       21.34        27.16        18.15         2.01        18.58        20.71 
TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       16.11        13.41        11.84         4.54        64.54        57.30 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52Q 
       49.28        43.92        25.32        26.43        83.57         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       12.72        43.89         0.20 

$`DEL PEAK 22(9P23) WILD-TYPE`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-22-1017 
        4.47         4.80        31.99         6.18        27.19        48.82 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-39-5039 TCGA-43-7658 TCGA-56-A4BY 
      129.01       133.74         1.55        17.88        78.18        17.85 
TCGA-60-2712 TCGA-60-2715 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
        9.01        35.34         8.02        20.78        42.08        30.81 
TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE 
       21.21        19.10        76.80        39.85        40.90         0.43 
TCGA-18-3408 TCGA-18-3421 TCGA-21-1070 TCGA-21-1076 TCGA-21-1078 TCGA-21-1081 
       75.75        86.96       119.54        60.89        15.58         9.34 
TCGA-21-5782 TCGA-21-5784 TCGA-22-0944 TCGA-22-1002 TCGA-22-4596 TCGA-22-4604 
       31.63        41.69         7.33         4.31         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-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-A5GW 
       16.64       173.82       151.27        14.07        54.44         0.30 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 
       74.66         9.07        60.30        50.66        39.32         1.12 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-39-5019 TCGA-39-5021 
        0.39         7.96         7.46         7.82       111.35        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-43-2576 
       55.20        82.52        36.39        68.38        55.56        40.21 
TCGA-43-2581 TCGA-43-6143 TCGA-43-6647 TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U 
       38.66        22.98        24.89         3.81         9.73        14.20 
TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-8304 
       10.65         0.39        28.34         8.75        27.45         3.48 
TCGA-56-8623 TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8388 TCGA-58-8391 TCGA-58-A46K 
       22.75        18.74        14.47        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-60-2714 TCGA-60-2716 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-63-7021 
       50.33        48.49        29.85        35.90        26.83        70.42 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2755 
       45.57        14.99        11.34        36.16        34.59         0.92 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 
       43.99        21.01         0.99         1.02         2.01        23.01 
TCGA-66-2773 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
        3.02        24.95        40.01         5.03        30.02        54.08 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 
        4.01         2.73         6.64        14.73        12.07        29.56 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7463 TCGA-77-8007 TCGA-77-8131 TCGA-77-8136 
      140.09         0.49        46.78         6.51        12.59        39.09 
TCGA-77-8139 TCGA-77-8150 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6561 
      104.09        54.41       126.18       150.25        27.62        40.24 
TCGA-85-6798 TCGA-85-7698 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 
        6.41        31.30        19.04        24.13        31.56        30.64 
TCGA-85-8277 TCGA-85-8353 TCGA-85-8355 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4PA 
       10.09         3.09         2.01        38.14        12.59        24.36 
TCGA-85-A512 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-8064 
       15.29        24.92        11.77        20.22        22.62         5.26 
TCGA-94-8491 TCGA-96-7544 TCGA-96-8170 TCGA-98-7454 TCGA-98-8022 TCGA-98-A53C 
       26.63        71.01        17.46        21.44        30.67        27.02 
TCGA-98-A53H TCGA-L3-A4E7 TCGA-LA-A446 TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK 
       20.32        12.89        13.18         1.22        13.74         4.21 
TCGA-NC-A5HL TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A5IB 
        2.89        14.73         3.65        33.07        11.18 

  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                       0.03                        0.30 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                     156.66                      173.82 
  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE 
                      21.04                       24.13 
[1] "0.0 - 156.7 (21.0)" "0.3 - 173.8 (24.1)"
[1] "hr=" "1"  
D52V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(9P23) MUTATED         1       62      101        1        47
  DEL PEAK 22(9P23) WILD-TYPE       1       27       51        1        18
                             vv
clus                          STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(9P23) MUTATED          55         2         45         11
  DEL PEAK 22(9P23) WILD-TYPE        40         1         18          8
                             vv
clus                          STAGE IV
  DEL PEAK 22(9P23) MUTATED          6
  DEL PEAK 22(9P23) WILD-TYPE        1
D52V3, multiclass
            clus
vv           DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  STAGE I                            1                           1
  STAGE IA                          62                          27
  STAGE IB                         101                          51
  STAGE II                           1                           1
  STAGE IIA                         47                          18
  STAGE IIB                         55                          40
  STAGE III                          2                           1
  STAGE IIIA                        45                          18
  STAGE IIIB                        11                           8
  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 22(9P23) MUTATED    79 187  50  16
  DEL PEAK 22(9P23) WILD-TYPE  33 107  21   8
D52V4, multiclass
    clus
vv   DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  T1                        79                          33
  T2                       187                         107
  T3                        50                          21
  T4                        16                           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 22(9P23) MUTATED   216  83  28   2
  DEL PEAK 22(9P23) WILD-TYPE 101  50  12   3
D52V5, multiclass
    clus
vv   DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  N0                       216                         101
  N1                        83                          50
  N2                        28                          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"
D52V6, binary
                             cls
clus                            0   1
  DEL PEAK 22(9P23) MUTATED   268   6
  DEL PEAK 22(9P23) WILD-TYPE 143   1
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED    268    6
  DEL PEAK 22(9P23) WILD-TYPE  143    1
   clus
vv  DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  0                       268                         143
  1                         6                           1
[1] 2 2
[1] FALSE
D52V7, binary
                             cls
clus                            0   1
  DEL PEAK 22(9P23) MUTATED    80 252
  DEL PEAK 22(9P23) WILD-TYPE  50 119
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED     80  252
  DEL PEAK 22(9P23) WILD-TYPE   50  119
        clus
vv       DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  FEMALE                        80                          50
  MALE                         252                         119
[1] 2 2
[1] FALSE
D52V8, binary
                             cls
clus                            0   1
  DEL PEAK 22(9P23) MUTATED   256  32
  DEL PEAK 22(9P23) WILD-TYPE 128  21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED    256   32
  DEL PEAK 22(9P23) WILD-TYPE  128   21
     clus
vv    DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  NO                        256                         128
  YES                        32                          21
[1] 2 2
[1] FALSE
D52V9, continuous
                             vv
clus                          LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(9P23) MUTATED                                       6
  DEL PEAK 22(9P23) WILD-TYPE                                     9
                             vv
clus                          LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 22(9P23) MUTATED                                        3
  DEL PEAK 22(9P23) WILD-TYPE                                      3
                             vv
clus                          LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 22(9P23) MUTATED                                         0
  DEL PEAK 22(9P23) WILD-TYPE                                       1
                             vv
clus                          LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(9P23) MUTATED                                                           323
  DEL PEAK 22(9P23) WILD-TYPE                                                         156
D52V10, multiclass
                                                             clus
vv                                                            DEL PEAK 22(9P23) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                               6
  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(9P23) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, continuous
D52V12, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 22(9P23) MUTATED   265   7   3  15
  DEL PEAK 22(9P23) WILD-TYPE 134   5   1   8
D52V13, multiclass
    clus
vv   DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  R0                       265                         134
  R1                         7                           5
  R2                         3                           1
  RX                        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                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(9P23) MUTATED       7                        24   227
  DEL PEAK 22(9P23) WILD-TYPE     2                         7   122
D52V14, multiclass
                           clus
vv                          DEL PEAK 22(9P23) MUTATED
  ASIAN                                             7
  BLACK OR AFRICAN AMERICAN                        24
  WHITE                                           227
                           clus
vv                          DEL PEAK 22(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"
D52V15, binary
                             cls
clus                            0   1
  DEL PEAK 22(9P23) MUTATED     4 213
  DEL PEAK 22(9P23) WILD-TYPE   4 104
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 22(9P23) MUTATED      4  213
  DEL PEAK 22(9P23) WILD-TYPE    4  104
                        clus
vv                       DEL PEAK 22(9P23) MUTATED DEL PEAK 22(9P23) WILD-TYPE
  HISPANIC OR LATINO                             4                           4
  NOT HISPANIC OR LATINO                       213                         104
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 23(9P21.3) MUTATION ANALYSIS
D53V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 23(9P21.3) MUTATED   221 162
  DEL PEAK 23(9P21.3) WILD-TYPE  59  52
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          383                           111 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                          162                            52 
$`DEL PEAK 23(9P21.3) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-21-A5DI TCGA-22-5471 
       12.20       123.19         4.80         6.18        32.19        60.66 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
       64.93        22.06        19.76        31.50        28.96        31.27 
TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V 
       22.49        18.38         7.76         2.93        11.61        12.03 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ 
       19.99        13.05         3.45        17.00        16.77        21.04 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH TCGA-77-A5GA 
        3.58        41.42         9.01        32.32        66.61        42.08 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
        9.50        14.07        21.04         0.16        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HD TCGA-NK-A5CT 
       57.07        19.36         2.76         5.69         0.07        65.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       16.80         0.43         8.58       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       92.15        36.07        92.42         2.79       154.32        49.94 
TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1077 TCGA-21-1080 TCGA-21-1082 
       46.88        99.16        70.16        34.78       122.43       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
       43.23        31.63        88.11        33.93        10.82         7.33 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 
       64.21         1.74        14.10        27.02        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 
       48.33        24.13        38.17        34.75        13.12        19.30 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
        9.57        11.77        63.55        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       86.30        11.74        18.84        30.12        62.86        56.32 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 
       97.94        79.53       173.82       103.53        14.07        63.35 
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-34-2608 TCGA-34-5231 TCGA-34-5232 
       27.16         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 
       16.93        44.75         4.96        38.79         4.04        26.43 
TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 
       33.90         4.01         0.43         8.12         6.81         0.39 
TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
        3.39        37.58        21.70       133.25       126.58       111.35 
TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       68.58        82.52       102.18         1.71        24.33         1.94 
TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 
       60.53        71.18        55.56        17.06        40.21        39.12 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 
       33.11        27.91        24.89        21.47         5.46        19.59 
TCGA-43-8115 TCGA-43-8116 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
       13.38        11.77        13.32        12.16        13.02         9.83 
TCGA-46-3769 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
        4.44        13.91         0.39        29.95         5.46        30.35 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 
       27.45        28.96        12.43        18.25        21.90        18.48 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       14.53        31.27        30.41        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
       17.49        33.24        14.96         4.93         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       14.07         1.35         1.81        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS 
       20.25        15.81        20.94        19.23        13.32         0.26 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
        0.03        13.25        29.95        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-60-2698 TCGA-60-2703 
       85.12        34.36        56.65        35.24        10.22        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2713 
       37.94        92.71        21.93        80.45        66.54        56.91 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       50.33        42.64         3.19        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
       26.83        11.77        52.67        70.13        70.42        68.15 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM 
       55.30       102.67        70.62        58.65        59.97        14.99 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW 
       25.28        89.29        78.28        16.37        36.16        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-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 
        2.01         0.92         0.99        21.01        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-66-2773 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        3.02         2.01        19.00        12.03         3.98        12.00 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 
        1.97        25.97        22.98         4.04        22.98        10.06 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
       54.08        49.05         2.73         6.94        13.35        16.18 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       12.07        12.33        29.56        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        73.22        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
       46.78        32.55        86.76        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       12.59        53.92        17.72        11.54        26.40        27.39 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 
        6.97        66.51        65.49        60.53        36.36       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 
      150.25        22.29         5.92        61.94        38.86         9.67 
TCGA-85-6560 TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
       41.39        36.53        34.95        32.91         1.38         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       29.95        18.94        25.15        26.79        30.64        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-85-8582 TCGA-85-8584 TCGA-85-8664 
       15.39         7.76        36.59        38.14        12.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ 
       22.59        30.28        34.13        30.97        19.86        30.48 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 
       19.73        27.16        16.21        15.85        14.96        15.29 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE TCGA-90-A59Q 
       29.92        12.39         3.65         2.93        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 
        2.70         3.48         4.01         2.30         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        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A 
       27.68        30.81        30.67        21.34        27.16        18.15 
TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
        2.01        18.58        20.71        16.11        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL 
       11.84         4.54        64.54        57.30         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
       49.28        43.92        25.32        14.73        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
        3.65         3.72        12.72        43.89         0.20 

$`DEL PEAK 23(9P21.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3416 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-33-4532 
        4.47        31.99        27.19        14.93        48.82       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-39-5039 TCGA-43-7658 TCGA-56-A4BY TCGA-56-A5DR 
      133.74         1.55        17.88        78.18        17.85         0.13 
TCGA-60-2715 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GB TCGA-98-A53D TCGA-J1-A4AH 
       35.34         8.02        20.78        30.81        21.21        19.10 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-18-3408 TCGA-18-3421 TCGA-21-1070 
       76.80        39.85        40.90        75.75        86.96       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-22-1002 TCGA-22-4596 TCGA-22-4605 TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 
        4.31         0.56        32.02        71.34        79.20        16.64 
TCGA-33-4583 TCGA-33-4587 TCGA-33-A5GW TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
      151.27        54.44         0.30        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 
       50.66        39.32         1.12         0.39         7.96         7.46 
TCGA-37-4133 TCGA-39-5022 TCGA-39-5034 TCGA-39-5035 TCGA-43-2581 TCGA-43-6143 
        7.82        55.20        36.39        68.38        38.66        22.98 
TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-51-4080 TCGA-52-7622 
        3.81         9.73        14.20        10.65         0.39        28.34 
TCGA-52-7811 TCGA-56-8623 TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8388 TCGA-58-A46N 
        8.75        22.75        18.74        14.47        13.55        29.92 
TCGA-60-2695 TCGA-60-2697 TCGA-60-2709 TCGA-60-2716 TCGA-63-A5ML TCGA-63-A5MN 
       21.11        12.23        49.48        48.49        45.57        11.34 
TCGA-66-2744 TCGA-66-2757 TCGA-66-2763 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 
        0.99        43.99         0.99        24.95        40.01         5.03 
TCGA-66-2792 TCGA-66-2795 TCGA-68-7756 TCGA-68-A59J TCGA-77-7139 TCGA-77-8007 
       30.02         4.01         6.64        14.73       140.09         6.51 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8150 TCGA-77-A5FZ TCGA-77-A5GF TCGA-85-6561 
       39.09       104.09        54.41       126.18        27.62        40.24 
TCGA-85-6798 TCGA-85-7698 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8277 
        6.41        31.30        19.04        24.13        31.56        10.09 
TCGA-85-8353 TCGA-85-8355 TCGA-85-A4PA TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED 
        3.09         2.01        24.36        24.92        11.77        20.22 
TCGA-92-8064 TCGA-98-7454 TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 TCGA-NC-A5HH 
        5.26        21.44        27.02        20.32        12.89         1.22 
TCGA-NC-A5HJ TCGA-O2-A52N TCGA-O2-A5IB 
       13.74        33.07        11.18 

  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                         0.03                          0.13 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                       173.82                        151.27 
  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE 
                        21.70                         21.99 
[1] "0.0 - 173.8 (21.7)" "0.1 - 151.3 (22.0)"
[1] "hr=" "1.1"
D53V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(9P21.3) MUTATED         1       69      116        1        57
  DEL PEAK 23(9P21.3) WILD-TYPE       1       20       36        1         8
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(9P21.3) MUTATED          67         2         52         14
  DEL PEAK 23(9P21.3) WILD-TYPE        28         1         11          5
                               vv
clus                            STAGE IV
  DEL PEAK 23(9P21.3) MUTATED          6
  DEL PEAK 23(9P21.3) WILD-TYPE        1
D53V3, multiclass
            clus
vv           DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  STAGE I                              1                             1
  STAGE IA                            69                            20
  STAGE IB                           116                            36
  STAGE II                             1                             1
  STAGE IIA                           57                             8
  STAGE IIB                           67                            28
  STAGE III                            2                             1
  STAGE IIIA                          52                            11
  STAGE IIIB                          14                             5
  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(9P21.3) MUTATED    89 227  54  18
  DEL PEAK 23(9P21.3) WILD-TYPE  23  67  17   6
D53V4, multiclass
    clus
vv   DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  T1                          89                            23
  T2                         227                            67
  T3                          54                            17
  T4                          18                             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 23(9P21.3) MUTATED   242 101  38   3
  DEL PEAK 23(9P21.3) WILD-TYPE  75  32   2   2
D53V5, multiclass
    clus
vv   DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  N0                         242                            75
  N1                         101                            32
  N2                          38                             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"
D53V6, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED   319   6
  DEL PEAK 23(9P21.3) WILD-TYPE  92   1
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED    319    6
  DEL PEAK 23(9P21.3) WILD-TYPE   92    1
   clus
vv  DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  0                         319                            92
  1                           6                             1
[1] 2 2
[1] FALSE
D53V7, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED    93 295
  DEL PEAK 23(9P21.3) WILD-TYPE  37  76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED     93  295
  DEL PEAK 23(9P21.3) WILD-TYPE   37   76
        clus
vv       DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  FEMALE                          93                            37
  MALE                           295                            76
[1] 2 2
[1] FALSE
D53V8, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED   295  40
  DEL PEAK 23(9P21.3) WILD-TYPE  89  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED    295   40
  DEL PEAK 23(9P21.3) WILD-TYPE   89   13
     clus
vv    DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  NO                          295                            89
  YES                          40                            13
[1] 2 2
[1] FALSE
D53V9, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(9P21.3) MUTATED                                       7
  DEL PEAK 23(9P21.3) WILD-TYPE                                     8
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 23(9P21.3) MUTATED                                        4
  DEL PEAK 23(9P21.3) WILD-TYPE                                      2
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 23(9P21.3) MUTATED                                         0
  DEL PEAK 23(9P21.3) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(9P21.3) MUTATED                                                           377
  DEL PEAK 23(9P21.3) WILD-TYPE                                                         102
D53V10, multiclass
                                                             clus
vv                                                            DEL PEAK 23(9P21.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         377
                                                             clus
vv                                                            DEL PEAK 23(9P21.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
D53V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 23(9P21.3) MUTATED   311   7   3  17
  DEL PEAK 23(9P21.3) WILD-TYPE  88   5   1   6
D53V13, multiclass
    clus
vv   DEL PEAK 23(9P21.3) MUTATED DEL PEAK 23(9P21.3) WILD-TYPE
  R0                         311                            88
  R1                           7                             5
  R2                           3                             1
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(9P21.3) MUTATED       8                        25   267
  DEL PEAK 23(9P21.3) WILD-TYPE     1                         6    82
D53V14, multiclass
                           clus
vv                          DEL PEAK 23(9P21.3) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          25
  WHITE                                             267
                           clus
vv                          DEL PEAK 23(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"
D53V15, binary
                               cls
clus                              0   1
  DEL PEAK 23(9P21.3) MUTATED     5 243
  DEL PEAK 23(9P21.3) WILD-TYPE   3  74
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(9P21.3) MUTATED      5  243
  DEL PEAK 23(9P21.3) WILD-TYPE    3   74
                        clus
vv                       DEL PEAK 23(9P21.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         243
                        clus
vv                       DEL PEAK 23(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            74
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 24(9P21.1) MUTATION ANALYSIS
D54V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 24(9P21.1) MUTATED   187 134
  DEL PEAK 24(9P21.1) WILD-TYPE  93  80
  DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE 
                          321                           173 
  DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE 
                          134                            80 
$`DEL PEAK 24(9P21.1) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-21-A5DI TCGA-22-5471 
       12.20       123.19         4.80         6.18        32.19        60.66 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
       64.93        22.06        19.76        31.50        28.96        31.27 
TCGA-43-5668 TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 
       18.38         7.76         2.93        11.61        12.03        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 
        3.45        17.00        16.77        21.04         3.58        41.42 
TCGA-60-2721 TCGA-63-A5MH TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 
       32.32        66.61         9.50        14.07        21.04         0.16 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 
       18.38        16.14        57.07        19.36         2.76         5.69 
TCGA-NC-A5HD TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3411 TCGA-18-3412 
        0.07        65.65        16.80         8.58       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       23.54        92.15        92.42         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-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
       33.93        10.82         7.33         4.31        64.21         1.74 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 
       14.10        27.02        20.48        35.08        48.33        38.17 
TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5477 
       34.75        13.12        19.30         9.57        11.77        44.25 
TCGA-22-5478 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
        0.79        11.74        18.84        30.12        62.86        56.32 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-6738 TCGA-33-AAS8 TCGA-33-AASB 
       97.94        79.53       103.53        63.35        36.62         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-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 
       32.88        65.23        81.24        16.93        44.75         4.96 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3789 TCGA-37-4130 
       38.79         4.04        26.43        33.90         0.43         8.12 
TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5016 
        6.81         0.39         3.39        37.58       133.25       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 
      111.35        68.58        82.52       102.18         1.71        24.33 
TCGA-39-5030 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 
        1.94        71.18        17.06        40.21        39.12        33.11 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 
       27.91        24.89        21.47         5.46        19.59        13.38 
TCGA-43-8116 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
       11.77        13.32        12.16        13.02         9.83         4.44 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 
       13.91         0.39        29.95         5.46        30.35        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       12.43        18.25        21.90        18.48        14.53        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       30.41        19.76         6.51         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       14.96         4.93         3.48        26.89        14.07         1.35 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
        1.81        13.81        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8387 TCGA-58-8390 
       20.94        19.23        13.32         0.26        13.25        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-60-2698 
       71.24        16.47        34.78        85.12        56.65        10.22 
TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2713 TCGA-60-2720 
       96.82        92.71        21.93        80.45        56.91         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 
       29.85        35.90        23.57        26.83        11.77        70.13 
TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       68.15        70.62        58.65        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       16.37        53.88        16.96        43.10         2.01        21.07 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 
        1.02         0.92         2.01         1.02         2.01         7.07 
TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2781 TCGA-66-2782 
       23.01        19.00         3.02        19.00         3.98        12.00 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 
        1.97        25.97        22.98         4.04        22.98        10.06 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 
        6.94        13.35        16.18        14.73        12.07        12.33 
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        73.22 
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        32.55        86.76 
TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 TCGA-77-8140 TCGA-77-8143 
       55.73       156.66        53.92        17.72        11.54        26.40 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G1 
       27.39         6.97        66.51        65.49        60.53       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 
       22.29         5.92        61.94        38.86         9.67        41.39 
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-85-8276 TCGA-85-8287 TCGA-85-8288 
       29.95        18.94        25.15        34.52         0.76        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 
       22.45        16.77         5.29        15.39        36.59        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR 
       22.59        30.28        34.13        30.97        19.86        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
       27.16        16.21        15.85        14.96        15.29        29.92 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       12.39         3.65         2.93        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        3.48         4.01         2.30         4.01         5.03        26.63 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
       14.14        17.69        71.01        18.31        17.46        27.68 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B 
       30.81        30.67        21.34        27.16        18.15         2.01 
TCGA-98-A53J TCGA-L3-A524 TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK 
       20.71        16.11        11.84        64.54        57.30         4.21 
TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N 
       43.92        14.73        26.43        83.57         3.65        33.07 
TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
        3.72        43.89         0.20 

$`DEL PEAK 24(9P21.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3416 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-33-4532 
        4.47        31.99        27.19        14.93        48.82       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-39-5039 TCGA-43-2578 TCGA-43-7658 TCGA-56-7221 
      133.74         1.55        17.88        22.49        78.18        19.99 
TCGA-56-A4BY TCGA-56-A5DR TCGA-60-2712 TCGA-60-2715 TCGA-68-8250 TCGA-77-7140 
       17.85         0.13         9.01        35.34         8.02        20.78 
TCGA-77-A5GA TCGA-77-A5GB TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HM 
       42.08        30.81        21.21        19.10        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3417 TCGA-18-3421 TCGA-21-1070 
       40.90         0.43        75.75        36.07        86.96       119.54 
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-21-5782 TCGA-21-5784 TCGA-22-0940 TCGA-22-4595 TCGA-22-4596 TCGA-22-4605 
       31.63        41.69        21.99        24.13         0.56        32.02 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 
       63.55        14.63        86.30        71.34        79.20        16.64 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW 
      173.82       151.27        14.07        54.44         4.70         0.30 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-7107 
       74.66         9.07        60.30        50.66        39.32         1.12 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-A5EN 
        4.01         0.39         7.96         7.46         7.82        21.70 
TCGA-39-5022 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-43-2581 
       55.20        60.53        36.39        68.38        55.56        38.66 
TCGA-43-6143 TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U TCGA-46-6025 TCGA-51-4080 
       22.98         3.81         9.73        14.20        10.65         0.39 
TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-8623 TCGA-56-A4ZK TCGA-56-A62T 
       28.34         8.75        27.45        22.75        18.74        14.47 
TCGA-58-8386 TCGA-58-8388 TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 
        0.03        13.55        34.36        35.24        29.92        21.11 
TCGA-60-2697 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2714 TCGA-60-2716 
       12.23        37.94        49.48        66.54        50.33        48.49 
TCGA-60-2719 TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MJ 
       42.64        52.67        70.42        55.30       102.67        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2744 
       45.57        14.99        11.34        36.16        34.59         0.99 
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-66-2767 TCGA-66-2777 TCGA-66-2780 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 
        2.01         2.01        12.03        24.95        40.01         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-77-6842 TCGA-77-7139 TCGA-77-8007 TCGA-77-8128 TCGA-77-8131 TCGA-77-8136 
       29.56       140.09         6.51        37.81        12.59        39.09 
TCGA-77-8139 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5GF 
      104.09        54.41        36.36       126.18       150.25        27.62 
TCGA-85-6561 TCGA-85-6798 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
       40.24         6.41        19.04        24.13        31.56        26.79 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 
       30.64        10.09         3.09        32.71         2.01         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4PA TCGA-85-A4QQ TCGA-90-6837 TCGA-90-7769 
       38.14        12.59        24.36        30.48        24.92        11.77 
TCGA-90-A4ED TCGA-92-8064 TCGA-98-7454 TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       20.22         5.26        21.44        27.02        20.32        18.58 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HJ 
       12.89        13.18        13.41         4.54         1.22        13.74 
TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-O2-A52S TCGA-O2-A5IB 
        2.89        49.28        25.32        12.72        11.18 

  DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE 
                         0.07                          0.03 
  DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE 
                       156.66                        173.82 
  DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE 
                        20.48                         24.92 
[1] "0.1 - 156.7 (20.5)" "0.0 - 173.8 (24.9)"
[1] "hr=" "1"  
D54V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(9P21.1) MUTATED         2       64      101        1        46
  DEL PEAK 24(9P21.1) WILD-TYPE       0       25       51        1        19
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(9P21.1) MUTATED          56         1         44          7
  DEL PEAK 24(9P21.1) WILD-TYPE        39         2         19         12
                               vv
clus                            STAGE IV
  DEL PEAK 24(9P21.1) MUTATED          3
  DEL PEAK 24(9P21.1) WILD-TYPE        4
D54V3, multiclass
            clus
vv           DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE
  STAGE I                              2                             0
  STAGE IA                            64                            25
  STAGE IB                           101                            51
  STAGE II                             1                             1
  STAGE IIA                           46                            19
  STAGE IIB                           56                            39
  STAGE III                            1                             2
  STAGE IIIA                          44                            19
  STAGE IIIB                           7                            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 24(9P21.1) MUTATED    78 189  48  11
  DEL PEAK 24(9P21.1) WILD-TYPE  34 105  23  13
D54V4, multiclass
    clus
vv   DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE
  T1                          78                            34
  T2                         189                           105
  T3                          48                            23
  T4                          11                            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 24(9P21.1) MUTATED   215  81  26   2
  DEL PEAK 24(9P21.1) WILD-TYPE 102  52  14   3
D54V5, multiclass
    clus
vv   DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE
  N0                         215                           102
  N1                          81                            52
  N2                          26                            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"
D54V6, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.1) MUTATED   264   3
  DEL PEAK 24(9P21.1) WILD-TYPE 147   4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.1) MUTATED    264    3
  DEL PEAK 24(9P21.1) WILD-TYPE  147    4
   clus
vv  DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE
  0                         264                           147
  1                           3                             4
[1] 2 2
[1] FALSE
D54V7, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.1) MUTATED    84 242
  DEL PEAK 24(9P21.1) WILD-TYPE  46 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.1) MUTATED     84  242
  DEL PEAK 24(9P21.1) WILD-TYPE   46  129
        clus
vv       DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE
  FEMALE                          84                            46
  MALE                           242                           129
[1] 2 2
[1] FALSE
D54V8, binary
                               cls
clus                              0   1
  DEL PEAK 24(9P21.1) MUTATED   252  31
  DEL PEAK 24(9P21.1) WILD-TYPE 132  22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.1) MUTATED    252   31
  DEL PEAK 24(9P21.1) WILD-TYPE  132   22
     clus
vv    DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE
  NO                          252                           132
  YES                          31                            22
[1] 2 2
[1] FALSE
D54V9, continuous
                               vv
clus                            LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(9P21.1) MUTATED                                       6
  DEL PEAK 24(9P21.1) WILD-TYPE                                     9
                               vv
clus                            LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 24(9P21.1) MUTATED                                        2
  DEL PEAK 24(9P21.1) WILD-TYPE                                      4
                               vv
clus                            LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 24(9P21.1) MUTATED                                         0
  DEL PEAK 24(9P21.1) WILD-TYPE                                       1
                               vv
clus                            LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(9P21.1) MUTATED                                                           318
  DEL PEAK 24(9P21.1) WILD-TYPE                                                         161
D54V10, multiclass
                                                             clus
vv                                                            DEL PEAK 24(9P21.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         318
                                                             clus
vv                                                            DEL PEAK 24(9P21.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           161
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
D54V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 24(9P21.1) MUTATED   254   7   3  17
  DEL PEAK 24(9P21.1) WILD-TYPE 145   5   1   6
D54V13, multiclass
    clus
vv   DEL PEAK 24(9P21.1) MUTATED DEL PEAK 24(9P21.1) WILD-TYPE
  R0                         254                           145
  R1                           7                             5
  R2                           3                             1
  RX                          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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(9P21.1) MUTATED       8                        23   232
  DEL PEAK 24(9P21.1) WILD-TYPE     1                         8   117
D54V14, multiclass
                           clus
vv                          DEL PEAK 24(9P21.1) MUTATED
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          23
  WHITE                                             232
                           clus
vv                          DEL PEAK 24(9P21.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               117
[1] 3 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(9P21.1) MUTATED     4 216
  DEL PEAK 24(9P21.1) WILD-TYPE   4 101
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 24(9P21.1) MUTATED      4  216
  DEL PEAK 24(9P21.1) WILD-TYPE    4  101
                        clus
vv                       DEL PEAK 24(9P21.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         216
                        clus
vv                       DEL PEAK 24(9P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           101
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 25(9Q21.11) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(9Q21.11) MUTATED   149  99
  DEL PEAK 25(9Q21.11) WILD-TYPE 131 115
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                           248                            246 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                            99                            115 
$`DEL PEAK 25(9Q21.11) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1017 TCGA-22-A5C4 
       12.20       123.19         6.18        32.19        48.82        22.06 
TCGA-33-4532 TCGA-33-6737 TCGA-34-2604 TCGA-34-2609 TCGA-43-7657 TCGA-43-8118 
      129.01        19.76        31.50        31.27         7.76         2.93 
TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-A4ZJ TCGA-60-2696 
       12.03        19.99        13.05         3.45        21.04         3.58 
TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-90-7766 TCGA-90-7964 
        9.01        32.32        66.61         8.02         9.50        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HD 
       21.04         0.16        18.38         2.76         5.69         0.07 
TCGA-NC-A5HM TCGA-NK-A5CT TCGA-O2-A52W TCGA-18-3411 TCGA-18-3417 TCGA-18-3419 
       39.85        65.65         8.58       117.57        36.07        92.42 
TCGA-18-3421 TCGA-21-1070 TCGA-21-1075 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       86.96       119.54        70.16       119.80        43.23        31.63 
TCGA-21-5786 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 
       33.93         4.31        64.21         1.74        27.02        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 TCGA-22-5473 
       35.08        48.33        34.75        13.12        19.30        63.55 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5481 TCGA-22-5483 TCGA-33-4547 TCGA-33-4582 
       14.63         0.79        79.20        18.84        79.53       103.53 
TCGA-33-4587 TCGA-33-6738 TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASI TCGA-34-2600 
       54.44        63.35         0.30       110.99        44.19        61.61 
TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
       32.88        65.23        81.24        16.93        44.75        39.32 
TCGA-34-5929 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-4130 TCGA-37-4135 
        4.96         4.04        26.43        33.90         8.12         6.81 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5019 TCGA-39-5024 TCGA-39-5028 
        0.39         3.39       133.25       111.35        82.52         1.71 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-3920 TCGA-43-5670 
       36.39        68.38        17.06        40.21        33.11        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-7656 TCGA-43-8115 
       22.98        24.89        21.47         5.46        19.59        13.38 
TCGA-43-8116 TCGA-46-3766 TCGA-46-3767 TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 
       11.77        12.16        13.02        13.91         5.46        30.35 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 
       28.96        12.43        18.25        21.90        18.48        31.27 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8503 
       30.41         0.10        17.49         3.48        26.89         1.35 
TCGA-56-8622 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
        1.81        13.81         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A5DS TCGA-58-8390 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
       19.23         0.26        29.95        16.47        34.78        85.12 
TCGA-60-2698 TCGA-60-2703 TCGA-60-2706 TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 
       10.22        96.82        92.71        80.45        50.33        42.64 
TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 TCGA-63-7022 
        3.19        35.90        23.57        11.77        70.13        68.15 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT 
      102.67        70.62        58.65        89.29        78.28        16.37 
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-66-2742 TCGA-66-2753 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2766 
       21.07         1.02         0.99        21.01         0.99         1.02 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 
        7.07        19.00         3.02        19.00        12.03         3.98 
TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 
       12.00         1.97        22.98         4.04        22.98        10.06 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
       49.05         2.73         6.94        13.35        16.18        14.73 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7463 TCGA-77-8007 
       29.56        73.12        75.09        23.28        46.78         6.51 
TCGA-77-8008 TCGA-77-8130 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
       86.76       156.66        39.09        17.72       104.09        11.54 
TCGA-77-8143 TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G6 
       26.40        54.41        60.53        36.36       132.36        22.29 
TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 TCGA-85-7843 TCGA-85-8048 
        5.92        38.86        41.39        34.95         1.15        25.15 
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        15.39 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR 
       18.08        22.59        34.13        30.97        19.86        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       27.16        16.21        15.85        29.92        12.39         3.65 
TCGA-90-7767 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-8065 TCGA-94-8035 
        2.93        22.62        10.59         2.70         2.30         4.01 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
       26.63        14.14        17.69        71.01        18.31        17.46 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53B TCGA-L3-A4E7 
       30.81        30.67        21.34        27.16         2.01        12.89 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK 
       13.41        11.84         4.54        64.54        57.30         4.21 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52Q 
       49.28        25.32        14.73        26.43         3.65         3.72 
TCGA-O2-A52V TCGA-O2-A5IB 
       43.89        11.18 

$`DEL PEAK 25(9Q21.11) WILD-TYPE`
TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-22-1000 TCGA-22-5471 
        4.47         4.80        31.99        27.19        14.93        60.66 
TCGA-22-5472 TCGA-33-4533 TCGA-33-4589 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 
       64.93       133.74         1.55        28.96        17.88        22.49 
TCGA-43-5668 TCGA-43-7658 TCGA-43-A474 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY 
       18.38        78.18        11.61        17.00        16.77        17.85 
TCGA-56-A5DR TCGA-60-2711 TCGA-60-2715 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
        0.13        41.42        35.34        20.78        42.08        30.81 
TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE 
       16.14        57.07        19.36        21.21        19.10        76.80 
TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 
       40.90        16.80         0.43        75.75        11.34        23.54 
TCGA-18-3415 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 
       92.15         2.79       154.32        49.94        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-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1012 
       88.11        41.69        10.82        21.99         7.33        14.10 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 
       24.13         0.56        38.17        32.02         9.57        11.77 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
       44.25        86.30        71.34        11.74        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 
       56.32        16.64        97.94       173.82       151.27        14.07 
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-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-7107 TCGA-34-8454 
       74.66         9.07        60.30        50.66         1.12        38.79 
TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 
        4.01         0.43         0.39         7.96         7.46         7.82 
TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 
       37.58        21.70       126.58        68.58        55.20       102.18 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-2581 
       24.33         1.94        60.53        71.18        55.56        38.66 
TCGA-43-3394 TCGA-43-6773 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3768 
       39.12         3.81         9.73        14.20        13.32         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
        4.44        10.65         0.39         0.39        29.95        28.34 
TCGA-52-7811 TCGA-52-7812 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 
        8.75        27.45        14.53        19.76         6.51        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8309 TCGA-56-8623 TCGA-56-8625 TCGA-56-A4BX 
       14.96         4.93        14.07        22.75        10.36        13.32 
TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 
       18.74        14.47         0.03        13.25        13.55        71.24 
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-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 
       37.94        21.93        49.48        66.54        56.91        48.49 
TCGA-60-2722 TCGA-60-2725 TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MJ 
       29.85        26.83        52.67        70.42        55.30        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-66-2744 TCGA-66-2754 
       45.57        14.99        11.34        25.28         0.99         2.01 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 
        0.92        43.99        25.05         2.01         2.01         2.01 
TCGA-66-2770 TCGA-66-2777 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2791 
       23.01         2.01        24.95        25.97        40.01         5.03 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7756 TCGA-70-6722 TCGA-70-6723 
       30.02        54.08         4.01         6.64        12.07        12.33 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       11.18       140.09         0.49        73.22        70.13       106.95 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 
        0.16        32.55        55.73        37.81        12.59        53.92 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-A5FZ TCGA-77-A5G3 
       27.39         6.97        66.51        65.49       126.18       150.25 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       61.94        27.62         9.67        40.24         6.41        36.53 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 
       31.30        32.91         1.38        29.95        18.94        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       24.13        31.56        26.79        30.64        34.52        10.09 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
        3.09        32.71         2.01         7.76        36.59        38.14 
TCGA-85-8584 TCGA-85-A4CL TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A511 TCGA-85-A512 
       12.59        30.28        24.36        30.48        14.96        15.29 
TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 
       24.92        11.77        20.22         3.48         4.01         5.26 
TCGA-94-8490 TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H 
        5.03        27.68        21.44        18.15        27.02        20.32 
TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HH TCGA-NC-A5HJ 
       18.58        20.71        16.11        13.18         1.22        13.74 
TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52S TCGA-XC-AA0X 
        2.89        43.92        83.57        33.07        12.72         0.20 

  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                        156.66                         173.82 
  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE 
                        21.025                         23.275 
[1] "0.1 - 156.7 (21.0)" "0.0 - 173.8 (23.3)"
[1] "hr=" "1.1"
D55V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(9Q21.11) MUTATED         1       50       71        1        33
  DEL PEAK 25(9Q21.11) WILD-TYPE       1       39       81        1        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(9Q21.11) MUTATED          50         2         31          7
  DEL PEAK 25(9Q21.11) WILD-TYPE        45         1         32         12
                                vv
clus                             STAGE IV
  DEL PEAK 25(9Q21.11) MUTATED          4
  DEL PEAK 25(9Q21.11) WILD-TYPE        3
D55V3, multiclass
            clus
vv           DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             50                             39
  STAGE IB                             71                             81
  STAGE II                              1                              1
  STAGE IIA                            33                             32
  STAGE IIB                            50                             45
  STAGE III                             2                              1
  STAGE IIIA                           31                             32
  STAGE IIIB                            7                             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
  DEL PEAK 25(9Q21.11) MUTATED    61 144  38   8
  DEL PEAK 25(9Q21.11) WILD-TYPE  51 150  33  16
D55V4, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  T1                           61                             51
  T2                          144                            150
  T3                           38                             33
  T4                            8                             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 25(9Q21.11) MUTATED   163  66  18   2
  DEL PEAK 25(9Q21.11) WILD-TYPE 154  67  22   3
D55V5, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  N0                          163                            154
  N1                           66                             67
  N2                           18                             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"
D55V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED   203   4
  DEL PEAK 25(9Q21.11) WILD-TYPE 208   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED    203    4
  DEL PEAK 25(9Q21.11) WILD-TYPE  208    3
   clus
vv  DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  0                          203                            208
  1                            4                              3
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED    72 179
  DEL PEAK 25(9Q21.11) WILD-TYPE  58 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED     72  179
  DEL PEAK 25(9Q21.11) WILD-TYPE   58  192
        clus
vv       DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  FEMALE                           72                             58
  MALE                            179                            192
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(9Q21.11) MUTATED   199  18
  DEL PEAK 25(9Q21.11) WILD-TYPE 185  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED    199   18
  DEL PEAK 25(9Q21.11) WILD-TYPE  185   35
     clus
vv    DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  NO                           199                            185
  YES                           18                             35
[1] 2 2
[1] FALSE
D55V9, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(9Q21.11) MUTATED                                       4
  DEL PEAK 25(9Q21.11) WILD-TYPE                                    11
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 25(9Q21.11) MUTATED                                        1
  DEL PEAK 25(9Q21.11) WILD-TYPE                                      5
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 25(9Q21.11) MUTATED                                         1
  DEL PEAK 25(9Q21.11) WILD-TYPE                                       0
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(9Q21.11) MUTATED                                                           245
  DEL PEAK 25(9Q21.11) WILD-TYPE                                                         234
D55V10, multiclass
                                                             clus
vv                                                            DEL PEAK 25(9Q21.11) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          245
                                                             clus
vv                                                            DEL PEAK 25(9Q21.11) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            234
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
D55V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(9Q21.11) MUTATED   197   2   2  10
  DEL PEAK 25(9Q21.11) WILD-TYPE 202  10   2  13
D55V13, multiclass
    clus
vv   DEL PEAK 25(9Q21.11) MUTATED DEL PEAK 25(9Q21.11) WILD-TYPE
  R0                          197                            202
  R1                            2                             10
  R2                            2                              2
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(9Q21.11) MUTATED       3                        16   176
  DEL PEAK 25(9Q21.11) WILD-TYPE     6                        15   173
D55V14, multiclass
                           clus
vv                          DEL PEAK 25(9Q21.11) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              176
                           clus
vv                          DEL PEAK 25(9Q21.11) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                173
[1] 3 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(9Q21.11) MUTATED     1 160
  DEL PEAK 25(9Q21.11) WILD-TYPE   7 157
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(9Q21.11) MUTATED      1  160
  DEL PEAK 25(9Q21.11) WILD-TYPE    7  157
                        clus
vv                       DEL PEAK 25(9Q21.11) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          160
                        clus
vv                       DEL PEAK 25(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                  7
  NOT HISPANIC OR LATINO                            157
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 26(10P15.3) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(10P15.3) MUTATED   135  90
  DEL PEAK 26(10P15.3) WILD-TYPE 145 124
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                           225                            269 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                            90                            124 
$`DEL PEAK 26(10P15.3) MUTATED`
TCGA-18-3406 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 
       12.20         6.18        27.19        32.19        14.93        60.66 
TCGA-22-A5C4 TCGA-33-4533 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 TCGA-43-8118 
       22.06       133.74        28.96        17.88        22.49         2.93 
TCGA-43-A56V TCGA-56-8305 TCGA-56-A4BY TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 
       12.03         3.45        17.85        66.61         8.02        20.78 
TCGA-77-A5GB TCGA-94-7033 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8020 
       30.81        21.04         0.16        16.14        19.36         2.76 
TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 
       19.10         0.07        39.85        40.90        65.65        16.80 
TCGA-18-3411 TCGA-18-3421 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
      117.57        86.96        99.16        70.16        60.89        34.78 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 TCGA-21-5786 TCGA-22-0940 
       31.73       122.43       119.80        31.63        33.93        21.99 
TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 
        1.74        27.02        20.48        35.08        24.13         0.56 
TCGA-22-4599 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       38.17         9.57        11.77        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-33-4582 TCGA-33-4583 
       86.30        11.74        18.84        56.32       103.53       151.27 
TCGA-33-4586 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-34-2596 TCGA-34-5236 
       14.07         0.30        36.62       110.99         2.63         9.07 
TCGA-34-5240 TCGA-34-5927 TCGA-34-8454 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3789 
       50.66        44.75        38.79        26.43        33.90         0.43 
TCGA-37-3792 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5019 
        0.39         6.81         3.39        21.70       133.25       111.35 
TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
       68.58       102.18        24.33         1.94        60.53        36.39 
TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 
       71.18        55.56        40.21        27.91        22.98        24.89 
TCGA-43-6770 TCGA-43-7656 TCGA-43-A56U TCGA-46-3769 TCGA-51-4080 TCGA-51-4081 
       21.47        19.59        14.20         4.44         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 TCGA-56-7223 
       28.34         5.46        30.35        28.96        18.25        14.53 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-8307 TCGA-56-8503 TCGA-56-8626 
       30.41        19.76         6.51        26.89         1.35         9.93 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8391 
       15.81        20.94        19.23        18.74        14.47        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-60-2713 
       37.94        92.71        80.45        49.48        66.54        56.91 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-63-7020 TCGA-63-A5MB TCGA-63-A5MJ 
       42.64        29.85        35.90        70.13       102.67        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MP TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 
       45.57        14.99        25.28         2.01         1.02         2.01 
TCGA-66-2755 TCGA-66-2757 TCGA-66-2759 TCGA-66-2766 TCGA-66-2770 TCGA-66-2771 
        0.92        43.99        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-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
        5.03        10.06         4.01        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 
        6.94        13.35        14.73        12.33        29.56        23.28 
TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7465 
       11.18       140.09         0.49        73.22         0.16        32.55 
TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
       55.73       156.66        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 
       11.54        27.39        65.49        36.36       150.25        22.29 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-7843 
       61.94        27.62         6.41        36.53        32.91         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 
       29.95        18.94        24.13        31.56        26.79        10.09 
TCGA-85-8287 TCGA-85-8351 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 TCGA-85-A4CN 
        0.76        16.77         3.09        15.39        36.59        34.13 
TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A512 TCGA-85-A5B5 
       19.86        30.48        19.73        16.21        15.29         3.65 
TCGA-90-7769 TCGA-90-A4EE TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-A5I6 
       11.77        22.62         4.01         5.26         2.30        17.69 
TCGA-96-8170 TCGA-98-8021 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53J TCGA-L3-A4E7 
       17.46        30.81        21.34        18.15        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP 
       16.11        13.41        11.84         2.89        43.92        25.32 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       33.07         3.72        12.72 

$`DEL PEAK 26(10P15.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-22-1017 TCGA-22-5472 
        4.47       123.19         4.80        31.99        48.82        64.93 
TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2609 TCGA-43-5668 
      129.01         1.55        19.76        31.50        31.27        18.38 
TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 
        7.76        78.18        11.61        19.99        13.05        17.00 
TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 
       16.77        21.04         0.13         3.58        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7943 
       35.34        32.32        42.08         9.50        14.07        18.38 
TCGA-96-7545 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HE TCGA-NK-A7XE TCGA-O2-A52W 
       57.07         5.69        21.21        76.80         0.43         8.58 
TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 
       75.75        11.34        23.54        92.15        36.07        92.42 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1078 
        2.79       154.32        49.94       119.54        46.88        15.58 
TCGA-21-1081 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 TCGA-22-0944 
        9.34        43.23        88.11        41.69        10.82         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-4594 TCGA-22-4601 TCGA-22-4604 
        4.31        64.21        14.10        48.33        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-5473 TCGA-22-5480 TCGA-22-5481 TCGA-22-5485 
       32.02        19.30        63.55        71.34        79.20        30.12 
TCGA-22-5489 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4587 
       62.86        16.64        97.94        79.53       173.82        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
       63.35         4.70         6.94        44.19       118.36        27.16 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 
       61.61        32.88        65.23        81.24        74.66        60.30 
TCGA-34-5241 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8455 TCGA-37-3783 
       16.93        39.32         4.96         1.12         4.04         4.01 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-A5EL 
        7.96         8.12         7.46         7.82         0.39        37.58 
TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5035 TCGA-39-5040 
      126.58        55.20        82.52         1.71        68.38        17.06 
TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 
       38.66        39.12        33.11         5.46         3.81        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
       11.77         9.73        13.32        12.16        13.02         9.83 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 
       10.65        13.91         0.39         8.75        27.45        12.43 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       21.90        18.48        31.27         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 
       14.96         4.93         3.48        14.07         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8386 
       13.81        10.36        20.25        13.32         0.26         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N 
       13.25        13.55        29.95        85.12        56.65        29.92 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2707 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 
       12.23        10.22        21.93        50.33        48.49         3.19 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 
       23.57        26.83        11.77        52.67        70.42        68.15 
TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS 
       55.30        70.62        58.65        11.34        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-66-2742 TCGA-66-2744 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 
       21.07         0.99         0.99        21.01         0.99         2.01 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2773 TCGA-66-2778 TCGA-66-2781 
        2.01         2.01         7.07         3.02        19.00         3.98 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 
       12.00        24.95         1.97        22.98        30.02        54.08 
TCGA-68-A59I TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 TCGA-77-7335 TCGA-77-7337 
       16.18        12.07        73.12        75.09        70.13       106.95 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8131 TCGA-77-8143 
       46.78         6.51        86.76        37.81        12.59        26.40 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
        6.97        66.51        54.41        60.53       126.18       132.36 
TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 
        5.92        38.86         9.67        41.39        40.24        34.95 
TCGA-85-7698 TCGA-85-7710 TCGA-85-8048 TCGA-85-8049 TCGA-85-8072 TCGA-85-8276 
       31.30         1.38        25.15        19.04        30.64        34.52 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 
       13.22        22.45         5.29        32.71         2.01         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB 
       38.14        12.59        18.08        22.59        30.28        30.97 
TCGA-85-A4PA TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L 
       24.36        27.16        15.85        14.96        29.92        12.39 
TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
       24.92         2.93        20.22        10.59         2.70         3.48 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        4.01         5.03        26.63        14.14        71.01        18.31 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53C 
       27.68        21.44        30.67        27.16         2.01        27.02 
TCGA-98-A53H TCGA-98-A53I TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       20.32        18.58        13.18         4.54        64.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HT 
       57.30        13.74         4.21        49.28        14.73        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       83.57         3.65        43.89        11.18         0.20 

  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                        156.66                         173.82 
  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE 
                         22.49                          21.04 
[1] "0.1 - 156.7 (22.5)" "0.0 - 173.8 (21.0)"
[1] "hr=" "1.2"
D56V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(10P15.3) MUTATED         1       34       76        0        33
  DEL PEAK 26(10P15.3) WILD-TYPE       1       55       76        2        32
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10P15.3) MUTATED          42         2         29          8
  DEL PEAK 26(10P15.3) WILD-TYPE        53         1         34         11
                                vv
clus                             STAGE IV
  DEL PEAK 26(10P15.3) MUTATED          1
  DEL PEAK 26(10P15.3) WILD-TYPE        6
D56V3, multiclass
            clus
vv           DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             34                             55
  STAGE IB                             76                             76
  STAGE II                              0                              2
  STAGE IIA                            33                             32
  STAGE IIB                            42                             53
  STAGE III                             2                              1
  STAGE IIIA                           29                             34
  STAGE IIIB                            8                             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
  DEL PEAK 26(10P15.3) MUTATED    48 143  27  10
  DEL PEAK 26(10P15.3) WILD-TYPE  64 151  44  14
D56V4, multiclass
    clus
vv   DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  T1                           48                             64
  T2                          143                            151
  T3                           27                             44
  T4                           10                             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 26(10P15.3) MUTATED   142  63  20   2
  DEL PEAK 26(10P15.3) WILD-TYPE 175  70  20   3
D56V5, multiclass
    clus
vv   DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  N0                          142                            175
  N1                           63                             70
  N2                           20                             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"
D56V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED   192   1
  DEL PEAK 26(10P15.3) WILD-TYPE 219   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED    192    1
  DEL PEAK 26(10P15.3) WILD-TYPE  219    6
   clus
vv  DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  0                          192                            219
  1                            1                              6
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED    57 171
  DEL PEAK 26(10P15.3) WILD-TYPE  73 200
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED     57  171
  DEL PEAK 26(10P15.3) WILD-TYPE   73  200
        clus
vv       DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  FEMALE                           57                             73
  MALE                            171                            200
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED   177  23
  DEL PEAK 26(10P15.3) WILD-TYPE 207  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED    177   23
  DEL PEAK 26(10P15.3) WILD-TYPE  207   30
     clus
vv    DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  NO                           177                            207
  YES                           23                             30
[1] 2 2
[1] FALSE
D56V9, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(10P15.3) MUTATED                                       8
  DEL PEAK 26(10P15.3) WILD-TYPE                                     7
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 26(10P15.3) MUTATED                                        2
  DEL PEAK 26(10P15.3) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 26(10P15.3) MUTATED                                         0
  DEL PEAK 26(10P15.3) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(10P15.3) MUTATED                                                           218
  DEL PEAK 26(10P15.3) WILD-TYPE                                                         261
D56V10, multiclass
                                                             clus
vv                                                            DEL PEAK 26(10P15.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          218
                                                             clus
vv                                                            DEL PEAK 26(10P15.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            261
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
D56V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(10P15.3) MUTATED   180   6   1  13
  DEL PEAK 26(10P15.3) WILD-TYPE 219   6   3  10
D56V13, multiclass
    clus
vv   DEL PEAK 26(10P15.3) MUTATED DEL PEAK 26(10P15.3) WILD-TYPE
  R0                          180                            219
  R1                            6                              6
  R2                            1                              3
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(10P15.3) MUTATED       2                        14   164
  DEL PEAK 26(10P15.3) WILD-TYPE     7                        17   185
D56V14, multiclass
                           clus
vv                          DEL PEAK 26(10P15.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              164
                           clus
vv                          DEL PEAK 26(10P15.3) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             17
  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"
D56V15, binary
                                cls
clus                               0   1
  DEL PEAK 26(10P15.3) MUTATED     3 143
  DEL PEAK 26(10P15.3) WILD-TYPE   5 174
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10P15.3) MUTATED      3  143
  DEL PEAK 26(10P15.3) WILD-TYPE    5  174
                        clus
vv                       DEL PEAK 26(10P15.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          143
                        clus
vv                       DEL PEAK 26(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            174
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 27(10P15.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(10P15.1) MUTATED   124  84
  DEL PEAK 27(10P15.1) WILD-TYPE 156 130
  DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE 
                           208                            286 
  DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE 
                            84                            130 
$`DEL PEAK 27(10P15.1) MUTATED`
TCGA-18-3406 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 
       12.20         6.18        27.19        32.19        14.93        60.66 
TCGA-33-4533 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 TCGA-43-8118 TCGA-43-A56V 
      133.74        28.96        17.88        22.49         2.93        12.03 
TCGA-56-8305 TCGA-56-A4BY TCGA-60-2711 TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GB 
        3.45        17.85        41.42        66.61         8.02        30.81 
TCGA-94-7033 TCGA-94-7557 TCGA-96-A4JK TCGA-98-8020 TCGA-J1-A4AH TCGA-NC-A5HD 
       21.04         0.16        19.36         2.76        19.10         0.07 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3411 TCGA-18-3421 
       39.85        40.90        65.65        16.80       117.57        86.96 
TCGA-18-4721 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1079 
      154.32        99.16        70.16        60.89        34.78        31.73 
TCGA-21-1080 TCGA-21-1082 TCGA-21-5782 TCGA-21-5786 TCGA-22-0940 TCGA-22-1011 
      122.43       119.80        31.63        33.93        21.99         1.74 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4599 TCGA-22-4601 
       27.02        20.48        35.08        24.13        38.17        34.75 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
        9.57        11.77        14.63        44.25         0.79        86.30 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       11.74        18.84        56.32       103.53       151.27        14.07 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-34-2596 TCGA-34-5236 TCGA-34-5240 
        0.30        36.62       110.99         2.63         9.07        50.66 
TCGA-34-5927 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 
       44.75        26.43        33.90         0.43         0.39         8.12 
TCGA-37-4135 TCGA-37-A5EN TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 
        6.81        21.70       111.35        68.58       102.18        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 
        1.94        60.53        36.39        71.18        55.56        40.21 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-7656 TCGA-43-A56U TCGA-46-3769 
       22.98        24.89        21.47        19.59        14.20         4.44 
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        14.53 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-8307 TCGA-56-8503 TCGA-56-8626 
       30.41        19.76         6.51        26.89         1.35         9.93 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8391 TCGA-58-8392 
       15.81        20.94        18.74        14.47        71.24        16.47 
TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 TCGA-60-2703 TCGA-60-2704 
       34.78        34.36        35.24        21.11        96.82        37.94 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2719 TCGA-60-2722 
       92.71        80.45        49.48        66.54        42.64        29.85 
TCGA-60-2723 TCGA-63-7020 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
       35.90        70.13       102.67        59.97        45.57        14.99 
TCGA-63-A5MP TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
       25.28         2.01         1.02         2.01         0.92        43.99 
TCGA-66-2766 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2786 
        1.02        23.01        19.00         2.01        12.03        25.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 TCGA-66-2800 
       40.01        22.98         4.04         5.03        10.06        49.05 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 
        2.73         6.64        13.35        14.73        12.33        29.56 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 
       23.28        11.18       140.09         0.49        73.22         0.16 
TCGA-77-7465 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       32.55        55.73       156.66        53.92        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 
      104.09        11.54        27.39        36.36       150.25        22.29 
TCGA-77-A5GF TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 
       27.62         6.41        36.53        32.91        29.95        18.94 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8277 TCGA-85-8287 TCGA-85-8351 
       24.13        31.56        26.79        10.09         0.76        16.77 
TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QQ 
        3.09        15.39        36.59        34.13        19.86        30.48 
TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE 
       19.73        16.21        15.29         3.65        11.77        22.62 
TCGA-92-8063 TCGA-92-8064 TCGA-94-8035 TCGA-94-A5I6 TCGA-96-8170 TCGA-98-8021 
        4.01         5.26         4.01        17.69        17.46        30.81 
TCGA-98-8023 TCGA-98-A53A TCGA-98-A53J TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HL 
       21.34        18.15        20.71        13.18        11.84         2.89 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-O2-A52N TCGA-O2-A52Q 
       43.92        25.32        33.07         3.72 

$`DEL PEAK 27(10P15.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-22-1017 TCGA-22-5472 
        4.47       123.19         4.80        31.99        48.82        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2609 
       22.06       129.01         1.55        19.76        31.50        31.27 
TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 
       18.38         7.76        78.18        11.61        19.99        13.05 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2712 
       17.00        16.77        21.04         0.13         3.58         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 
       35.34        32.32        20.78        42.08         9.50        14.07 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HE 
       18.38        16.14        57.07         5.69        21.21        76.80 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 
        0.43         8.58        75.75        11.34        23.54        92.15 
TCGA-18-3417 TCGA-18-3419 TCGA-18-4086 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 
       36.07        92.42         2.79        49.94       119.54        46.88 
TCGA-21-1078 TCGA-21-1081 TCGA-21-1083 TCGA-21-5783 TCGA-21-5784 TCGA-21-5787 
       15.58         9.34        43.23        88.11        41.69        10.82 
TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-4594 TCGA-22-4596 
        7.33         4.31        64.21        14.10        48.33         0.56 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-5473 TCGA-22-5480 TCGA-22-5481 
       13.12        32.02        19.30        63.55        71.34        79.20 
TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       30.12        62.86        16.64        97.94        79.53       173.82 
TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ 
       54.44        63.35         4.70         6.94        44.19       118.36 
TCGA-33-AASL TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       27.16        61.61        32.88        65.23        81.24        74.66 
TCGA-34-5239 TCGA-34-5241 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       60.30        16.93        39.32         4.96         1.12        38.79 
TCGA-34-8455 TCGA-37-3783 TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 
        4.04         4.01         7.96         7.46         7.82         0.39 
TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 
        3.39        37.58       133.25       126.58        55.20        82.52 
TCGA-39-5028 TCGA-39-5035 TCGA-39-5040 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
        1.71        68.38        17.06        38.66        39.12        33.11 
TCGA-43-5670 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
       27.91         5.46         3.81        13.38        11.77         9.73 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 
       13.32        12.16        13.02         9.83        10.65        13.91 
TCGA-51-4079 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 
        0.39         5.46         8.75        27.45        28.96        12.43 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 TCGA-56-7731 TCGA-56-7822 TCGA-56-7823 
       21.90        18.48        31.27         0.10        17.49        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 
       14.96         4.93         3.48        14.07         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS 
       13.81        10.36        20.25        19.23        13.32         0.26 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-A46J TCGA-58-A46L 
        0.03        13.25        13.55        29.95        85.12        56.65 
TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2707 TCGA-60-2713 TCGA-60-2714 
       29.92        12.23        10.22        21.93        56.91        50.33 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
       48.49         3.19        23.57        26.83        11.77        52.67 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MN 
       70.42        68.15        55.30        70.62        58.65        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-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 TCGA-66-2758 
       16.96        43.10        21.07         0.99         0.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       25.05         0.99         2.01         2.01         2.01         7.07 
TCGA-66-2773 TCGA-66-2778 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
        3.02        19.00         3.98        12.00        24.95         1.97 
TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-68-7757 TCGA-68-A59I 
       22.98        30.02        54.08         4.01         6.94        16.18 
TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 
       12.07        73.12        75.09        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-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
       66.51        54.41        65.49        60.53       126.18       132.36 
TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
        5.92        61.94        38.86         9.67        41.39        40.24 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 
       34.95        31.30         1.38         1.15        25.15        19.04 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 
       30.64        34.52        13.22        22.45         5.29        32.71 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
        2.01         7.76        38.14        12.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 
       30.28        30.97        24.36        27.16        15.85        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A59Q 
       29.92        12.39        24.92         2.93        20.22        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8065 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        2.70         3.48         2.30         5.03        26.63        14.14 
TCGA-96-7544 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-A538 
       71.01        18.31        27.68        21.44        30.67        27.16 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 
        2.01        27.02        20.32        18.58        12.89        16.11 
TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ 
       13.41         4.54        64.54         1.22        57.30        13.74 
TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
        4.21        49.28        14.73        26.43        83.57         3.65 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89        11.18         0.20 

  DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE 
                          0.07                           0.03 
  DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE 
                        156.66                         173.82 
  DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE 
                        22.995                         20.550 
[1] "0.1 - 156.7 (23.0)" "0.0 - 173.8 (20.6)"
[1] "hr=" "1.2"
D57V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(10P15.1) MUTATED         1       35       71        0        28
  DEL PEAK 27(10P15.1) WILD-TYPE       1       54       81        2        37
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(10P15.1) MUTATED          39         1         26          7
  DEL PEAK 27(10P15.1) WILD-TYPE        56         2         37         12
                                vv
clus                             STAGE IV
  DEL PEAK 27(10P15.1) MUTATED          1
  DEL PEAK 27(10P15.1) WILD-TYPE        6
D57V3, multiclass
            clus
vv           DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE
  STAGE I                               1                              1
  STAGE IA                             35                             54
  STAGE IB                             71                             81
  STAGE II                              0                              2
  STAGE IIA                            28                             37
  STAGE IIB                            39                             56
  STAGE III                             1                              2
  STAGE IIIA                           26                             37
  STAGE IIIB                            7                             12
  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(10P15.1) MUTATED    48 131  23   9
  DEL PEAK 27(10P15.1) WILD-TYPE  64 163  48  15
D57V4, multiclass
    clus
vv   DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE
  T1                           48                             64
  T2                          131                            163
  T3                           23                             48
  T4                            9                             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(10P15.1) MUTATED   135  56  17   2
  DEL PEAK 27(10P15.1) WILD-TYPE 182  77  23   3
D57V5, multiclass
    clus
vv   DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE
  N0                          135                            182
  N1                           56                             77
  N2                           17                             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"
D57V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.1) MUTATED   178   1
  DEL PEAK 27(10P15.1) WILD-TYPE 233   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.1) MUTATED    178    1
  DEL PEAK 27(10P15.1) WILD-TYPE  233    6
   clus
vv  DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE
  0                          178                            233
  1                            1                              6
[1] 2 2
[1] FALSE
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.1) MUTATED    51 160
  DEL PEAK 27(10P15.1) WILD-TYPE  79 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.1) MUTATED     51  160
  DEL PEAK 27(10P15.1) WILD-TYPE   79  211
        clus
vv       DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE
  FEMALE                           51                             79
  MALE                            160                            211
[1] 2 2
[1] FALSE
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(10P15.1) MUTATED   166  20
  DEL PEAK 27(10P15.1) WILD-TYPE 218  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.1) MUTATED    166   20
  DEL PEAK 27(10P15.1) WILD-TYPE  218   33
     clus
vv    DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE
  NO                           166                            218
  YES                           20                             33
[1] 2 2
[1] FALSE
D57V9, continuous
                                vv
clus                             LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(10P15.1) MUTATED                                       7
  DEL PEAK 27(10P15.1) WILD-TYPE                                     8
                                vv
clus                             LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  DEL PEAK 27(10P15.1) MUTATED                                        2
  DEL PEAK 27(10P15.1) WILD-TYPE                                      4
                                vv
clus                             LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  DEL PEAK 27(10P15.1) MUTATED                                         0
  DEL PEAK 27(10P15.1) WILD-TYPE                                       1
                                vv
clus                             LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(10P15.1) MUTATED                                                           202
  DEL PEAK 27(10P15.1) WILD-TYPE                                                         277
D57V10, multiclass
                                                             clus
vv                                                            DEL PEAK 27(10P15.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          202
                                                             clus
vv                                                            DEL PEAK 27(10P15.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            277
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
D57V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(10P15.1) MUTATED   168   6   1  11
  DEL PEAK 27(10P15.1) WILD-TYPE 231   6   3  12
D57V13, multiclass
    clus
vv   DEL PEAK 27(10P15.1) MUTATED DEL PEAK 27(10P15.1) WILD-TYPE
  R0                          168                            231
  R1                            6                              6
  R2                            1                              3
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(10P15.1) MUTATED       2                        13   152
  DEL PEAK 27(10P15.1) WILD-TYPE     7                        18   197
D57V14, multiclass
                           clus
vv                          DEL PEAK 27(10P15.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              152
                           clus
vv                          DEL PEAK 27(10P15.1) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             18
  WHITE                                                197
[1] 3 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(10P15.1) MUTATED     3 131
  DEL PEAK 27(10P15.1) WILD-TYPE   5 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(10P15.1) MUTATED      3  131
  DEL PEAK 27(10P15.1) WILD-TYPE    5  186
                        clus
vv                       DEL PEAK 27(10P15.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          131
                        clus
vv                       DEL PEAK 27(10P15.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            186
[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   151 114
  DEL PEAK 28(10Q23.31) WILD-TYPE 129 100
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            265                             229 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                            114                             100 
$`DEL PEAK 28(10Q23.31) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1000 
       12.20         4.47         4.80         6.18        32.19        14.93 
TCGA-33-4533 TCGA-33-6737 TCGA-34-2605 TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 
      133.74        19.76        28.96        22.49        18.38        78.18 
TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY 
       11.61        12.03        19.99         3.45        17.00        17.85 
TCGA-60-2715 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GB TCGA-94-7033 
       35.34        66.61         8.02        20.78        30.81        21.04 
TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A539 TCGA-J1-A4AH 
       18.38        16.14        57.07        19.36         5.69        19.10 
TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W 
        0.07        39.85        40.90        16.80         0.43         8.58 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 
      117.57        11.34        92.15       154.32        49.94        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1081 TCGA-21-1082 
       99.16        70.16        60.89        34.78         9.34       119.80 
TCGA-21-5783 TCGA-22-0940 TCGA-22-0944 TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 
       88.11        21.99         7.33        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        86.30        11.74        18.84        30.12 
TCGA-22-5489 TCGA-22-5491 TCGA-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 
       62.86        56.32        97.94       103.53       151.27        14.07 
TCGA-33-4587 TCGA-33-6738 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD 
       54.44        63.35         0.30        36.62         6.94       110.99 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 TCGA-34-5236 TCGA-34-5927 TCGA-34-5929 
      118.36        27.16         2.63         9.07        44.75         4.96 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EN 
       26.43        33.90         0.39         6.81         3.39        21.70 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5029 
      133.25       126.58       111.35        68.58       102.18        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 
        1.94        60.53        71.18        55.56        17.06        40.21 
TCGA-43-3394 TCGA-43-3920 TCGA-43-6770 TCGA-43-A56U TCGA-46-3765 TCGA-46-3768 
       39.12        33.11        21.47        14.20        13.32         9.83 
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-56-7222 TCGA-56-7223 
       30.35        28.96        12.43        18.25        18.48        14.53 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 TCGA-56-8304 TCGA-56-8307 
       30.41        19.76         6.51        33.24         3.48        26.89 
TCGA-56-8309 TCGA-56-8622 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BX 
       14.07         1.81        10.36        20.25        15.81        13.32 
TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 
       18.74        14.47         0.03        13.55        71.24        16.47 
TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-60-2695 TCGA-60-2698 
       34.78        85.12        34.36        35.24        21.11        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-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2725 TCGA-63-7020 TCGA-63-7022 
       42.64         3.19        29.85        26.83        70.13        68.15 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-66-2727 
      102.67        70.62        58.65        59.97        45.57        16.96 
TCGA-66-2737 TCGA-66-2753 TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 
        2.01         1.02         2.01         0.99        43.99        21.01 
TCGA-66-2759 TCGA-66-2763 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 
       25.05         0.99        23.01        19.00         3.02        19.00 
TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2789 TCGA-66-2791 
       12.00        24.95         1.97        40.01         4.04         5.03 
TCGA-66-2792 TCGA-66-2793 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
       30.02        10.06        49.05         2.73         6.64         6.94 
TCGA-68-8251 TCGA-68-A59J TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-7139 
       13.35        14.73        12.33        29.56        73.12       140.09 
TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 
      106.95        46.78        32.55        55.73       156.66        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-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G7 
       66.51        54.41        65.49        36.36       150.25         5.92 
TCGA-77-A5GF TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
       27.62        41.39        40.24         6.41        36.53        31.30 
TCGA-85-7699 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
       32.91        29.95        18.94        19.04        24.13        31.56 
TCGA-85-8277 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8479 TCGA-85-8580 
       10.09        16.77         3.09        32.71        15.39        36.59 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ 
       18.08        30.28        34.13        30.97        19.86        30.48 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 
       27.16        16.21        15.85        14.96        12.39         3.65 
TCGA-92-7341 TCGA-92-8064 TCGA-94-8035 TCGA-94-A5I6 TCGA-96-8170 TCGA-98-8021 
        3.48         5.26         4.01        17.69        17.46        30.81 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       21.34        27.16        18.15        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HI 
       16.11        13.18        13.41        11.84         1.22        57.30 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52V TCGA-O2-A5IB 
       49.28        43.92        26.43        83.57        43.89        11.18 
TCGA-XC-AA0X 
        0.20 

$`DEL PEAK 28(10Q23.31) WILD-TYPE`
TCGA-18-3409 TCGA-18-3416 TCGA-18-5595 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 
      123.19        31.99        27.19        48.82        60.66        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 
       22.06       129.01         1.55        31.50        31.27        17.88 
TCGA-43-7657 TCGA-43-8118 TCGA-56-8201 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR 
        7.76         2.93        13.05        16.77        21.04         0.13 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-77-A5GA TCGA-90-7766 
        3.58        41.42         9.01        32.32        42.08         9.50 
TCGA-90-7964 TCGA-94-7557 TCGA-98-8020 TCGA-98-A53D TCGA-NC-A5HE TCGA-NK-A5CT 
       14.07         0.16         2.76        21.21        76.80        65.65 
TCGA-18-3408 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       75.75        23.54        36.07        92.42        86.96         2.79 
TCGA-21-1070 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 TCGA-21-5782 
      119.54        15.58        31.73       122.43        43.23        31.63 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 
       41.69        33.93        10.82         4.31        14.10        27.02 
TCGA-22-4591 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 
       20.48         0.56        34.75        13.12        32.02        19.30 
TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5492 TCGA-33-4547 TCGA-33-4566 
       44.25        71.34        79.20        16.64        79.53       173.82 
TCGA-33-A4WN TCGA-33-AASI TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
        4.70        44.19        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 TCGA-34-7107 
       74.66        60.30        50.66        16.93        39.32         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4130 
       38.79         4.04         4.01         0.43         7.96         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-A5EL TCGA-39-5022 TCGA-39-5024 
        7.46         7.82         0.39        37.58        55.20        82.52 
TCGA-39-5028 TCGA-39-5034 TCGA-39-5035 TCGA-43-2581 TCGA-43-5670 TCGA-43-6143 
        1.71        36.39        68.38        38.66        27.91        22.98 
TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       24.89         5.46         3.81        19.59        13.38        11.77 
TCGA-43-A475 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-46-6026 TCGA-52-7811 
        9.73        12.16        13.02         4.44        13.91         8.75 
TCGA-52-7812 TCGA-56-6545 TCGA-56-7579 TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 
       27.45        21.90        31.27         0.10        17.49        14.96 
TCGA-56-8083 TCGA-56-8503 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-A49D 
        4.93         1.35        22.75        13.81         9.93        20.94 
TCGA-56-A4BW TCGA-56-A5DS TCGA-58-8387 TCGA-58-8390 TCGA-58-A46L TCGA-58-A46N 
       19.23         0.26        13.25        29.95        56.65        29.92 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2707 TCGA-60-2714 TCGA-60-2716 TCGA-60-2723 
       12.23        96.82        21.93        50.33        48.49        35.90 
TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MM 
       23.57        11.77        52.67        70.42        55.30        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       11.34        25.28        89.29        78.28        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 
       53.88        34.59        43.10        21.07         0.99         0.92 
TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2777 
        2.01         1.02         2.01         2.01         7.07         2.01 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2786 TCGA-66-2788 TCGA-66-2790 TCGA-66-2794 
       12.03         3.98        25.97        22.98        22.98        54.08 
TCGA-66-2795 TCGA-68-A59I TCGA-70-6722 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
        4.01        16.18        12.07        75.09        23.28        11.18 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-8007 TCGA-77-8008 
        0.49        73.22        70.13         0.16         6.51        86.76 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8145 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
       37.81        12.59         6.97        60.53       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6175 TCGA-85-7697 TCGA-85-7710 
       22.29        61.94        38.86         9.67        34.95         1.38 
TCGA-85-7843 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 
        1.15        25.15        26.79        30.64        34.52         0.76 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 
       13.22        22.45         5.29         2.01         7.76        38.14 
TCGA-85-8584 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A512 TCGA-85-A513 
       12.59        22.59        24.36        19.73        15.29        29.92 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       24.92         2.93        11.77        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ 
        2.70         4.01         2.30         5.03        26.63        14.14 
TCGA-96-7544 TCGA-96-8169 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-A53B 
       71.01        18.31        27.68        21.44        30.67         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HK 
       27.02        20.32         4.54        64.54        13.74         4.21 
TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q 
        2.89        25.32        14.73         3.65        33.07         3.72 
TCGA-O2-A52S 
       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 
                         156.66                          173.82 
  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE 
                          22.49                           21.21 
[1] "0.0 - 156.7 (22.5)" "0.1 - 173.8 (21.2)"
[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       86        1        35
  DEL PEAK 28(10Q23.31) WILD-TYPE       1       41       66        1        30
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(10Q23.31) MUTATED          48         1         34         11
  DEL PEAK 28(10Q23.31) WILD-TYPE        47         2         29          8
                                 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                              41
  STAGE IB                              86                              66
  STAGE II                               1                               1
  STAGE IIA                             35                              30
  STAGE IIB                             48                              47
  STAGE III                              1                               2
  STAGE IIIA                            34                              29
  STAGE IIIB                            11                               8
  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    64 158  37   9
  DEL PEAK 28(10Q23.31) WILD-TYPE  48 136  34  15
D58V4, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  T1                            64                              48
  T2                           158                             136
  T3                            37                              34
  T4                             9                              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   167  72  21   4
  DEL PEAK 28(10Q23.31) WILD-TYPE 150  61  19   1
D58V5, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  N0                           167                             150
  N1                            72                              61
  N2                            21                              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   223   1
  DEL PEAK 28(10Q23.31) WILD-TYPE 188   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED    223    1
  DEL PEAK 28(10Q23.31) WILD-TYPE  188    6
   clus
vv  DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  0                           223                             188
  1                             1                               6
[1] 2 2
[1] FALSE
D58V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED    61 207
  DEL PEAK 28(10Q23.31) WILD-TYPE  69 164
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED     61  207
  DEL PEAK 28(10Q23.31) WILD-TYPE   69  164
        clus
vv       DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  FEMALE                            61                              69
  MALE                             207                             164
[1] 2 2
[1] FALSE
D58V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(10Q23.31) MUTATED   211  29
  DEL PEAK 28(10Q23.31) WILD-TYPE 173  24
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED    211   29
  DEL PEAK 28(10Q23.31) WILD-TYPE  173   24
     clus
vv    DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  NO                            211                             173
  YES                            29                              24
[1] 2 2
[1] FALSE
D58V9, 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 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                                                           256
  DEL PEAK 28(10Q23.31) WILD-TYPE                                                         223
D58V10, multiclass
                                                             clus
vv                                                            DEL PEAK 28(10Q23.31) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           256
                                                             clus
vv                                                            DEL PEAK 28(10Q23.31) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             223
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, continuous
D58V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(10Q23.31) MUTATED   217   5   2  12
  DEL PEAK 28(10Q23.31) WILD-TYPE 182   7   2  11
D58V13, multiclass
    clus
vv   DEL PEAK 28(10Q23.31) MUTATED DEL PEAK 28(10Q23.31) WILD-TYPE
  R0                           217                             182
  R1                             5                               7
  R2                             2                               2
  RX                            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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(10Q23.31) MUTATED       5                        20   184
  DEL PEAK 28(10Q23.31) WILD-TYPE     4                        11   165
D58V14, multiclass
                           clus
vv                          DEL PEAK 28(10Q23.31) MUTATED
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               184
                           clus
vv                          DEL PEAK 28(10Q23.31) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                              11
  WHITE                                                 165
[1] 3 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     4 168
  DEL PEAK 28(10Q23.31) WILD-TYPE   4 149
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(10Q23.31) MUTATED      4  168
  DEL PEAK 28(10Q23.31) WILD-TYPE    4  149
                        clus
vv                       DEL PEAK 28(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           168
                        clus
vv                       DEL PEAK 28(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             149
[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   139 103
  DEL PEAK 29(11P15.5) WILD-TYPE 141 111
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           242                            252 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                           103                            111 
$`DEL PEAK 29(11P15.5) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-21-A5DI TCGA-22-1017 
       12.20       123.19         4.80        31.99        32.19        48.82 
TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 TCGA-34-2605 
       60.66        22.06       129.01       133.74        19.76        28.96 
TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 
       22.49        18.38         7.76        11.61        12.03        13.05 
TCGA-56-8308 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH 
       17.00        21.04         0.13         9.01        32.32        66.61 
TCGA-68-8250 TCGA-77-A5GA TCGA-90-7964 TCGA-94-7033 TCGA-98-8020 TCGA-NC-A5HD 
        8.02        42.08        14.07        21.04         2.76         0.07 
TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3408 
       76.80        40.90        65.65        16.80         8.58        75.75 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-5592 
       11.34        23.54        36.07        92.42        86.96        49.94 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 TCGA-21-1082 
      119.54        46.88        60.89        34.78       122.43       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-4593 TCGA-22-4595 
       43.23        31.63        33.93        10.82        35.08        24.13 
TCGA-22-4596 TCGA-22-4601 TCGA-22-4607 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
        0.56        34.75        19.30        63.55        44.25         0.79 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-33-4538 TCGA-33-4547 
       86.30        79.20        11.74        18.84        97.94        79.53 
TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 TCGA-33-AASB TCGA-33-AASI TCGA-34-2600 
      103.53        54.44        63.35         6.94        44.19        61.61 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5236 TCGA-34-5241 TCGA-34-5928 TCGA-34-5929 
       65.23        81.24         9.07        16.93        39.32         4.96 
TCGA-34-8454 TCGA-37-3783 TCGA-37-3789 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
       38.79         4.01         0.43         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EN TCGA-39-5011 TCGA-39-5019 TCGA-39-5022 
        6.81         0.39        21.70       133.25       111.35        55.20 
TCGA-39-5027 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-43-2581 
      102.18        60.53        36.39        68.38        55.56        38.66 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-8115 TCGA-46-3768 
       33.11        27.91        22.98        19.59        13.38         9.83 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 
        4.44        10.65        13.91         5.46        30.35        28.96 
TCGA-56-6545 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7822 TCGA-56-8307 
       21.90        18.48        31.27        30.41        17.49        26.89 
TCGA-56-8503 TCGA-56-8624 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZK 
        1.35        13.81        20.25        15.81        20.94        18.74 
TCGA-56-A62T TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-60-2695 TCGA-60-2698 
       14.47        13.25        29.95        71.24        21.11        10.22 
TCGA-60-2703 TCGA-60-2708 TCGA-60-2714 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 
       96.82        80.45        50.33         3.19        35.90        23.57 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML 
       11.77        52.67        70.13       102.67        59.97        45.57 
TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2742 TCGA-66-2758 TCGA-66-2759 
       16.37        53.88        34.59        21.07        21.01        25.05 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 TCGA-66-2773 
        0.99         1.02         2.01         7.07        19.00         3.02 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2785 TCGA-66-2788 TCGA-66-2789 
       12.03         3.98        12.00         1.97        22.98         4.04 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2795 TCGA-66-2800 TCGA-68-7757 
        5.03        30.02        10.06         4.01        49.05         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6723 TCGA-77-6844 TCGA-77-6845 
       13.35        16.18        14.73        12.33        75.09        23.28 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
      140.09         0.49       106.95         0.16        46.78        32.55 
TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8133 TCGA-77-8138 
        6.51        86.76        55.73       156.66        53.92        17.72 
TCGA-77-8140 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
       11.54        26.40        66.51        54.41        65.49        60.53 
TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6561 
       36.36        22.29         5.92        61.94        27.62        40.24 
TCGA-85-7696 TCGA-85-7697 TCGA-85-7699 TCGA-85-7843 TCGA-85-7950 TCGA-85-8048 
       36.53        34.95        32.91         1.15        18.94        25.15 
TCGA-85-8276 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8479 
       34.52        13.22        16.77         5.29         3.09        15.39 
TCGA-85-8481 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A4QR 
        7.76        30.28        34.13        19.86        30.48        19.73 
TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 
       15.29         3.65        11.77        10.59         4.01         2.30 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        4.01         5.03        26.63        14.14        71.01        18.31 
TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J TCGA-LA-A7SW TCGA-MF-A522 
       21.34        18.15         2.01        20.71        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN 
        4.54        64.54        57.30        13.74         2.89        49.28 
TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q 
       43.92        14.73        26.43        83.57        33.07         3.72 
TCGA-O2-A52V TCGA-XC-AA0X 
       43.89         0.20 

$`DEL PEAK 29(11P15.5) WILD-TYPE`
TCGA-18-3407 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 TCGA-22-5472 TCGA-33-4589 
        4.47         6.18        27.19        14.93        64.93         1.55 
TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-7658 TCGA-43-8118 TCGA-56-7221 
       31.50        31.27        17.88        78.18         2.93        19.99 
TCGA-56-8305 TCGA-56-8504 TCGA-56-A4BY TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 
        3.45        16.77        17.85         3.58        41.42        35.34 
TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
       20.78        30.81         9.50         0.16        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HM 
       57.07        19.36         5.69        21.21        19.10        39.85 
TCGA-NK-A7XE TCGA-18-3411 TCGA-18-3415 TCGA-18-4086 TCGA-18-4721 TCGA-21-1072 
        0.43       117.57        92.15         2.79       154.32        99.16 
TCGA-21-1075 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-5783 TCGA-21-5784 
       70.16        15.58        31.73         9.34        88.11        41.69 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       21.99         7.33         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 
       27.02        20.48        48.33        38.17        13.12        32.02 
TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 TCGA-22-5480 TCGA-22-5485 TCGA-22-5489 
        9.57        11.77        14.63        71.34        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-A4WN 
       56.32        16.64       173.82       151.27        14.07         4.70 
TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 
        0.30        36.62       110.99       118.36        27.16         2.63 
TCGA-34-2608 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-7107 
       32.88        74.66        60.30        50.66        44.75         1.12 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3792 TCGA-37-4129 TCGA-37-5819 
        4.04        26.43        33.90         0.39         7.96         3.39 
TCGA-37-A5EL TCGA-39-5016 TCGA-39-5021 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 
       37.58       126.58        68.58        82.52         1.71        24.33 
TCGA-39-5030 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-6647 
        1.94        71.18        17.06        40.21        39.12        24.89 
TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
       21.47         5.46         3.81        11.77         9.73        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
       13.32        12.16        13.02         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-5898 TCGA-56-7223 
       28.34         8.75        27.45        12.43        18.25        14.53 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
       19.76         6.51         0.10        33.24        14.96         4.93 
TCGA-56-8304 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8626 
        3.48        14.07         1.81        22.75        10.36         9.93 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8386 TCGA-58-8388 TCGA-58-8392 
       19.23        13.32         0.26         0.03        13.55        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-60-2697 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 
       12.23        37.94        92.71        21.93        49.48        66.54 
TCGA-60-2713 TCGA-60-2716 TCGA-60-2719 TCGA-60-2722 TCGA-60-2725 TCGA-63-7021 
       56.91        48.49        42.64        29.85        26.83        70.42 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN 
       68.15        55.30        70.62        58.65        14.99        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-66-2727 TCGA-66-2734 
       25.28        89.29        78.28        36.16        16.96        43.10 
TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
        2.01         0.99         1.02         2.01         0.92         0.99 
TCGA-66-2757 TCGA-66-2765 TCGA-66-2767 TCGA-66-2770 TCGA-66-2777 TCGA-66-2778 
       43.99         2.01         2.01        23.01         2.01        19.00 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2790 TCGA-66-2794 TCGA-68-7755 
       24.95        25.97        40.01        22.98        54.08         2.73 
TCGA-68-7756 TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-7138 TCGA-77-7142 
        6.64        12.07        29.56        73.12        11.18        73.22 
TCGA-77-7335 TCGA-77-8128 TCGA-77-8131 TCGA-77-8136 TCGA-77-8139 TCGA-77-8144 
       70.13        37.81        12.59        39.09       104.09        27.39 
TCGA-77-8145 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5GH TCGA-85-6175 
        6.97       126.18       132.36       150.25        38.86         9.67 
TCGA-85-6560 TCGA-85-6798 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-8049 
       41.39         6.41        31.30         1.38        29.95        19.04 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 
       24.13        31.56        26.79        30.64        10.09         0.76 
TCGA-85-8350 TCGA-85-8354 TCGA-85-8355 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
       22.45        32.71         2.01        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z 
       18.08        22.59        30.97        24.36        27.16        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 TCGA-90-7767 
       15.85        14.96        29.92        12.39        24.92         2.93 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-A5I6 
       20.22        22.62         2.70         3.48         5.26        17.69 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 
       17.46        27.68        21.44        30.81        30.67        27.16 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       27.02        20.32        18.58        12.89        16.11        13.18 
TCGA-NC-A5HH TCGA-NC-A5HK TCGA-NC-A5HP TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A5IB 
        1.22         4.21        25.32         3.65        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 
                        156.66                         173.82 
  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE 
                        22.175                         21.325 
[1] "0.1 - 156.7 (22.2)" "0.0 - 173.8 (21.3)"
[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       36       72        1        31
  DEL PEAK 29(11P15.5) WILD-TYPE       0       53       80        1        34
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(11P15.5) MUTATED          51         1         36          9
  DEL PEAK 29(11P15.5) WILD-TYPE        44         2         27         10
                                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                             36                             53
  STAGE IB                             72                             80
  STAGE II                              1                              1
  STAGE IIA                            31                             34
  STAGE IIB                            51                             44
  STAGE III                             1                              2
  STAGE IIIA                           36                             27
  STAGE IIIB                            9                             10
  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    47 142  44  12
  DEL PEAK 29(11P15.5) WILD-TYPE  65 152  27  12
D59V4, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  T1                           47                             65
  T2                          142                            152
  T3                           44                             27
  T4                           12                             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   153  71  18   2
  DEL PEAK 29(11P15.5) WILD-TYPE 164  62  22   3
D59V5, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  N0                          153                            164
  N1                           71                             62
  N2                           18                             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   204   4
  DEL PEAK 29(11P15.5) WILD-TYPE 207   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED    204    4
  DEL PEAK 29(11P15.5) WILD-TYPE  207    3
   clus
vv  DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  0                          204                            207
  1                            4                              3
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED    57 188
  DEL PEAK 29(11P15.5) WILD-TYPE  73 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED     57  188
  DEL PEAK 29(11P15.5) WILD-TYPE   73  183
        clus
vv       DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  FEMALE                           57                             73
  MALE                            188                            183
[1] 2 2
[1] FALSE
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED   185  29
  DEL PEAK 29(11P15.5) WILD-TYPE 199  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED    185   29
  DEL PEAK 29(11P15.5) WILD-TYPE  199   24
     clus
vv    DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  NO                           185                            199
  YES                           29                             24
[1] 2 2
[1] FALSE
D59V9, 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 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                                                           234
  DEL PEAK 29(11P15.5) WILD-TYPE                                                         245
D59V10, multiclass
                                                             clus
vv                                                            DEL PEAK 29(11P15.5) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          234
                                                             clus
vv                                                            DEL PEAK 29(11P15.5) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            245
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, continuous
D59V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(11P15.5) MUTATED   193   7   2  10
  DEL PEAK 29(11P15.5) WILD-TYPE 206   5   2  13
D59V13, multiclass
    clus
vv   DEL PEAK 29(11P15.5) MUTATED DEL PEAK 29(11P15.5) WILD-TYPE
  R0                          193                            206
  R1                            7                              5
  R2                            2                              2
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(11P15.5) MUTATED       2                        18   168
  DEL PEAK 29(11P15.5) WILD-TYPE     7                        13   181
D59V14, multiclass
                           clus
vv                          DEL PEAK 29(11P15.5) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           18
  WHITE                                              168
                           clus
vv                          DEL PEAK 29(11P15.5) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             13
  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"
D59V15, binary
                                cls
clus                               0   1
  DEL PEAK 29(11P15.5) MUTATED     2 149
  DEL PEAK 29(11P15.5) WILD-TYPE   6 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(11P15.5) MUTATED      2  149
  DEL PEAK 29(11P15.5) WILD-TYPE    6  168
                        clus
vv                       DEL PEAK 29(11P15.5) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          149
                        clus
vv                       DEL PEAK 29(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            168
[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    89  72
  DEL PEAK 30(11Q22.1) WILD-TYPE 191 142
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                           161                            333 
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                            72                            142 
$`DEL PEAK 30(11Q22.1) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3416 TCGA-18-5595 TCGA-33-4589 TCGA-34-2605 
       12.20       123.19        31.99        27.19         1.55        28.96 
TCGA-43-7657 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8504 
        7.76         2.93        11.61        12.03        19.99        16.77 
TCGA-56-A4BY TCGA-60-2712 TCGA-63-A5MH TCGA-68-8250 TCGA-90-7766 TCGA-96-7545 
       17.85         9.01        66.61         8.02         9.50        57.07 
TCGA-98-8020 TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3412 
        2.76        76.80        65.65        16.80         8.58        11.34 
TCGA-18-3417 TCGA-18-3421 TCGA-21-1076 TCGA-21-1080 TCGA-21-5783 TCGA-21-5787 
       36.07        86.96        60.89       122.43        88.11        10.82 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-4593 TCGA-22-4601 
       21.99         4.31         1.74        14.10        35.08        34.75 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 TCGA-22-5481 TCGA-33-AASB 
       11.77        63.55        44.25         0.79        79.20         6.94 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-5232 TCGA-34-5239 TCGA-34-5928 
       27.16         2.63        61.61        81.24        60.30        39.32 
TCGA-34-8454 TCGA-37-4130 TCGA-37-A5EN TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 
       38.79         8.12        21.70       126.58       111.35        68.58 
TCGA-39-5022 TCGA-39-5027 TCGA-39-5031 TCGA-39-5037 TCGA-43-2581 TCGA-43-3920 
       55.20       102.18        60.53        55.56        38.66        33.11 
TCGA-43-6771 TCGA-43-8116 TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
        5.46        11.77         9.83        10.65        13.91         0.39 
TCGA-52-7809 TCGA-56-7222 TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 
        5.46        18.48        14.53        30.41        19.76        17.49 
TCGA-56-8082 TCGA-56-8503 TCGA-56-8624 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX 
       14.96         1.35        13.81        15.81        19.23        13.32 
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-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 
       10.22        80.45        29.85        35.90        26.83        11.77 
TCGA-63-7023 TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MS TCGA-66-2727 TCGA-66-2758 
       55.30        59.97        45.57        78.28        16.96        21.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2781 TCGA-66-2790 TCGA-66-2794 
        1.02         2.01         2.01         3.98        22.98        54.08 
TCGA-66-2800 TCGA-68-8251 TCGA-68-A59J TCGA-77-7139 TCGA-77-7338 TCGA-77-7465 
       49.05        13.35        14.73       140.09         0.16        32.55 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8133 TCGA-77-8136 
       86.76        55.73        37.81       156.66        53.92        39.09 
TCGA-77-8138 TCGA-77-8143 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 
       17.72        26.40        66.51        54.41        65.49       150.25 
TCGA-77-A5G6 TCGA-85-6798 TCGA-85-7696 TCGA-85-7699 TCGA-85-8048 TCGA-85-8071 
       22.29         6.41        36.53        32.91        25.15        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 
       30.64        34.52        10.09         5.29        32.71         2.01 
TCGA-85-8479 TCGA-85-8664 TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 
       15.39        18.08        19.86        30.48        27.16        14.96 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8064 
        3.65         2.93        22.62        10.59         3.48         5.26 
TCGA-94-8491 TCGA-94-A5I6 TCGA-96-8169 TCGA-96-A4JL TCGA-98-A538 TCGA-98-A53I 
       26.63        17.69        18.31        27.68        27.16        18.58 
TCGA-98-A53J TCGA-MF-A522 TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HO 
       20.71        11.84        64.54        13.74         2.89        43.92 
TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       83.57        33.07        12.72        43.89        11.18 

$`DEL PEAK 30(11Q22.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3410 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 
        4.47         4.80         6.18        32.19        14.93        48.82 
TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-6737 
       60.66        64.93        22.06       129.01       133.74        19.76 
TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 
       31.50        31.27        17.88        22.49        18.38        78.18 
TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       13.05         3.45        17.00        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       41.42        35.34        32.32        20.78        42.08        30.81 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK 
       14.07        21.04         0.16        18.38        16.14        19.36 
TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NC-A5HR 
        5.69        21.21        19.10         0.07        39.85        40.90 
TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3411 TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 
        0.43        75.75       117.57        23.54        92.15        92.42 
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-21-1082 
       70.16        34.78        15.58        31.73         9.34       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1005 
       43.23        31.63        41.69        33.93         7.33        64.21 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 
       27.02        20.48        48.33        24.13         0.56        38.17 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5474 TCGA-22-5479 
       13.12        32.02        19.30         9.57        14.63        86.30 
TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 
       71.34        11.74        18.84        30.12        62.86        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 
       16.64        97.94        79.53       173.82       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       14.07        54.44        63.35         4.70         0.30        36.62 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-2608 TCGA-34-5231 TCGA-34-5234 
      110.99        44.19       118.36        32.88        65.23        74.66 
TCGA-34-5236 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 
        9.07        50.66        16.93        44.75         4.96         1.12 
TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
        4.04        26.43        33.90         4.01         0.43         0.39 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        7.96         7.46         7.82         6.81         0.39         3.39 
TCGA-37-A5EL TCGA-39-5011 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
       37.58       133.25        82.52         1.71        24.33         1.94 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 
       36.39        68.38        71.18        17.06        40.21        39.12 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 
       27.91        22.98        24.89        21.47         3.81        19.59 
TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       13.38         9.73        14.20        13.32        12.16        13.02 
TCGA-46-3769 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7810 TCGA-52-7811 
        4.44         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-56-7579 
       27.45        28.96        12.43        18.25        21.90        31.27 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 
        6.51         0.10        33.24         4.93         3.48        26.89 
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-A5DS TCGA-56-A62T TCGA-58-8388 TCGA-58-8392 TCGA-58-8393 
       20.94         0.26        14.47        13.55        16.47        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-60-2703 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-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2724 
       56.91        50.33        48.49        42.64         3.19        23.57 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG 
       52.67        70.13        70.42        68.15       102.67        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-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-66-2753 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-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 
       25.05         0.99         2.01         7.07        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-66-2785 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-66-2793 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-A59I TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
       16.18        12.07        12.33        29.56        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 
       23.28        11.18         0.49        73.22        70.13       106.95 
TCGA-77-7463 TCGA-77-8007 TCGA-77-8131 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 
       46.78         6.51        12.59       104.09        11.54        27.39 
TCGA-77-8145 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 
        6.97        60.53        36.36       126.18       132.36         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 
       61.94        27.62        38.86         9.67        41.39        40.24 
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-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       19.04        24.13        31.56         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
       16.77         3.09         7.76        36.59        38.14        12.59 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR 
       22.59        30.28        34.13        30.97        24.36        19.73 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       16.21        15.85        15.29        29.92        12.39        24.92 
TCGA-90-7769 TCGA-90-A4ED TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 
       11.77        20.22         2.70         4.01         2.30         4.01 
TCGA-94-8490 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 
        5.03        14.14        71.01        17.46        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       30.67        21.34        18.15         2.01        27.02        20.32 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HH 
       12.89        16.11        13.18        13.41         4.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
       57.30         4.21        49.28        25.32        14.73        26.43 
TCGA-NK-A5CX TCGA-O2-A52Q TCGA-XC-AA0X 
        3.65         3.72         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 
                        156.66                         173.82 
  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE 
                          21.7                           21.9 
[1] "0.0 - 156.7 (21.7)" "0.1 - 173.8 (21.9)"
[1] "hr=" "1"  
D60V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(11Q22.1) MUTATED         2       24       45        1        27
  DEL PEAK 30(11Q22.1) WILD-TYPE       0       65      107        1        38
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(11Q22.1) MUTATED          31         2         22          5
  DEL PEAK 30(11Q22.1) WILD-TYPE        64         1         41         14
                                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                             24                             65
  STAGE IB                             45                            107
  STAGE II                              1                              1
  STAGE IIA                            27                             38
  STAGE IIB                            31                             64
  STAGE III                             2                              1
  STAGE IIIA                           22                             41
  STAGE IIIB                            5                             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 30(11Q22.1) MUTATED    31 105  19   8
  DEL PEAK 30(11Q22.1) WILD-TYPE  81 189  52  16
D60V4, multiclass
    clus
vv   DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  T1                           31                             81
  T2                          105                            189
  T3                           19                             52
  T4                            8                             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 30(11Q22.1) MUTATED    93  56  12   1
  DEL PEAK 30(11Q22.1) WILD-TYPE 224  77  28   4
D60V5, multiclass
    clus
vv   DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  N0                           93                            224
  N1                           56                             77
  N2                           12                             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   133   2
  DEL PEAK 30(11Q22.1) WILD-TYPE 278   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q22.1) MUTATED    133    2
  DEL PEAK 30(11Q22.1) WILD-TYPE  278    5
   clus
vv  DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  0                          133                            278
  1                            2                              5
[1] 2 2
[1] FALSE
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q22.1) MUTATED    38 125
  DEL PEAK 30(11Q22.1) WILD-TYPE  92 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q22.1) MUTATED     38  125
  DEL PEAK 30(11Q22.1) WILD-TYPE   92  246
        clus
vv       DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  FEMALE                           38                             92
  MALE                            125                            246
[1] 2 2
[1] FALSE
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q22.1) MUTATED   132  14
  DEL PEAK 30(11Q22.1) WILD-TYPE 252  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q22.1) MUTATED    132   14
  DEL PEAK 30(11Q22.1) WILD-TYPE  252   39
     clus
vv    DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  NO                           132                            252
  YES                           14                             39
[1] 2 2
[1] FALSE
D60V9, 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 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                                                           156
  DEL PEAK 30(11Q22.1) WILD-TYPE                                                         323
D60V10, multiclass
                                                             clus
vv                                                            DEL PEAK 30(11Q22.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          156
                                                             clus
vv                                                            DEL PEAK 30(11Q22.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            323
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
D60V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(11Q22.1) MUTATED   128   2   1   6
  DEL PEAK 30(11Q22.1) WILD-TYPE 271  10   3  17
D60V13, multiclass
    clus
vv   DEL PEAK 30(11Q22.1) MUTATED DEL PEAK 30(11Q22.1) WILD-TYPE
  R0                          128                            271
  R1                            2                             10
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(11Q22.1) MUTATED       2                        11   114
  DEL PEAK 30(11Q22.1) WILD-TYPE     7                        20   235
D60V14, multiclass
                           clus
vv                          DEL PEAK 30(11Q22.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           11
  WHITE                                              114
                           clus
vv                          DEL PEAK 30(11Q22.1) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             20
  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"
D60V15, binary
                                cls
clus                               0   1
  DEL PEAK 30(11Q22.1) MUTATED     2 107
  DEL PEAK 30(11Q22.1) WILD-TYPE   6 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(11Q22.1) MUTATED      2  107
  DEL PEAK 30(11Q22.1) WILD-TYPE    6  210
                        clus
vv                       DEL PEAK 30(11Q22.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          107
                        clus
vv                       DEL PEAK 30(11Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            210
[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    99  83
  DEL PEAK 31(11Q25) WILD-TYPE 181 131
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                         182                          312 
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                          83                          131 
$`DEL PEAK 31(11Q25) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3416 TCGA-18-5595 TCGA-33-4532 TCGA-33-4533 
       12.20       123.19        31.99        27.19       129.01       133.74 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-43-7657 TCGA-43-7658 TCGA-43-A474 
        1.55        19.76        28.96         7.76        78.18        11.61 
TCGA-43-A56V TCGA-56-7221 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-60-2712 
       12.03        19.99        17.00        16.77        17.85         9.01 
TCGA-60-2715 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-90-7766 TCGA-96-7545 
       35.34        66.61         8.02        20.78         9.50        57.07 
TCGA-98-8020 TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W 
        2.76         0.07        76.80        65.65        16.80         8.58 
TCGA-18-3408 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-21-1076 
       75.75        11.34        23.54        36.07        86.96        60.89 
TCGA-21-1080 TCGA-21-1082 TCGA-21-5783 TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 
      122.43       119.80        88.11        10.82        21.99         4.31 
TCGA-22-1011 TCGA-22-1016 TCGA-22-4593 TCGA-22-4601 TCGA-22-4613 TCGA-22-5473 
        1.74        27.02        35.08        34.75        11.77        63.55 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5481 TCGA-22-5489 TCGA-33-4587 TCGA-33-AASB 
       44.25         0.79        79.20        62.86        54.44         6.94 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-5232 TCGA-34-5236 TCGA-34-5239 
       27.16         2.63        61.61        81.24         9.07        60.30 
TCGA-34-5928 TCGA-34-A5IX TCGA-37-3789 TCGA-37-4135 TCGA-37-A5EN TCGA-39-5016 
       39.32        33.90         0.43         6.81        21.70       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5031 TCGA-39-5037 
      111.35        68.58        55.20       102.18        60.53        55.56 
TCGA-43-2581 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-8116 
       38.66        33.11        24.89        21.47         5.46        11.77 
TCGA-46-3768 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-52-7809 TCGA-56-7222 
        9.83        10.65        13.91         0.39         5.46        18.48 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-56-8624 TCGA-56-8625 
       14.53        30.41        19.76        17.49        13.81        10.36 
TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-58-8390 TCGA-58-A46J 
       15.81        19.23        13.32        18.74        29.95        85.12 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2708 TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 
       21.11        10.22        80.45        29.85        26.83        11.77 
TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MS TCGA-66-2727 
       55.30       102.67        59.97        45.57        78.28        16.96 
TCGA-66-2753 TCGA-66-2756 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 
        1.02         0.99        43.99        21.01        25.05         2.01 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2773 TCGA-66-2790 TCGA-66-2792 TCGA-66-2794 
        2.01         2.01         3.02        22.98        30.02        54.08 
TCGA-66-2800 TCGA-68-8251 TCGA-68-A59J TCGA-70-6722 TCGA-77-7139 TCGA-77-7142 
       49.05        13.35        14.73        12.07       140.09        73.22 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        0.16        32.55        86.76        55.73        37.81       156.66 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8143 TCGA-77-8148 
       12.59        53.92        39.09        17.72        26.40        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G3 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
       54.41        65.49       150.25         6.41        36.53        31.30 
TCGA-85-7699 TCGA-85-8048 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       32.91        25.15        26.79        30.64        34.52        10.09 
TCGA-85-8287 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8664 
        0.76         5.29        32.71         2.01         7.76        18.08 
TCGA-85-A4JC TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7767 
       19.86        27.16        16.21        14.96         3.65         2.93 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-94-8491 TCGA-94-A5I6 
       22.62        10.59         3.48         4.01        26.63        17.69 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J TCGA-MF-A522 TCGA-NC-A5HG 
       21.34        27.16        18.58        20.71        11.84        64.54 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52S 
       13.74         4.21        43.92        83.57        33.07        12.72 
TCGA-O2-A52V TCGA-O2-A5IB 
       43.89        11.18 

$`DEL PEAK 31(11Q25) WILD-TYPE`
TCGA-18-3407 TCGA-18-3410 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 
        4.47         4.80         6.18        32.19        14.93        48.82 
TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-34-2604 TCGA-34-2609 TCGA-39-5039 
       60.66        64.93        22.06        31.50        31.27        17.88 
TCGA-43-2578 TCGA-43-5668 TCGA-43-8118 TCGA-56-8201 TCGA-56-8305 TCGA-56-A4ZJ 
       22.49        18.38         2.93        13.05         3.45        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2721 TCGA-77-A5GA TCGA-77-A5GB 
        0.13         3.58        41.42        32.32        42.08        30.81 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK 
       14.07        21.04         0.16        18.38        16.14        19.36 
TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE 
        5.69        21.21        19.10        39.85        40.90         0.43 
TCGA-18-3411 TCGA-18-3415 TCGA-18-3419 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
      117.57        92.15        92.42         2.79       154.32        49.94 
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-21-1079 TCGA-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 
       31.73         9.34        43.23        31.63        41.69        33.93 
TCGA-22-0944 TCGA-22-1005 TCGA-22-1012 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
        7.33        64.21        14.10        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-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 
       14.63        86.30        71.34        11.74        18.84        30.12 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 
       56.32        16.64        97.94        79.53       173.82       103.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
      151.27        14.07        63.35         4.70         0.30        36.62 
TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-2608 TCGA-34-5231 TCGA-34-5234 
      110.99        44.19       118.36        32.88        65.23        74.66 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       50.66        16.93        44.75         4.96         1.12        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
        4.04        26.43         4.01         0.39         7.96         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL TCGA-39-5011 
        7.46         7.82         0.39         3.39        37.58       133.25 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 
       82.52         1.71        24.33         1.94        36.39        68.38 
TCGA-39-5036 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 
       71.18        17.06        40.21        39.12        27.91        22.98 
TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 
        3.81        19.59        13.38         9.73        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       12.16        13.02         4.44         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        12.43        18.25 
TCGA-56-6545 TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 
       21.90        31.27         6.51         0.10        33.24        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 
        4.93         3.48        26.89        14.07         1.35         1.81 
TCGA-56-8623 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A5DS TCGA-56-A62T 
       22.75         9.93        20.25        20.94         0.26        14.47 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
        0.03        13.25        13.55        71.24        16.47        34.78 
TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2703 
       34.36        56.65        35.24        29.92        12.23        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       37.94        92.71        21.93        49.48        66.54        56.91 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 
       50.33        48.49        42.64         3.19        35.90        23.57 
TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MI 
       52.67        70.13        70.42        68.15        70.62        58.65 
TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MV 
       14.99        11.34        25.28        89.29        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       53.88        34.59        43.10         2.01        21.07         0.99 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2763 TCGA-66-2766 TCGA-66-2769 TCGA-66-2770 
        2.01         0.92         0.99         1.02         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-66-2788 TCGA-66-2789 
       24.95         1.97        25.97        40.01        22.98         4.04 
TCGA-66-2791 TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 
        5.03        10.06         4.01         2.73         6.64         6.94 
TCGA-68-A59I TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       16.18        12.33        29.56        73.12        75.09        23.28 
TCGA-77-7138 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-8007 
       11.18         0.49        70.13       106.95        46.78         6.51 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 TCGA-77-8156 
      104.09        11.54        27.39         6.97        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      126.18       132.36        22.29         5.92        61.94        27.62 
TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 TCGA-85-7710 
       38.86         9.67        41.39        40.24        34.95         1.38 
TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 
        1.15        29.95        18.94        19.04        24.13        31.56 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 
       13.22        22.45        16.77         3.09        15.39        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB 
       38.14        12.59        22.59        30.28        34.13        30.97 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 
       24.36        30.48        19.73        15.85        15.29        29.92 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-92-7340 TCGA-92-8064 
       12.39        24.92        11.77        20.22         2.70         5.26 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 
        2.30         4.01         5.03        14.14        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A53A 
       17.46        27.68        21.44        30.81        30.67        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
        2.01        27.02        20.32        12.89        16.11        13.18 
TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN 
       13.41         4.54         1.22        57.30         2.89        49.28 
TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52Q TCGA-XC-AA0X 
       25.32        14.73        26.43         3.65         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 
                      156.66                       173.82 
  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE 
                       22.80                        21.14 
[1] "0.1 - 156.7 (22.8)" "0.0 - 173.8 (21.1)"
[1] "hr=" "1"  
D61V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(11Q25) MUTATED         2       26       56        1        24
  DEL PEAK 31(11Q25) WILD-TYPE       0       63       96        1        41
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(11Q25) MUTATED          40         2         24          6
  DEL PEAK 31(11Q25) WILD-TYPE        55         1         39         13
                              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                           63
  STAGE IB                           56                           96
  STAGE II                            1                            1
  STAGE IIA                          24                           41
  STAGE IIB                          40                           55
  STAGE III                           2                            1
  STAGE IIIA                         24                           39
  STAGE IIIB                          6                           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
  DEL PEAK 31(11Q25) MUTATED    33 116  25  10
  DEL PEAK 31(11Q25) WILD-TYPE  79 178  46  14
D61V4, multiclass
    clus
vv   DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  T1                         33                           79
  T2                        116                          178
  T3                         25                           46
  T4                         10                           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  62  12   1
  DEL PEAK 31(11Q25) WILD-TYPE 209  71  28   4
D61V5, multiclass
    clus
vv   DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  N0                        108                          209
  N1                         62                           71
  N2                         12                           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   149   2
  DEL PEAK 31(11Q25) WILD-TYPE 262   5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(11Q25) MUTATED    149    2
  DEL PEAK 31(11Q25) WILD-TYPE  262    5
   clus
vv  DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  0                        149                          262
  1                          2                            5
[1] 2 2
[1] FALSE
D61V7, binary
                              cls
clus                             0   1
  DEL PEAK 31(11Q25) MUTATED    40 144
  DEL PEAK 31(11Q25) WILD-TYPE  90 227
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(11Q25) MUTATED     40  144
  DEL PEAK 31(11Q25) WILD-TYPE   90  227
        clus
vv       DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  FEMALE                         40                           90
  MALE                          144                          227
[1] 2 2
[1] FALSE
D61V8, binary
                              cls
clus                             0   1
  DEL PEAK 31(11Q25) MUTATED   147  19
  DEL PEAK 31(11Q25) WILD-TYPE 237  34
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(11Q25) MUTATED    147   19
  DEL PEAK 31(11Q25) WILD-TYPE  237   34
     clus
vv    DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  NO                         147                          237
  YES                         19                           34
[1] 2 2
[1] FALSE
D61V9, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 31(11Q25) MUTATED                                       6
  DEL PEAK 31(11Q25) WILD-TYPE                                     9
                              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                                                           176
  DEL PEAK 31(11Q25) WILD-TYPE                                                         303
D61V10, multiclass
                                                             clus
vv                                                            DEL PEAK 31(11Q25) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        176
                                                             clus
vv                                                            DEL PEAK 31(11Q25) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          303
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, continuous
D61V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 31(11Q25) MUTATED   141   3   1  11
  DEL PEAK 31(11Q25) WILD-TYPE 258   9   3  12
D61V13, multiclass
    clus
vv   DEL PEAK 31(11Q25) MUTATED DEL PEAK 31(11Q25) WILD-TYPE
  R0                        141                          258
  R1                          3                            9
  R2                          1                            3
  RX                         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                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(11Q25) MUTATED       3                        13   127
  DEL PEAK 31(11Q25) WILD-TYPE     6                        18   222
D61V14, multiclass
                           clus
vv                          DEL PEAK 31(11Q25) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                         13
  WHITE                                            127
                           clus
vv                          DEL PEAK 31(11Q25) WILD-TYPE
  ASIAN                                                6
  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"
D61V15, binary
                              cls
clus                             0   1
  DEL PEAK 31(11Q25) MUTATED     2 117
  DEL PEAK 31(11Q25) WILD-TYPE   6 200
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(11Q25) MUTATED      2  117
  DEL PEAK 31(11Q25) WILD-TYPE    6  200
                        clus
vv                       DEL PEAK 31(11Q25) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                        117
                        clus
vv                       DEL PEAK 31(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          200
[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    50  34
  DEL PEAK 32(12Q24.31) WILD-TYPE 230 180
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                             84                             410 
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                             34                             180 
$`DEL PEAK 32(12Q24.31) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-18-4083 TCGA-33-4533 TCGA-43-5668 TCGA-43-A56V 
        4.47       123.19         6.18       133.74        18.38        12.03 
TCGA-68-8250 TCGA-77-A5GA TCGA-77-A5GB TCGA-94-7033 TCGA-O2-A52W TCGA-18-3408 
        8.02        42.08        30.81        21.04         8.58        75.75 
TCGA-18-3415 TCGA-18-4086 TCGA-21-1072 TCGA-21-1082 TCGA-22-4595 TCGA-22-5473 
       92.15         2.79        99.16       119.80        24.13        63.55 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5485 TCGA-33-A5GW TCGA-33-AASL TCGA-34-5232 
        0.79        86.30        30.12         0.30        27.16        81.24 
TCGA-34-A5IX TCGA-37-4129 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-43-2581 
       33.90         7.96         0.39        37.58        21.70        38.66 
TCGA-43-5670 TCGA-43-6143 TCGA-46-6026 TCGA-52-7809 TCGA-56-5898 TCGA-56-7222 
       27.91        22.98        13.91         5.46        18.25        18.48 
TCGA-56-7223 TCGA-56-7822 TCGA-56-8624 TCGA-56-A49D TCGA-60-2698 TCGA-60-2703 
       14.53        17.49        13.81        20.94        10.22        96.82 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-63-A5MB TCGA-63-A5ML TCGA-66-2763 
       29.85        35.90        26.83       102.67        45.57         0.99 
TCGA-66-2766 TCGA-66-2773 TCGA-66-2781 TCGA-68-7757 TCGA-77-7138 TCGA-77-8007 
        1.02         3.02         3.98         6.94        11.18         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 TCGA-77-8139 
       86.76        55.73       156.66        12.59        17.72       104.09 
TCGA-77-8144 TCGA-77-8148 TCGA-77-8153 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7696 
       27.39        66.51        65.49        38.86        41.39        36.53 
TCGA-85-7710 TCGA-85-8350 TCGA-85-8353 TCGA-85-8354 TCGA-85-A50M TCGA-85-A50Z 
        1.38        22.45         3.09        32.71        27.16        16.21 
TCGA-85-A513 TCGA-90-A4ED TCGA-94-A4VJ TCGA-94-A5I6 TCGA-98-8021 TCGA-98-A538 
       29.92        20.22        14.14        17.69        30.81        27.16 
TCGA-98-A53J TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HP TCGA-NK-A5CR TCGA-O2-A52V 
       20.71        13.18        11.84        25.32        83.57        43.89 

$`DEL PEAK 32(12Q24.31) WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
       12.20         4.80        31.99        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 
       48.82        60.66        64.93        22.06       129.01         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 
       19.76        31.50        28.96        31.27        17.88        22.49 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 
        7.76        78.18         2.93        11.61        19.99        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR 
        3.45        17.00        16.77        17.85        21.04         0.13 
TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
        3.58        41.42         9.01        35.34        32.32        66.61 
TCGA-77-7140 TCGA-90-7766 TCGA-90-7964 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
       20.78         9.50        14.07         0.16        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH 
       57.07        19.36         2.76         5.69        21.21        19.10 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 
        0.07        76.80        39.85        40.90        65.65        16.80 
TCGA-NK-A7XE TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 
        0.43       117.57        11.34        23.54        36.07        92.42 
TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 
       86.96       154.32        49.94       119.54        46.88        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-21-5786 TCGA-21-5787 
       43.23        31.63        88.11        41.69        33.93        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       21.99         7.33         4.31        64.21         1.74        14.10 
TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4599 
       27.02        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-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 
       14.63        44.25        71.34        79.20        11.74        18.84 
TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
       62.86        56.32        16.64        97.94        79.53       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
      103.53       151.27        14.07        54.44        63.35         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-34-2608 TCGA-34-5231 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
       61.61        32.88        65.23        74.66         9.07        60.30 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
       50.66        16.93        44.75        39.32         4.96         1.12 
TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
       38.79         4.04        26.43         4.01         0.43         0.39 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 
        8.12         7.46         7.82         6.81         3.39       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
      126.58       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 
        1.71        24.33         1.94        60.53        36.39        68.38 
TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 
       71.18        55.56        17.06        40.21        39.12        33.11 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       24.89        21.47         5.46         3.81        19.59        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       11.77         9.73        14.20        13.32        12.16        13.02 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        9.83         4.44        10.65         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        12.43 
TCGA-56-6545 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       21.90        31.27        30.41        19.76         6.51         0.10 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
       33.24        14.96         4.93         3.48        26.89        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-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T 
       15.81        19.23        13.32        18.74         0.26        14.47 
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-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-60-2697 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 
       21.11        12.23        37.94        92.71        21.93        80.45 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       49.48        66.54        56.91        50.33        48.49        42.64 
TCGA-60-2720 TCGA-60-2724 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 
        3.19        23.57        11.77        52.67        70.13        70.42 
TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM 
       68.15        55.30        70.62        58.65        59.97        14.99 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV 
       11.34        25.28        89.29        78.28        16.37        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-66-2753 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-66-2765 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-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2782 
       23.01        19.00         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-66-2794 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-68-8251 TCGA-68-A59I TCGA-68-A59J 
       49.05         2.73         6.64        13.35        16.18        14.73 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       12.07        12.33        29.56        73.12        75.09        23.28 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
      140.09         0.49        73.22        70.13       106.95         0.16 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8128 TCGA-77-8133 TCGA-77-8136 TCGA-77-8140 
       46.78        32.55        37.81        53.92        39.09        11.54 
TCGA-77-8143 TCGA-77-8145 TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       26.40         6.97        54.41        60.53        36.36       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      132.36       150.25        22.29         5.92        61.94        27.62 
TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
        9.67        40.24         6.41        34.95        31.30        32.91 
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-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 
       31.56        26.79        30.64        34.52        10.09         0.76 
TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
       13.22        16.77         5.29         2.01        15.39         7.76 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       36.59        38.14        12.59        18.08        22.59        30.28 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       34.13        30.97        19.86        24.36        30.48        19.73 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       15.85        14.96        15.29        12.39         3.65        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
        2.93        11.77        22.62        10.59         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        4.01         5.26         2.30         4.01         5.03        26.63 
TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 
       71.01        18.31        17.46        27.68        21.44        30.67 
TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       21.34        18.15         2.01        27.02        20.32        18.58 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       12.89        16.11        13.41         4.54        64.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO 
       57.30        13.74         4.21         2.89        49.28        43.92 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S 
       14.73        26.43         3.65        33.07         3.72        12.72 
TCGA-O2-A5IB TCGA-XC-AA0X 
       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 
                         156.66                          173.82 
  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE 
                         23.555                          21.390 
[1] "0.3 - 156.7 (23.6)" "0.0 - 173.8 (21.4)"
[1] "hr=" "1.2"
D62V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(12Q24.31) MUTATED         1       15       34        1         7
  DEL PEAK 32(12Q24.31) WILD-TYPE       1       74      118        1        58
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(12Q24.31) MUTATED          17         0          8          1
  DEL PEAK 32(12Q24.31) WILD-TYPE        78         3         55         18
                                 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                              15                              74
  STAGE IB                              34                             118
  STAGE II                               1                               1
  STAGE IIA                              7                              58
  STAGE IIB                             17                              78
  STAGE III                              0                               3
  STAGE IIIA                             8                              55
  STAGE IIIB                             1                              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 32(12Q24.31) MUTATED    19  53  13   1
  DEL PEAK 32(12Q24.31) WILD-TYPE  93 241  58  23
D62V4, multiclass
    clus
vv   DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  T1                            19                              93
  T2                            53                             241
  T3                            13                              58
  T4                             1                              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    59  19   5   0
  DEL PEAK 32(12Q24.31) WILD-TYPE 258 114  35   5
D62V5, multiclass
    clus
vv   DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  N0                            59                             258
  N1                            19                             114
  N2                             5                              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    70   1
  DEL PEAK 32(12Q24.31) WILD-TYPE 341   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.31) MUTATED     70    1
  DEL PEAK 32(12Q24.31) WILD-TYPE  341    6
   clus
vv  DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  0                            70                             341
  1                             1                               6
[1] 2 2
[1] FALSE
D62V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(12Q24.31) MUTATED    17  69
  DEL PEAK 32(12Q24.31) WILD-TYPE 113 302
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.31) MUTATED     17   69
  DEL PEAK 32(12Q24.31) WILD-TYPE  113  302
        clus
vv       DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  FEMALE                            17                             113
  MALE                              69                             302
[1] 2 2
[1] FALSE
D62V8, binary
                                 cls
clus                                0   1
  DEL PEAK 32(12Q24.31) MUTATED    71   4
  DEL PEAK 32(12Q24.31) WILD-TYPE 313  49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.31) MUTATED     71    4
  DEL PEAK 32(12Q24.31) WILD-TYPE  313   49
     clus
vv    DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  NO                             71                             313
  YES                             4                              49
[1] 2 2
[1] FALSE
D62V9, 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 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                                                            83
  DEL PEAK 32(12Q24.31) WILD-TYPE                                                         396
D62V10, multiclass
                                                             clus
vv                                                            DEL PEAK 32(12Q24.31) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            83
                                                             clus
vv                                                            DEL PEAK 32(12Q24.31) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             396
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, continuous
D62V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(12Q24.31) MUTATED    64   0   1   4
  DEL PEAK 32(12Q24.31) WILD-TYPE 335  12   3  19
D62V13, multiclass
    clus
vv   DEL PEAK 32(12Q24.31) MUTATED DEL PEAK 32(12Q24.31) WILD-TYPE
  R0                            64                             335
  R1                             0                              12
  R2                             1                               3
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(12Q24.31) MUTATED       3                         8    49
  DEL PEAK 32(12Q24.31) WILD-TYPE     6                        23   300
D62V14, multiclass
                           clus
vv                          DEL PEAK 32(12Q24.31) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                49
                           clus
vv                          DEL PEAK 32(12Q24.31) WILD-TYPE
  ASIAN                                                   6
  BLACK OR AFRICAN AMERICAN                              23
  WHITE                                                 300
[1] 3 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  54
  DEL PEAK 32(12Q24.31) WILD-TYPE   8 263
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(12Q24.31) MUTATED      0   54
  DEL PEAK 32(12Q24.31) WILD-TYPE    8  263
                        clus
vv                       DEL PEAK 32(12Q24.31) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            54
                        clus
vv                       DEL PEAK 32(12Q24.31) WILD-TYPE
  HISPANIC OR LATINO                                   8
  NOT HISPANIC OR LATINO                             263
[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   186 139
  DEL PEAK 33(13Q12.11) WILD-TYPE  94  75
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            325                             169 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                            139                              75 
$`DEL PEAK 33(13Q12.11) MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1000 
      123.19         4.80        31.99         6.18        32.19        14.93 
TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 
       60.66        64.93        22.06       129.01         1.55        19.76 
TCGA-34-2604 TCGA-34-2605 TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 TCGA-43-A474 
       31.50        28.96        22.49        18.38        78.18        11.61 
TCGA-56-8308 TCGA-56-A4BY TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 
       17.00        17.85         3.58        41.42         9.01        32.32 
TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
       66.61         8.02        42.08         9.50        14.07        21.04 
TCGA-94-7557 TCGA-94-A5I4 TCGA-96-7545 TCGA-98-8020 TCGA-98-A539 TCGA-J1-A4AH 
        0.16        16.14        57.07         2.76         5.69        19.10 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3411 
        0.07        76.80        39.85        65.65        16.80       117.57 
TCGA-18-3412 TCGA-18-3415 TCGA-18-3419 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 
       11.34        92.15        92.42       154.32       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 TCGA-21-5783 
       99.16        70.16        60.89       122.43       119.80        88.11 
TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 TCGA-22-1011 TCGA-22-1016 
       33.93        10.82        21.99         4.31         1.74        27.02 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 
       20.48        35.08        48.33        24.13         0.56        34.75 
TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 
       13.12        32.02        19.30        11.77        63.55        44.25 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
        0.79        71.34        79.20        11.74        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       56.32        16.64        97.94       151.27        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI 
       63.35         4.70         0.30        36.62         6.94        44.19 
TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5928 TCGA-34-5929 
        2.63        32.88        65.23        81.24        39.32         4.96 
TCGA-34-8454 TCGA-34-8455 TCGA-37-3792 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
       38.79         4.04         0.39         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-5819 TCGA-39-5016 TCGA-39-5022 TCGA-39-5028 TCGA-39-5029 
        6.81         3.39       126.58        55.20         1.71        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 
        1.94        60.53        71.18        40.21        38.66        39.12 
TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-8115 TCGA-43-8116 
       33.11        22.98        24.89        21.47        13.38        11.77 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 
       14.20        13.32        12.16         4.44        10.65         0.39 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 
       28.34         5.46         8.75        28.96        18.25        21.90 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-8082 
       18.48        31.27        19.76         6.51        17.49        14.96 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        3.48        26.89        14.07        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 
       20.25        15.81        20.94        18.74        14.47         0.03 
TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46M TCGA-60-2703 
       13.55        71.24        34.78        34.36        35.24        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2714 
       37.94        92.71        21.93        80.45        66.54        50.33 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 
       42.64         3.19        29.85        35.90        23.57        26.83 
TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB 
       11.77        52.67        70.13        70.42        68.15       102.67 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MR 
       70.62        58.65        59.97        45.57        11.34        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2734 
       78.28        16.37        53.88        34.59        16.96        43.10 
TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 
        1.02         2.01         0.92         0.99        21.01        25.05 
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-66-2778 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-66-2790 TCGA-66-2791 TCGA-66-2792 
       25.97        40.01        22.98        22.98         5.03        30.02 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 
        4.01        49.05         2.73         6.64         6.94        13.35 
TCGA-68-A59I TCGA-70-6723 TCGA-77-6842 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 
       16.18        12.33        29.56        75.09        23.28        11.18 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
      140.09         0.49        73.22       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
       32.55         6.51        55.73        37.81       156.66        12.59 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
       53.92        17.72       104.09        11.54        26.40        27.39 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 
       66.51        54.41        65.49        60.53        36.36       132.36 
TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 
      150.25        22.29         5.92        61.94        27.62         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 
       41.39        40.24        34.95        31.30        32.91         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 
       29.95        18.94        19.04        31.56        30.64        10.09 
TCGA-85-8287 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
        0.76        13.22        16.77         5.29         3.09        32.71 
TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4QQ 
       15.39        36.59        18.08        22.59        34.13        30.48 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A53L 
       19.73        27.16        16.21        15.85        15.29        12.39 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
        3.65         2.93        11.77        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 
        3.48         4.01         5.26         4.01         5.03        26.63 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       17.69        71.01        18.31        21.44        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J 
       21.34        27.16        18.15         2.01        18.58        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
       12.89        16.11        13.41         4.54        64.54        57.30 
TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
       13.74         4.21         2.89        43.92        25.32        14.73 
TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       26.43        83.57         3.65         3.72        12.72        43.89 
TCGA-XC-AA0X 
        0.20 

$`DEL PEAK 33(13Q12.11) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-5595 TCGA-22-1017 TCGA-33-4533 TCGA-34-2609 
       12.20         4.47        27.19        48.82       133.74        31.27 
TCGA-39-5039 TCGA-43-7657 TCGA-43-8118 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 
       17.88         7.76         2.93        12.03        19.99        13.05 
TCGA-56-8305 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2715 TCGA-77-7140 
        3.45        16.77        21.04         0.13        35.34        20.78 
TCGA-77-A5GB TCGA-94-7943 TCGA-96-A4JK TCGA-98-A53D TCGA-NC-A5HR TCGA-NK-A7XE 
       30.81        18.38        19.36        21.21        40.90         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 
        8.58        75.75        23.54        36.07        86.96         2.79 
TCGA-18-5592 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1083 
       49.94        34.78        15.58        31.73         9.34        43.23 
TCGA-21-5782 TCGA-21-5784 TCGA-22-0944 TCGA-22-1005 TCGA-22-1012 TCGA-22-4599 
       31.63        41.69         7.33        64.21        14.10        38.17 
TCGA-22-4609 TCGA-22-5474 TCGA-22-5479 TCGA-22-5483 TCGA-33-4547 TCGA-33-4566 
        9.57        14.63        86.30        18.84        79.53       173.82 
TCGA-33-4582 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-5234 
      103.53       110.99       118.36        27.16        61.61        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-7107 
        9.07        60.30        50.66        16.93        44.75         1.12 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 TCGA-37-4141 
       26.43        33.90         4.01         0.43         7.96         0.39 
TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 
       37.58        21.70       133.25       111.35        68.58        82.52 
TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-5670 
      102.18        36.39        68.38        55.56        17.06        27.91 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-A475 TCGA-46-3767 TCGA-46-3768 
        5.46         3.81        19.59         9.73        13.02         9.83 
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        12.43 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7731 TCGA-56-7823 TCGA-56-8083 TCGA-56-8503 
       14.53        30.41         0.10        33.24         4.93         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8387 
        1.81        22.75        19.23        13.32         0.26        13.25 
TCGA-58-8390 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 
       29.95        16.47        85.12        56.65        29.92        21.11 
TCGA-60-2697 TCGA-60-2698 TCGA-60-2709 TCGA-60-2713 TCGA-60-2716 TCGA-63-7023 
       12.23        10.22        49.48        56.91        48.49        55.30 
TCGA-63-A5MM TCGA-63-A5MP TCGA-63-A5MV TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       14.99        25.28        36.16         2.01        21.07         0.99 
TCGA-66-2757 TCGA-66-2763 TCGA-66-2765 TCGA-66-2770 TCGA-66-2781 TCGA-66-2789 
       43.99         0.99         2.01        23.01         3.98         4.04 
TCGA-66-2793 TCGA-66-2794 TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 TCGA-77-7335 
       10.06        54.08        14.73        12.07        73.12        70.13 
TCGA-77-8008 TCGA-77-8136 TCGA-77-8145 TCGA-77-A5FZ TCGA-77-A5GH TCGA-85-6798 
       86.76        39.09         6.97       126.18        38.86         6.41 
TCGA-85-7696 TCGA-85-7710 TCGA-85-8048 TCGA-85-8052 TCGA-85-8071 TCGA-85-8276 
       36.53         1.38        25.15        24.13        26.79        34.52 
TCGA-85-8350 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4CL 
       22.45         2.01         7.76        38.14        12.59        30.28 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 
       30.97        19.86        24.36        14.96        29.92        24.92 
TCGA-90-A4ED TCGA-92-8065 TCGA-94-A4VJ TCGA-96-8170 TCGA-96-A4JL TCGA-98-A53C 
       20.22         2.30        14.14        17.46        27.68        27.02 
TCGA-98-A53H TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HN TCGA-O2-A52N 
       20.32        13.18        11.84         1.22        49.28        33.07 
TCGA-O2-A5IB 
       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 
                         156.66                          173.82 
  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE 
                           21.9                            21.7 
[1] "0.0 - 156.7 (21.9)" "0.1 - 173.8 (21.7)"
[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       51      104        1        42
  DEL PEAK 33(13Q12.11) WILD-TYPE       2       38       48        1        23
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(13Q12.11) MUTATED          63         2         51         10
  DEL PEAK 33(13Q12.11) WILD-TYPE        32         1         12          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                              51                              38
  STAGE IB                             104                              48
  STAGE II                               1                               1
  STAGE IIA                             42                              23
  STAGE IIB                             63                              32
  STAGE III                              2                               1
  STAGE IIIA                            51                              12
  STAGE IIIB                            10                               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    65 204  48  14
  DEL PEAK 33(13Q12.11) WILD-TYPE  47  90  23  10
D63V4, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  T1                            65                              47
  T2                           204                              90
  T3                            48                              23
  T4                            14                              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 33(13Q12.11) MUTATED   206  89  29   4
  DEL PEAK 33(13Q12.11) WILD-TYPE 111  44  11   1
D63V5, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  N0                           206                             111
  N1                            89                              44
  N2                            29                              11
  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   274   4
  DEL PEAK 33(13Q12.11) WILD-TYPE 137   3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED    274    4
  DEL PEAK 33(13Q12.11) WILD-TYPE  137    3
   clus
vv  DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  0                           274                             137
  1                             4                               3
[1] 2 2
[1] FALSE
D63V7, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED    85 246
  DEL PEAK 33(13Q12.11) WILD-TYPE  45 125
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED     85  246
  DEL PEAK 33(13Q12.11) WILD-TYPE   45  125
        clus
vv       DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  FEMALE                            85                              45
  MALE                             246                             125
[1] 2 2
[1] FALSE
D63V8, binary
                                 cls
clus                                0   1
  DEL PEAK 33(13Q12.11) MUTATED   256  36
  DEL PEAK 33(13Q12.11) WILD-TYPE 128  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED    256   36
  DEL PEAK 33(13Q12.11) WILD-TYPE  128   17
     clus
vv    DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  NO                            256                             128
  YES                            36                              17
[1] 2 2
[1] FALSE
D63V9, 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 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                                                           320
  DEL PEAK 33(13Q12.11) WILD-TYPE                                                         159
D63V10, multiclass
                                                             clus
vv                                                            DEL PEAK 33(13Q12.11) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           320
                                                             clus
vv                                                            DEL PEAK 33(13Q12.11) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, continuous
D63V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 33(13Q12.11) MUTATED   266  10   3  17
  DEL PEAK 33(13Q12.11) WILD-TYPE 133   2   1   6
D63V13, multiclass
    clus
vv   DEL PEAK 33(13Q12.11) MUTATED DEL PEAK 33(13Q12.11) WILD-TYPE
  R0                           266                             133
  R1                            10                               2
  R2                             3                               1
  RX                            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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(13Q12.11) MUTATED       4                        21   221
  DEL PEAK 33(13Q12.11) WILD-TYPE     5                        10   128
D63V14, multiclass
                           clus
vv                          DEL PEAK 33(13Q12.11) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               221
                           clus
vv                          DEL PEAK 33(13Q12.11) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                              10
  WHITE                                                 128
[1] 3 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     7 193
  DEL PEAK 33(13Q12.11) WILD-TYPE   1 124
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 33(13Q12.11) MUTATED      7  193
  DEL PEAK 33(13Q12.11) WILD-TYPE    1  124
                        clus
vv                       DEL PEAK 33(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           193
                        clus
vv                       DEL PEAK 33(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             124
[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   198 141
  DEL PEAK 34(13Q14.2) WILD-TYPE  82  73
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           339                            155 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                           141                             73 
$`DEL PEAK 34(13Q14.2) MUTATED`
TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1000 
      123.19         4.80        31.99         6.18        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 
       48.82        60.66        64.93        22.06       133.74         1.55 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 
       31.50        28.96        31.27        22.49        18.38         7.76 
TCGA-43-7658 TCGA-43-A474 TCGA-56-8305 TCGA-56-8308 TCGA-56-A4BY TCGA-60-2696 
       78.18        11.61         3.45        17.00        17.85         3.58 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 
       41.42         9.01        32.32        66.61         8.02        20.78 
TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-A5I4 
       42.08         9.50        14.07        21.04         0.16        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HE 
       57.07        19.36         2.76         5.69         0.07        76.80 
TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
       39.85        65.65        16.80        92.42        86.96         2.79 
TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
      154.32       119.54        46.88        99.16        70.16        60.89 
TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5786 
      122.43       119.80        43.23        31.63        88.11        33.93 
TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 
       10.82        21.99         4.31         1.74        27.02        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 
       35.08        48.33        24.13         0.56        34.75        13.12 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 TCGA-22-5477 TCGA-22-5478 
       32.02        19.30        11.77        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-33-4538 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 
       16.64        97.94       103.53       151.27        14.07        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI 
       63.35         4.70         0.30        36.62         6.94        44.19 
TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5927 TCGA-34-5928 
        2.63        32.88        65.23        81.24        44.75        39.32 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
        4.96         1.12        38.79         4.04        26.43        33.90 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4135 TCGA-37-5819 TCGA-39-5011 
        0.39         7.96         7.46         6.81         3.39       133.25 
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        60.53        71.18 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 
       17.06        40.21        38.66        33.11        22.98        24.89 
TCGA-43-6770 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-46-3765 TCGA-46-3766 
       21.47        19.59        13.38        11.77        13.32        12.16 
TCGA-46-3767 TCGA-46-3769 TCGA-46-6025 TCGA-51-4079 TCGA-52-7622 TCGA-52-7809 
       13.02         4.44        10.65         0.39        28.34         5.46 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 
        8.75        27.45        28.96        18.25        21.90        18.48 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7823 TCGA-56-8082 TCGA-56-8304 
       31.27        19.76         6.51        33.24        14.96         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 
       26.89        14.07        13.81        10.36        20.25        15.81 
TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-8388 TCGA-58-8390 
       20.94        18.74        14.47         0.03        13.55        29.95 
TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-60-2703 
       71.24        34.78        85.12        34.36        35.24        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2710 TCGA-60-2713 
       37.94        92.71        21.93        80.45        66.54        56.91 
TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       50.33        42.64         3.19        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
       26.83        11.77        52.67        70.13        70.42        68.15 
TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN 
      102.67        70.62        58.65        59.97        45.57        11.34 
TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       25.28        89.29        78.28        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 
       43.10         1.02         2.01         0.92         0.99        43.99 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 
       21.01        25.05         0.99         2.01         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-66-2783 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-66-2790 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-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-70-6723 
        2.73         6.64         6.94        13.35        16.18        12.33 
TCGA-77-6842 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       29.56        75.09        11.18       140.09         0.49        73.22 
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        32.55         6.51 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 
       37.81       156.66        12.59        53.92        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        66.51        54.41        65.49 
TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       60.53        36.36       132.36       150.25        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 TCGA-85-7698 
       61.94        27.62         9.67        40.24        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 
       26.79        30.64        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        15.39        36.59        18.08 
TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       22.59        34.13        19.73        27.16        16.21        15.85 
TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4EE 
       15.29        12.39         3.65         2.93        11.77        22.62 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-8035 TCGA-94-8490 
        2.70         3.48         4.01         5.26         4.01         5.03 
TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-98-7454 TCGA-98-8021 
       26.63        17.69        71.01        18.31        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53I TCGA-98-A53J 
       30.67        21.34        27.16         2.01        18.58        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG 
       12.89        16.11        13.18        13.41         4.54        64.54 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP 
       57.30        13.74         4.21         2.89        43.92        25.32 
TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S 
       14.73        26.43        83.57         3.65         3.72        12.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         0.20 

$`DEL PEAK 34(13Q14.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-5595 TCGA-33-4532 TCGA-33-6737 TCGA-39-5039 
       12.20         4.47        27.19       129.01        19.76        17.88 
TCGA-43-8118 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8504 TCGA-56-A4ZJ 
        2.93        12.03        19.99        13.05        16.77        21.04 
TCGA-56-A5DR TCGA-60-2715 TCGA-77-A5GB TCGA-94-7943 TCGA-98-A53D TCGA-J1-A4AH 
        0.13        35.34        30.81        18.38        21.21        19.10 
TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 
       40.90         0.43         8.58        75.75       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-5592 TCGA-21-1077 TCGA-21-1078 
       23.54        92.15        36.07        49.94        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-33-4547 
       38.17         9.57        14.63        86.30        71.34        79.53 
TCGA-33-4566 TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-5234 
      173.82       110.99       118.36        27.16        61.61        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-37-3783 TCGA-37-3789 
        9.07        60.30        50.66        16.93         4.01         0.43 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 
        8.12         7.82         0.39        37.58        21.70       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5024 TCGA-39-5027 TCGA-39-5034 TCGA-39-5035 
      111.35        68.58        82.52       102.18        36.39        68.38 
TCGA-39-5037 TCGA-43-3394 TCGA-43-5670 TCGA-43-6771 TCGA-43-6773 TCGA-43-A475 
       55.56        39.12        27.91         5.46         3.81         9.73 
TCGA-43-A56U TCGA-46-3768 TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7810 
       14.20         9.83        13.91         0.39        29.95        30.35 
TCGA-56-5897 TCGA-56-7223 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8083 
       12.43        14.53        30.41         0.10        17.49         4.93 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8626 TCGA-56-A4BW TCGA-56-A4BX 
        1.35         1.81        22.75         9.93        19.23        13.32 
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-60-2716 TCGA-63-7023 TCGA-63-A5MM 
       12.23        10.22        49.48        48.49        55.30        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-70-6722 
        1.02        23.01         4.04        54.08        14.73        12.07 
TCGA-77-6843 TCGA-77-6845 TCGA-77-8008 TCGA-77-8009 TCGA-77-8136 TCGA-77-8145 
       73.12        23.28        86.76        55.73        39.09         6.97 
TCGA-77-A5FZ TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7710 
      126.18        38.86        41.39         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 
       38.14        12.59        30.28        30.97        19.86        24.36 
TCGA-85-A4QQ TCGA-85-A511 TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED TCGA-90-A59Q 
       30.48        14.96        29.92        24.92        20.22        10.59 
TCGA-92-8065 TCGA-94-A4VJ TCGA-96-8170 TCGA-96-A4JL TCGA-98-A53A TCGA-98-A53C 
        2.30        14.14        17.46        27.68        18.15        27.02 
TCGA-98-A53H TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HN TCGA-O2-A52N 
       20.32        11.84         1.22        49.28        33.07 

  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 
                        156.66                         173.82 
  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE 
                         22.06                          21.07 
[1] "0.0 - 156.7 (22.1)" "0.1 - 173.8 (21.1)"
[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       58      106        2        44
  DEL PEAK 34(13Q14.2) WILD-TYPE       2       31       46        0        21
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(13Q14.2) MUTATED          63         3         48         12
  DEL PEAK 34(13Q14.2) WILD-TYPE        32         0         15          7
                                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                             58                             31
  STAGE IB                            106                             46
  STAGE II                              2                              0
  STAGE IIA                            44                             21
  STAGE IIB                            63                             32
  STAGE III                             3                              0
  STAGE IIIA                           48                             15
  STAGE IIIB                           12                              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
  DEL PEAK 34(13Q14.2) MUTATED    74 207  48  15
  DEL PEAK 34(13Q14.2) WILD-TYPE  38  87  23   9
D64V4, multiclass
    clus
vv   DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  T1                           74                             38
  T2                          207                             87
  T3                           48                             23
  T4                           15                              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 34(13Q14.2) MUTATED   214  94  29   4
  DEL PEAK 34(13Q14.2) WILD-TYPE 103  39  11   1
D64V5, multiclass
    clus
vv   DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  N0                          214                            103
  N1                           94                             39
  N2                           29                             11
  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   287   4
  DEL PEAK 34(13Q14.2) WILD-TYPE 124   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED    287    4
  DEL PEAK 34(13Q14.2) WILD-TYPE  124    3
   clus
vv  DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  0                          287                            124
  1                            4                              3
[1] 2 2
[1] FALSE
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(13Q14.2) MUTATED    94 250
  DEL PEAK 34(13Q14.2) WILD-TYPE  36 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED     94  250
  DEL PEAK 34(13Q14.2) WILD-TYPE   36  121
        clus
vv       DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  FEMALE                           94                             36
  MALE                            250                            121
[1] 2 2
[1] FALSE
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(13Q14.2) MUTATED   263  39
  DEL PEAK 34(13Q14.2) WILD-TYPE 121  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED    263   39
  DEL PEAK 34(13Q14.2) WILD-TYPE  121   14
     clus
vv    DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  NO                           263                            121
  YES                           39                             14
[1] 2 2
[1] FALSE
D64V9, 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 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                                                           334
  DEL PEAK 34(13Q14.2) WILD-TYPE                                                         145
D64V10, multiclass
                                                             clus
vv                                                            DEL PEAK 34(13Q14.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          334
                                                             clus
vv                                                            DEL PEAK 34(13Q14.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, continuous
D64V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(13Q14.2) MUTATED   273  10   3  17
  DEL PEAK 34(13Q14.2) WILD-TYPE 126   2   1   6
D64V13, multiclass
    clus
vv   DEL PEAK 34(13Q14.2) MUTATED DEL PEAK 34(13Q14.2) WILD-TYPE
  R0                          273                            126
  R1                           10                              2
  R2                            3                              1
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(13Q14.2) MUTATED       4                        20   235
  DEL PEAK 34(13Q14.2) WILD-TYPE     5                        11   114
D64V14, multiclass
                           clus
vv                          DEL PEAK 34(13Q14.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           20
  WHITE                                              235
                           clus
vv                          DEL PEAK 34(13Q14.2) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                114
[1] 3 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     8 204
  DEL PEAK 34(13Q14.2) WILD-TYPE   0 113
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(13Q14.2) MUTATED      8  204
  DEL PEAK 34(13Q14.2) WILD-TYPE    0  113
                        clus
vv                       DEL PEAK 34(13Q14.2) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                          204
                        clus
vv                       DEL PEAK 34(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                            113
[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    92  81
  DEL PEAK 35(14Q11.2) WILD-TYPE 188 133
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                           173                            321 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                            81                            133 
$`DEL PEAK 35(14Q11.2) MUTATED`
TCGA-18-3416 TCGA-34-2604 TCGA-34-2605 TCGA-43-7657 TCGA-43-7658 TCGA-56-8305 
       31.99        31.50        28.96         7.76        78.18         3.45 
TCGA-56-A4BY TCGA-60-2696 TCGA-60-2712 TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GA 
       17.85         3.58         9.01        66.61         8.02        42.08 
TCGA-90-7766 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 
        9.50        21.04         0.16        18.38        16.14        57.07 
TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NK-A5CT TCGA-18-4086 TCGA-21-1071 
       19.10         0.07        76.80        65.65         2.79        46.88 
TCGA-21-1083 TCGA-21-5784 TCGA-21-5786 TCGA-22-0940 TCGA-22-1012 TCGA-22-1016 
       43.23        41.69        33.93        21.99        14.10        27.02 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4596 TCGA-22-4601 TCGA-22-5473 TCGA-22-5474 
       35.08        48.33         0.56        34.75        63.55        14.63 
TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5491 TCGA-33-4538 
       44.25        71.34        79.20        18.84        56.32        97.94 
TCGA-33-4547 TCGA-33-4583 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 
       79.53       151.27        54.44         4.70         0.30        36.62 
TCGA-33-AASD TCGA-33-AASL TCGA-34-2596 TCGA-34-2600 TCGA-34-5241 TCGA-34-5927 
      110.99        27.16         2.63        61.61        16.93        44.75 
TCGA-34-5928 TCGA-34-5929 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 TCGA-37-4130 
       39.32         4.96        38.79        33.90         4.01         8.12 
TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5016 TCGA-39-5024 
        7.82         6.81         3.39        21.70       126.58        82.52 
TCGA-39-5030 TCGA-39-5035 TCGA-39-5040 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
        1.94        68.38        17.06        39.12        33.11        27.91 
TCGA-43-6770 TCGA-43-7656 TCGA-43-A475 TCGA-43-A56U TCGA-46-3768 TCGA-46-6026 
       21.47        19.59         9.73        14.20         9.83        13.91 
TCGA-51-4079 TCGA-52-7809 TCGA-56-5897 TCGA-56-7582 TCGA-56-7822 TCGA-56-8082 
        0.39         5.46        12.43        19.76        17.49        14.96 
TCGA-56-8307 TCGA-56-8309 TCGA-56-A4BW TCGA-58-8388 TCGA-58-8390 TCGA-58-A46K 
       26.89        14.07        19.23        13.55        29.95        34.36 
TCGA-60-2695 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       21.11        37.94        49.48        66.54        56.91        50.33 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MP 
       26.83        11.77        52.67        55.30       102.67        25.28 
TCGA-63-A5MT TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 
       16.37        16.96         1.02         2.01         0.92        43.99 
TCGA-66-2758 TCGA-66-2766 TCGA-66-2769 TCGA-66-2773 TCGA-66-2777 TCGA-66-2786 
       21.01         1.02         7.07         3.02         2.01        25.97 
TCGA-66-2787 TCGA-66-2789 TCGA-66-2793 TCGA-68-7757 TCGA-68-8251 TCGA-70-6722 
       40.01         4.04        10.06         6.94        13.35        12.07 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 TCGA-77-7141 TCGA-77-7338 
       29.56        73.12        75.09       140.09         0.49         0.16 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8140 TCGA-77-8143 TCGA-77-8156 
       32.55         6.51        86.76        11.54        26.40        36.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 
       22.29         5.92        27.62        38.86        41.39         6.41 
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-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8352 
       31.56        30.64        10.09         0.76        13.22         5.29 
TCGA-85-8580 TCGA-85-A4JC TCGA-85-A511 TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 
       36.59        19.86        14.96        12.39         2.93        11.77 
TCGA-90-A4ED TCGA-90-A59Q TCGA-94-8491 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       20.22        10.59        26.63        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53J TCGA-LA-A446 TCGA-NC-A5HJ 
       30.67        21.34        18.15        20.71        13.18        13.74 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NK-A5CR TCGA-O2-A52Q TCGA-XC-AA0X 
        4.21         2.89        83.57         3.72         0.20 

$`DEL PEAK 35(14Q11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19         4.80         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 
       32.19        14.93        48.82        60.66        64.93        22.06 
TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2609 TCGA-39-5039 
      129.01       133.74         1.55        19.76        31.27        17.88 
TCGA-43-2578 TCGA-43-5668 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 
       22.49        18.38         2.93        11.61        12.03        19.99 
TCGA-56-8201 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2711 
       13.05        17.00        16.77        21.04         0.13        41.42 
TCGA-60-2715 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GB TCGA-90-7964 TCGA-96-A4JK 
       35.34        32.32        20.78        30.81        14.07        19.36 
TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5D1 
        2.76         5.69        21.21        39.85        40.90        16.80 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
        0.43         8.58        75.75       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 
       92.15        36.07        92.42        86.96       154.32        49.94 
TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
      119.54        99.16        70.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 
       31.73       122.43         9.34       119.80        31.63        88.11 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-4591 
       10.82         7.33         4.31        64.21         1.74        20.48 
TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       24.13        38.17        13.12        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
       11.77         0.79        86.30        11.74        30.12        62.86 
TCGA-22-5492 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 TCGA-33-AASB 
       16.64       173.82       103.53        14.07        63.35         6.94 
TCGA-33-AASI TCGA-33-AASJ TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       44.19       118.36        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 
        9.07        60.30        50.66         1.12         4.04        26.43 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-37-4141 TCGA-37-A5EL 
        0.43         0.39         7.96         7.46         0.39        37.58 
TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 TCGA-39-5028 
      133.25       111.35        68.58        55.20       102.18         1.71 
TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 
       24.33        60.53        36.39        71.18        55.56        40.21 
TCGA-43-2581 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 
       38.66        22.98        24.89         5.46         3.81        13.38 
TCGA-43-8116 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-46-6025 
       11.77        13.32        12.16        13.02         4.44        10.65 
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-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       28.96        18.25        21.90        18.48        14.53        31.27 
TCGA-56-7580 TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 
       30.41         6.51         0.10        33.24         4.93         3.48 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
        1.35         1.81        22.75        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
       20.25        15.81        20.94        13.32        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 
       14.47         0.03        13.25        71.24        16.47        34.78 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 
       85.12        56.65        35.24        29.92        12.23        10.22 
TCGA-60-2703 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2716 TCGA-60-2719 
       96.82        92.71        21.93        80.45        48.49        42.64 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-63-7020 TCGA-63-7021 
        3.19        29.85        35.90        23.57        70.13        70.42 
TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM 
       68.15        70.62        58.65        59.97        45.57        14.99 
TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       11.34        89.29        78.28        36.16        53.88        34.59 
TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 TCGA-66-2759 
       43.10         2.01        21.07         0.99         0.99        25.05 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 
        0.99         2.01         2.01         2.01        23.01        19.00 
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-66-2788 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
       22.98        22.98         5.03        30.02        54.08         4.01 
TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I TCGA-68-A59J TCGA-70-6723 
       49.05         2.73         6.64        16.18        14.73        12.33 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 
       23.28        11.18        73.22        70.13       106.95        46.78 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       55.73        37.81       156.66        12.59        53.92        39.09 
TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       17.72       104.09        27.39         6.97        66.51        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G8 
       65.49        60.53       126.18       132.36       150.25        61.94 
TCGA-85-6175 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
        9.67        40.24        36.53        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-8071 TCGA-85-8276 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
        1.38        26.79        34.52        22.45        16.77         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 
       32.71         2.01        15.39         7.76        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA 
       18.08        22.59        30.28        34.13        30.97        24.36 
TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 
       30.48        19.73        27.16        16.21        15.85        15.29 
TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-A4EE TCGA-92-7340 TCGA-92-7341 
       29.92         3.65        24.92        22.62         2.70         3.48 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ 
        4.01         5.26         2.30         4.01         5.03        14.14 
TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-98-A538 TCGA-98-A53B 
       17.69        71.01        18.31        17.46        27.16         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW 
       27.02        20.32        18.58        12.89        16.11        13.41 
TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HN 
       11.84         4.54        64.54         1.22        57.30        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CX TCGA-O2-A52N 
       43.92        25.32        14.73        26.43         3.65        33.07 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       12.72        43.89        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                         173.82 
  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE 
                         21.01                          22.62 
[1] "0.1 - 151.3 (21.0)" "0.0 - 173.8 (22.6)"
[1] "hr=" "1.3"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(14Q11.2) MUTATED         0       36       55        0        28
  DEL PEAK 35(14Q11.2) WILD-TYPE       2       53       97        2        37
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(14Q11.2) MUTATED          27         1         22          5
  DEL PEAK 35(14Q11.2) WILD-TYPE        68         2         41         14
                                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                             36                             53
  STAGE IB                             55                             97
  STAGE II                              0                              2
  STAGE IIA                            28                             37
  STAGE IIB                            27                             68
  STAGE III                             1                              2
  STAGE IIIA                           22                             41
  STAGE IIIB                            5                             14
  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    46 103  20   6
  DEL PEAK 35(14Q11.2) WILD-TYPE  66 191  51  18
D65V4, multiclass
    clus
vv   DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  T1                           46                             66
  T2                          103                            191
  T3                           20                             51
  T4                            6                             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   112  48  13   1
  DEL PEAK 35(14Q11.2) WILD-TYPE 205  85  27   4
D65V5, multiclass
    clus
vv   DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  N0                          112                            205
  N1                           48                             85
  N2                           13                             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   144   0
  DEL PEAK 35(14Q11.2) WILD-TYPE 267   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED    144    0
  DEL PEAK 35(14Q11.2) WILD-TYPE  267    7
   clus
vv  DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  0                          144                            267
  1                            0                              7
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q11.2) MUTATED    44 131
  DEL PEAK 35(14Q11.2) WILD-TYPE  86 240
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED     44  131
  DEL PEAK 35(14Q11.2) WILD-TYPE   86  240
        clus
vv       DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  FEMALE                           44                             86
  MALE                            131                            240
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 35(14Q11.2) MUTATED   132  15
  DEL PEAK 35(14Q11.2) WILD-TYPE 252  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED    132   15
  DEL PEAK 35(14Q11.2) WILD-TYPE  252   38
     clus
vv    DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  NO                           132                            252
  YES                           15                             38
[1] 2 2
[1] FALSE
D65V9, 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 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                                                           169
  DEL PEAK 35(14Q11.2) WILD-TYPE                                                         310
D65V10, multiclass
                                                             clus
vv                                                            DEL PEAK 35(14Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          169
                                                             clus
vv                                                            DEL PEAK 35(14Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            310
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, continuous
D65V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(14Q11.2) MUTATED   142   3   1   7
  DEL PEAK 35(14Q11.2) WILD-TYPE 257   9   3  16
D65V13, multiclass
    clus
vv   DEL PEAK 35(14Q11.2) MUTATED DEL PEAK 35(14Q11.2) WILD-TYPE
  R0                          142                            257
  R1                            3                              9
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(14Q11.2) MUTATED       4                        13   122
  DEL PEAK 35(14Q11.2) WILD-TYPE     5                        18   227
D65V14, multiclass
                           clus
vv                          DEL PEAK 35(14Q11.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              122
                           clus
vv                          DEL PEAK 35(14Q11.2) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             18
  WHITE                                                227
[1] 3 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     2 113
  DEL PEAK 35(14Q11.2) WILD-TYPE   6 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(14Q11.2) MUTATED      2  113
  DEL PEAK 35(14Q11.2) WILD-TYPE    6  204
                        clus
vv                       DEL PEAK 35(14Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          113
                        clus
vv                       DEL PEAK 35(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            204
[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    84  82
  DEL PEAK 36(15Q11.2) WILD-TYPE 196 132
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                           166                            328 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                            82                            132 
$`DEL PEAK 36(15Q11.2) MUTATED`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3416 TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 
       12.20         4.80        31.99        14.93        48.82        60.66 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 
       22.06       129.01       133.74         1.55        19.76        31.50 
TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-A56V TCGA-56-8305 TCGA-60-2712 
       22.49        18.38         7.76        12.03         3.45         9.01 
TCGA-63-A5MH TCGA-NC-A5HD TCGA-NC-A5HM TCGA-O2-A52W TCGA-18-3408 TCGA-18-3412 
       66.61         0.07        39.85         8.58        75.75        11.34 
TCGA-18-3415 TCGA-18-3419 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 
       92.15        92.42        49.94       119.54        46.88        99.16 
TCGA-21-1083 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1012 TCGA-22-1016 
       43.23        10.82        21.99         7.33        14.10        27.02 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-5477 TCGA-22-5480 
       48.33        24.13         0.56        38.17        44.25        71.34 
TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-AAS8 TCGA-33-AASI 
       79.53       103.53        14.07        54.44        36.62        44.19 
TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 
      118.36        27.16        61.61         4.96        38.79        26.43 
TCGA-37-3783 TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 
        4.01         7.82         0.39         3.39        21.70       133.25 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
      126.58        68.58         1.71        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5040 TCGA-43-2581 TCGA-43-5670 TCGA-46-3769 TCGA-46-6026 
       36.39        17.06        38.66        27.91         4.44        13.91 
TCGA-51-4079 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 TCGA-56-7580 TCGA-56-7822 
        0.39         5.46        30.35        28.96        30.41        17.49 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BW 
        3.48        26.89        14.07        10.36        20.94        19.23 
TCGA-56-A62T TCGA-58-8386 TCGA-58-A46J TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 
       14.47         0.03        85.12        10.22        96.82        80.45 
TCGA-60-2714 TCGA-60-2720 TCGA-60-2723 TCGA-60-2726 TCGA-63-7022 TCGA-63-A5MB 
       50.33         3.19        35.90        11.77        68.15       102.67 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MS TCGA-63-A5MY TCGA-66-2737 
       58.65        59.97        45.57        78.28        34.59         2.01 
TCGA-66-2742 TCGA-66-2754 TCGA-66-2766 TCGA-66-2767 TCGA-66-2790 TCGA-66-2791 
       21.07         2.01         1.02         2.01        22.98         5.03 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
       10.06        54.08        49.05        16.18        14.73        12.07 
TCGA-77-6842 TCGA-77-7139 TCGA-77-7141 TCGA-77-7337 TCGA-77-8007 TCGA-77-8009 
       29.56       140.09         0.49       106.95         6.51        55.73 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8145 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5GH 
       37.81       156.66         6.97        65.49        36.36        38.86 
TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7843 TCGA-85-8072 TCGA-85-8287 
        9.67        41.39        36.53         1.15        30.64         0.76 
TCGA-85-8288 TCGA-85-8352 TCGA-85-8479 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4QQ 
       13.22         5.29        15.39        12.59        22.59        30.48 
TCGA-85-A50M TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-7767 TCGA-90-A4ED 
       27.16        14.96        29.92        12.39         2.93        20.22 
TCGA-90-A4EE TCGA-92-7340 TCGA-92-8064 TCGA-92-8065 TCGA-94-8491 TCGA-MF-A522 
       22.62         2.70         5.26         2.30        26.63        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
        4.54        64.54        57.30        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX 
       49.28        43.92        25.32        14.73        83.57         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB 
       33.07         3.72        12.72        11.18 

$`DEL PEAK 36(15Q11.2) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-5472 
        4.47       123.19         6.18        27.19        32.19        64.93 
TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 
       28.96        31.27        17.88        78.18         2.93        11.61 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ 
       19.99        13.05        17.00        16.77        17.85        21.04 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 
        0.13         3.58        41.42        35.34        32.32         8.02 
TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
       20.78        42.08        30.81         9.50        14.07        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
        0.16        18.38        16.14        57.07        19.36         2.76 
TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5CT 
        5.69        21.21        19.10        76.80        40.90        65.65 
TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3411 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 
       16.80         0.43       117.57        23.54        36.07        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 
        2.79       154.32        70.16        60.89        34.78        15.58 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 
       31.73       122.43         9.34       119.80        31.63        88.11 
TCGA-21-5784 TCGA-21-5786 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-4591 
       41.69        33.93         4.31        64.21         1.74        20.48 
TCGA-22-4593 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 
       35.08        34.75        13.12        32.02        19.30         9.57 
TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 
       11.77        63.55        14.63         0.79        86.30        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-33-4538 TCGA-33-4566 TCGA-33-4583 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW 
       97.94       173.82       151.27        63.35         4.70         0.30 
TCGA-33-AASB TCGA-33-AASD TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
        6.94       110.99         2.63        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 
       74.66         9.07        60.30        50.66        16.93        44.75 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3789 TCGA-37-3792 
       39.32         1.12         4.04        33.90         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-A5EL TCGA-39-5019 
        7.96         8.12         7.46         6.81        37.58       111.35 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
       55.20        82.52       102.18        68.38        71.18        55.56 
TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 
       40.21        39.12        33.11        22.98        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
        5.46         3.81        19.59        13.38        11.77         9.73 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 
       14.20        13.32        12.16        13.02         9.83        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        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
       18.25        21.90        18.48        14.53        31.27        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8503 
        6.51         0.10        33.24        14.96         4.93         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
        1.81        22.75        13.81         9.93        20.25        15.81 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 
       13.32        18.74         0.26        13.25        13.55        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       71.24        16.47        34.78        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       29.92        21.11        12.23        37.94        92.71        21.93 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2719 TCGA-60-2722 
       49.48        66.54        56.91        48.49        42.64        29.85 
TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 
       23.57        26.83        52.67        70.13        70.42        55.30 
TCGA-63-A5MG TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MT 
       70.62        14.99        11.34        25.28        89.29        16.37 
TCGA-63-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 
       36.16        53.88        16.96        43.10         0.99         1.02 
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-66-2768 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-66-2783 
        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-66-2789 TCGA-66-2792 
        1.97        25.97        40.01        22.98         4.04        30.02 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-70-6723 
        4.01         2.73         6.64         6.94        13.35        12.33 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 
       73.12        75.09        23.28        11.18        73.22        70.13 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 TCGA-77-8131 TCGA-77-8133 
        0.16        46.78        32.55        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 
       66.51        54.41        60.53       126.18       132.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 
       22.29         5.92        61.94        27.62        40.24         6.41 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
       34.95        31.30        32.91         1.38        29.95        18.94 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
       25.15        19.04        24.13        31.56        26.79        34.52 
TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       10.09        22.45        16.77         3.09        32.71         2.01 
TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4CN 
        7.76        36.59        38.14        18.08        30.28        34.13 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 
       30.97        19.86        24.36        19.73        16.21        15.85 
TCGA-85-A512 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A59Q TCGA-92-7341 
       15.29         3.65        24.92        11.77        10.59         3.48 
TCGA-92-8063 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 
        4.01         4.01         5.03        14.14        17.69        71.01 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 
       18.31        17.46        27.68        21.44        30.81        30.67 
TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       21.34        27.16        18.15         2.01        27.02        20.32 
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-A5HH TCGA-NC-A5HT TCGA-O2-A52V TCGA-XC-AA0X 
        1.22        26.43        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 
                        156.66                         173.82 
  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE 
                        22.605                         21.160 
[1] "0.0 - 156.7 (22.6)" "0.1 - 173.8 (21.2)"
[1] "hr=" "1.1"
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       65      110        2        44
                                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        61         0         35         11
                                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                             65
  STAGE IB                             42                            110
  STAGE II                              0                              2
  STAGE IIA                            21                             44
  STAGE IIB                            34                             61
  STAGE III                             3                              0
  STAGE IIIA                           28                             35
  STAGE IIIB                            8                             11
  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    30 102  25  10
  DEL PEAK 36(15Q11.2) WILD-TYPE  82 192  46  14
D66V4, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  T1                           30                             82
  T2                          102                            192
  T3                           25                             46
  T4                           10                             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    91  51  21   2
  DEL PEAK 36(15Q11.2) WILD-TYPE 226  82  19   3
D66V5, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  N0                           91                            226
  N1                           51                             82
  N2                           21                             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   135   3
  DEL PEAK 36(15Q11.2) WILD-TYPE 276   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED    135    3
  DEL PEAK 36(15Q11.2) WILD-TYPE  276    4
   clus
vv  DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  0                          135                            276
  1                            3                              4
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED    50 117
  DEL PEAK 36(15Q11.2) WILD-TYPE  80 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED     50  117
  DEL PEAK 36(15Q11.2) WILD-TYPE   80  254
        clus
vv       DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  FEMALE                           50                             80
  MALE                            117                            254
[1] 2 2
[1] FALSE
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED   122  20
  DEL PEAK 36(15Q11.2) WILD-TYPE 262  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED    122   20
  DEL PEAK 36(15Q11.2) WILD-TYPE  262   33
     clus
vv    DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  NO                           122                            262
  YES                           20                             33
[1] 2 2
[1] FALSE
D66V9, 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 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                                                           161
  DEL PEAK 36(15Q11.2) WILD-TYPE                                                         318
D66V10, multiclass
                                                             clus
vv                                                            DEL PEAK 36(15Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          161
                                                             clus
vv                                                            DEL PEAK 36(15Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            318
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, continuous
D66V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(15Q11.2) MUTATED   131   5   2   6
  DEL PEAK 36(15Q11.2) WILD-TYPE 268   7   2  17
D66V13, multiclass
    clus
vv   DEL PEAK 36(15Q11.2) MUTATED DEL PEAK 36(15Q11.2) WILD-TYPE
  R0                          131                            268
  R1                            5                              7
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(15Q11.2) MUTATED       5                        13   113
  DEL PEAK 36(15Q11.2) WILD-TYPE     4                        18   236
D66V14, multiclass
                           clus
vv                          DEL PEAK 36(15Q11.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              113
                           clus
vv                          DEL PEAK 36(15Q11.2) WILD-TYPE
  ASIAN                                                  4
  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"
D66V15, binary
                                cls
clus                               0   1
  DEL PEAK 36(15Q11.2) MUTATED     2 101
  DEL PEAK 36(15Q11.2) WILD-TYPE   6 216
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(15Q11.2) MUTATED      2  101
  DEL PEAK 36(15Q11.2) WILD-TYPE    6  216
                        clus
vv                       DEL PEAK 36(15Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          101
                        clus
vv                       DEL PEAK 36(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            216
[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    88  80
  DEL PEAK 37(15Q21.1) WILD-TYPE 192 134
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                           168                            326 
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                            80                            134 
$`DEL PEAK 37(15Q21.1) MUTATED`
TCGA-18-3406 TCGA-18-3416 TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-33-4533 
       12.20        31.99        14.93        48.82        60.66       133.74 
TCGA-33-4589 TCGA-34-2604 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-A56V 
        1.55        31.50        22.49        18.38         7.76        12.03 
TCGA-56-8305 TCGA-60-2712 TCGA-63-A5MH TCGA-68-8250 TCGA-96-A4JK TCGA-NC-A5HD 
        3.45         9.01        66.61         8.02        19.36         0.07 
TCGA-NC-A5HM TCGA-O2-A52W TCGA-18-3408 TCGA-18-3412 TCGA-18-3419 TCGA-18-5592 
       39.85         8.58        75.75        11.34        92.42        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-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4594 TCGA-22-4595 
        7.33        14.10        27.02        20.48        48.33        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-5477 TCGA-22-5480 TCGA-33-4582 TCGA-33-4586 
        0.56        38.17        44.25        71.34       103.53        14.07 
TCGA-33-4587 TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ 
       54.44        36.62         6.94       110.99        44.19       118.36 
TCGA-33-AASL TCGA-34-2600 TCGA-34-5929 TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 
       27.16        61.61         4.96        38.79        26.43         4.01 
TCGA-37-4133 TCGA-37-4141 TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 
        7.82         0.39         3.39       133.25       126.58        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        60.53        36.39        17.06 
TCGA-43-2581 TCGA-43-5670 TCGA-43-8116 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
       38.66        27.91        11.77         9.83         4.44        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-52-7810 TCGA-52-7812 TCGA-56-7580 TCGA-56-7822 
       13.91         0.39        30.35        27.45        30.41        17.49 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8625 TCGA-56-8629 TCGA-56-A49D 
        3.48        26.89        14.07        10.36        15.81        20.94 
TCGA-56-A4BW TCGA-56-A62T TCGA-58-8386 TCGA-60-2698 TCGA-60-2703 TCGA-60-2708 
       19.23        14.47         0.03        10.22        96.82        80.45 
TCGA-60-2714 TCGA-60-2720 TCGA-60-2723 TCGA-60-2726 TCGA-63-7022 TCGA-63-A5MB 
       50.33         3.19        35.90        11.77        68.15       102.67 
TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MS TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2737 
       59.97        45.57        78.28        53.88        34.59         2.01 
TCGA-66-2742 TCGA-66-2754 TCGA-66-2756 TCGA-66-2766 TCGA-66-2767 TCGA-66-2790 
       21.07         2.01         0.99         1.02         2.01        22.98 
TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 TCGA-68-A59I TCGA-68-A59J 
        5.03        10.06        54.08        49.05        16.18        14.73 
TCGA-70-6722 TCGA-77-6842 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7337 
       12.07        29.56        23.28       140.09         0.49       106.95 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8145 TCGA-77-8153 
        6.51        55.73        37.81       156.66         6.97        65.49 
TCGA-77-8156 TCGA-77-A5G6 TCGA-77-A5GH TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 
       36.36        22.29        38.86         9.67        41.39        36.53 
TCGA-85-7843 TCGA-85-8072 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8479 
        1.15        30.64        34.52         0.76        13.22        15.39 
TCGA-85-8584 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A511 
       12.59        22.59        30.28        30.48        27.16        14.96 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-8064 
       12.39         3.65         2.93        20.22        22.62         5.26 
TCGA-92-8065 TCGA-94-8491 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI 
        2.30        26.63        11.84         4.54        64.54        57.30 
TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
        4.21         2.89        49.28        43.92        25.32        14.73 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A5IB 
       83.57         3.65        33.07         3.72        12.72        11.18 

$`DEL PEAK 37(15Q21.1) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI 
        4.47       123.19         4.80         6.18        27.19        32.19 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 
       64.93        22.06       129.01        19.76        28.96        31.27 
TCGA-39-5039 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 
       17.88        78.18         2.93        11.61        19.99        13.05 
TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       17.00        16.77        17.85        21.04         0.13         3.58 
TCGA-60-2711 TCGA-60-2715 TCGA-60-2721 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       41.42        35.34        32.32        20.78        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
        9.50        14.07        21.04         0.16        18.38        16.14 
TCGA-96-7545 TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE 
       57.07         2.76         5.69        21.21        19.10        76.80 
TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3411 TCGA-18-3414 
       40.90        65.65        16.80         0.43       117.57        23.54 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1075 
       92.15        36.07        86.96         2.79       154.32        70.16 
TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 
       60.89        34.78        15.58        31.73         9.34       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-1002 
       43.23        31.63        88.11        41.69        21.99         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-4593 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       64.21         1.74        35.08        34.75        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 
       19.30         9.57        11.77        63.55        14.63         0.79 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 
       86.30        79.20        11.74        18.84        30.12        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 
       56.32        16.64        97.94        79.53       173.82       151.27 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 
       63.35         4.70         0.30         2.63        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       81.24        74.66         9.07        60.30        50.66        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3789 
       44.75        39.32         1.12         4.04        33.90         0.43 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-A5EL 
        0.39         7.96         8.12         7.46         6.81        37.58 
TCGA-37-A5EN TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5035 
       21.70       111.35        55.20        82.52       102.18        68.38 
TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 
       71.18        55.56        40.21        39.12        33.11        22.98 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       24.89        21.47         5.46         3.81        19.59        13.38 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-51-4080 
        9.73        14.20        13.32        12.16        13.02         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 
       29.95        28.34         5.46         8.75        28.96        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7582 
       18.25        21.90        18.48        14.53        31.27        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8503 
        6.51         0.10        33.24        14.96         4.93         1.35 
TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BX 
        1.81        22.75        13.81         9.93        20.25        13.32 
TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
       18.74         0.26        13.25        13.55        29.95        71.24 
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-60-2697 TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 
       29.92        21.11        12.23        37.94        92.71        21.93 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2719 TCGA-60-2722 
       49.48        66.54        56.91        48.49        42.64        29.85 
TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 
       23.57        26.83        52.67        70.13        70.42        55.30 
TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       70.62        58.65        14.99        11.34        25.28        89.29 
TCGA-63-A5MT TCGA-63-A5MV TCGA-66-2727 TCGA-66-2734 TCGA-66-2744 TCGA-66-2753 
       16.37        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-70-6723 TCGA-77-6843 
        2.73         6.64         6.94        13.35        12.33        73.12 
TCGA-77-6844 TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 
       75.09        11.18        73.22        70.13         0.16        46.78 
TCGA-77-7465 TCGA-77-8008 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 
       32.55        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        66.51        54.41 
TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 
       60.53       126.18       132.36       150.25         5.92        61.94 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       27.62        40.24         6.41        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-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       31.56        26.79        10.09        22.45        16.77         5.29 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 
        3.09        32.71         2.01         7.76        36.59        38.14 
TCGA-85-8664 TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QR 
       18.08        34.13        30.97        19.86        24.36        19.73 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-7769 
       16.21        15.85        15.29        29.92        24.92        11.77 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-94-8035 TCGA-94-8490 
       10.59         2.70         3.48         4.01         4.01         5.03 
TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
       14.14        17.69        71.01        18.31        17.46        27.68 
TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53A 
       21.44        30.81        30.67        21.34        27.16        18.15 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
        2.01        27.02        20.32        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HT 
       16.11        13.18        13.41         1.22        13.74        26.43 
TCGA-O2-A52V TCGA-XC-AA0X 
       43.89         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 
                        156.66                         173.82 
  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE 
                        22.540                         21.455 
[1] "0.0 - 156.7 (22.5)" "0.1 - 173.8 (21.5)"
[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        21
  DEL PEAK 37(15Q21.1) WILD-TYPE       0       62      111        2        44
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(15Q21.1) MUTATED          33         3         28          8
  DEL PEAK 37(15Q21.1) WILD-TYPE        62         0         35         11
                                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                             62
  STAGE IB                             41                            111
  STAGE II                              0                              2
  STAGE IIA                            21                             44
  STAGE IIB                            33                             62
  STAGE III                             3                              0
  STAGE IIIA                           28                             35
  STAGE IIIB                            8                             11
  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    33 101  25  10
  DEL PEAK 37(15Q21.1) WILD-TYPE  79 193  46  14
D67V4, multiclass
    clus
vv   DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  T1                           33                             79
  T2                          101                            193
  T3                           25                             46
  T4                           10                             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 37(15Q21.1) MUTATED    94  51  21   2
  DEL PEAK 37(15Q21.1) WILD-TYPE 223  82  19   3
D67V5, multiclass
    clus
vv   DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  N0                           94                            223
  N1                           51                             82
  N2                           21                             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"
D67V6, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q21.1) MUTATED   134   3
  DEL PEAK 37(15Q21.1) WILD-TYPE 277   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q21.1) MUTATED    134    3
  DEL PEAK 37(15Q21.1) WILD-TYPE  277    4
   clus
vv  DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  0                          134                            277
  1                            3                              4
[1] 2 2
[1] FALSE
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q21.1) MUTATED    48 121
  DEL PEAK 37(15Q21.1) WILD-TYPE  82 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q21.1) MUTATED     48  121
  DEL PEAK 37(15Q21.1) WILD-TYPE   82  250
        clus
vv       DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  FEMALE                           48                             82
  MALE                            121                            250
[1] 2 2
[1] FALSE
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q21.1) MUTATED   122  22
  DEL PEAK 37(15Q21.1) WILD-TYPE 262  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q21.1) MUTATED    122   22
  DEL PEAK 37(15Q21.1) WILD-TYPE  262   31
     clus
vv    DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  NO                           122                            262
  YES                           22                             31
[1] 2 2
[1] FALSE
D67V9, 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 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                                                           164
  DEL PEAK 37(15Q21.1) WILD-TYPE                                                         315
D67V10, multiclass
                                                             clus
vv                                                            DEL PEAK 37(15Q21.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          164
                                                             clus
vv                                                            DEL PEAK 37(15Q21.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            315
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, continuous
D67V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(15Q21.1) MUTATED   134   4   2   6
  DEL PEAK 37(15Q21.1) WILD-TYPE 265   8   2  17
D67V13, multiclass
    clus
vv   DEL PEAK 37(15Q21.1) MUTATED DEL PEAK 37(15Q21.1) WILD-TYPE
  R0                          134                            265
  R1                            4                              8
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(15Q21.1) MUTATED       4                        16   113
  DEL PEAK 37(15Q21.1) WILD-TYPE     5                        15   236
D67V14, multiclass
                           clus
vv                          DEL PEAK 37(15Q21.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              113
                           clus
vv                          DEL PEAK 37(15Q21.1) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             15
  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"
D67V15, binary
                                cls
clus                               0   1
  DEL PEAK 37(15Q21.1) MUTATED     3 102
  DEL PEAK 37(15Q21.1) WILD-TYPE   5 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(15Q21.1) MUTATED      3  102
  DEL PEAK 37(15Q21.1) WILD-TYPE    5  215
                        clus
vv                       DEL PEAK 37(15Q21.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          102
                        clus
vv                       DEL PEAK 37(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            215
[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  75
  DEL PEAK 38(16P13.3) WILD-TYPE 171 139
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                           184                            310 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                            75                            139 
$`DEL PEAK 38(16P13.3) MUTATED`
TCGA-18-3410 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-6737 TCGA-34-2609 TCGA-43-7657 
        4.80        22.06       133.74        19.76        31.27         7.76 
TCGA-43-8118 TCGA-56-8201 TCGA-56-8305 TCGA-56-A4BY TCGA-63-A5MH TCGA-94-7557 
        2.93        13.05         3.45        17.85        66.61         0.16 
TCGA-96-A4JK TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NK-A5CT TCGA-O2-A52W 
       19.36         5.69        19.10         0.07        65.65         8.58 
TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 TCGA-18-5592 TCGA-21-1070 
       92.15        36.07        86.96       154.32        49.94       119.54 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1080 TCGA-21-1082 TCGA-21-5786 
       70.16        60.89        34.78       122.43       119.80        33.93 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 
       21.99         4.31        14.10        48.33        24.13        38.17 
TCGA-22-4604 TCGA-22-4613 TCGA-22-5478 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 
       13.12        11.77         0.79        71.34        11.74        30.12 
TCGA-33-4582 TCGA-33-4587 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL 
      103.53        54.44         6.94        44.19       118.36        27.16 
TCGA-34-2596 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
        2.63         9.07        60.30        16.93        44.75        39.32 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-5819 TCGA-39-5011 TCGA-39-5016 TCGA-39-5021 
        4.04        33.90         3.39       133.25       126.58        68.58 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5040 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 
      102.18         1.71        17.06        39.12        27.91        22.98 
TCGA-43-7656 TCGA-43-8116 TCGA-43-A56U TCGA-46-3765 TCGA-51-4080 TCGA-52-7622 
       19.59        11.77        14.20        13.32         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        21.90        31.27 
TCGA-56-7580 TCGA-56-7822 TCGA-56-8082 TCGA-56-8307 TCGA-56-8503 TCGA-56-8629 
       30.41        17.49        14.96        26.89         1.35        15.81 
TCGA-56-A49D TCGA-56-A4BX TCGA-58-8386 TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J 
       20.94        13.32         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-63-6202 TCGA-63-7023 
       35.90        23.57        26.83        11.77        52.67        55.30 
TCGA-63-A5MB TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
      102.67        45.57        25.28        53.88        34.59        16.96 
TCGA-66-2734 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2757 TCGA-66-2758 
       43.10         1.02         2.01         0.92        43.99        21.01 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2773 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 
        0.99         1.02         3.02         3.98        12.00        25.97 
TCGA-66-2787 TCGA-66-2792 TCGA-66-2800 TCGA-68-7756 TCGA-68-8251 TCGA-68-A59J 
       40.01        30.02        49.05         6.64        13.35        14.73 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7139 TCGA-77-7142 TCGA-77-8130 
       12.33        29.56        23.28       140.09        73.22       156.66 
TCGA-77-8136 TCGA-77-8140 TCGA-77-8143 TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 
       39.09        11.54        26.40        65.49        60.53        36.36 
TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6798 TCGA-85-7698 TCGA-85-7699 
        5.92        27.62        38.86         6.41        31.30        32.91 
TCGA-85-7843 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8277 TCGA-85-8351 
        1.15        18.94        24.13        31.56        10.09        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8664 
        5.29         3.09         2.01        15.39        36.59        18.08 
TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A53L TCGA-85-A5B5 
       30.28        34.13        19.86        19.73        12.39         3.65 
TCGA-90-7767 TCGA-90-A4EE TCGA-92-7340 TCGA-92-8064 TCGA-94-8035 TCGA-96-7544 
        2.93        22.62         2.70         5.26         4.01        71.01 
TCGA-96-8169 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 
       18.31        21.34        18.15        18.58        12.89        16.11 
TCGA-LA-A7SW TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HO 
       13.41        64.54        13.74         4.21        49.28        43.92 
TCGA-NC-A5HT TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A5IB 
       26.43        33.07        12.72        11.18 

$`DEL PEAK 38(16P13.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19        31.99         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-33-4532 
       32.19        14.93        48.82        60.66        64.93       129.01 
TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 
        1.55        31.50        28.96        17.88        22.49        18.38 
TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8308 TCGA-56-8504 
       78.18        11.61        12.03        19.99        17.00        16.77 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       21.04         0.13         3.58        41.42         9.01        35.34 
TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 
       32.32         8.02        20.78        42.08        30.81         9.50 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-98-8020 
       14.07        21.04        18.38        16.14        57.07         2.76 
TCGA-98-A53D TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE 
       21.21        76.80        39.85        40.90        16.80         0.43 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3419 TCGA-18-4086 
       75.75       117.57        11.34        23.54        92.42         2.79 
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-22-0944 TCGA-22-1005 
       31.63        88.11        41.69        10.82         7.33        64.21 
TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 TCGA-22-4601 
        1.74        27.02        20.48        35.08         0.56        34.75 
TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       32.02        19.30         9.57        63.55        14.63        44.25 
TCGA-22-5479 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
       86.30        79.20        18.84        62.86        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 
       97.94        79.53       173.82       151.27        14.07        63.35 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-34-2600 TCGA-34-2608 
        4.70         0.30        36.62       110.99        61.61        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 TCGA-34-5929 TCGA-34-7107 
       65.23        81.24        74.66        50.66         4.96         1.12 
TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       38.79        26.43         4.01         0.43         0.39         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL 
        8.12         7.46         7.82         6.81         0.39        37.58 
TCGA-37-A5EN TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 
       21.70       111.35        55.20        82.52        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 
       60.53        36.39        68.38        71.18        55.56        40.21 
TCGA-43-2581 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       38.66        33.11        24.89        21.47         5.46         3.81 
TCGA-43-8115 TCGA-43-A475 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
       13.38         9.73        12.16        13.02         9.83         4.44 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7811 TCGA-56-5897 
       10.65        13.91         0.39        29.95         8.75        12.43 
TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       18.25        18.48        14.53        19.76         6.51         0.10 
TCGA-56-7823 TCGA-56-8083 TCGA-56-8304 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 
       33.24         4.93         3.48        14.07         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4ZK 
       13.81        10.36         9.93        20.25        19.23        18.74 
TCGA-56-A5DS TCGA-56-A62T TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
        0.26        14.47        13.25        13.55        29.95        71.24 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       35.24        29.92        12.23        10.22        96.82        37.94 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       92.71        21.93        49.48        66.54        56.91        50.33 
TCGA-60-2716 TCGA-60-2722 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MG 
       48.49        29.85        70.13        70.42        68.15        70.62 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS 
       58.65        59.97        14.99        11.34        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MV TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2756 
       16.37        36.16         2.01        21.07         0.99         0.99 
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-66-2783 TCGA-66-2785 
       19.00         2.01        19.00        12.03        24.95         1.97 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 
       22.98         4.04        22.98         5.03        10.06        54.08 
TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-A59I TCGA-70-6722 TCGA-77-6843 
        4.01         2.73         6.94        16.18        12.07        73.12 
TCGA-77-6844 TCGA-77-7138 TCGA-77-7141 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 
       75.09        11.18         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        32.55         6.51        86.76        55.73        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 
       66.51        54.41       126.18       132.36       150.25        22.29 
TCGA-77-A5G8 TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 
       61.94         9.67        41.39        40.24        36.53        34.95 
TCGA-85-7710 TCGA-85-7844 TCGA-85-8048 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 
        1.38        29.95        25.15        19.04        26.79        30.64 
TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8354 TCGA-85-8481 
       34.52         0.76        13.22        22.45        32.71         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ 
       38.14        12.59        22.59        30.97        24.36        30.48 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
       27.16        16.21        15.85        14.96        15.29        29.92 
TCGA-90-6837 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 
       24.92        11.77        20.22        10.59         3.48         4.01 
TCGA-92-8065 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8170 
        2.30         5.03        26.63        14.14        17.69        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53B 
       27.68        21.44        30.81        30.67        27.16         2.01 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HF 
       27.02        20.32        20.71        13.18        11.84         4.54 
TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR 
        1.22        57.30         2.89        25.32        14.73        83.57 
TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
        3.65         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 
                        156.66                         173.82 
  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE 
                        22.340                         21.325 
[1] "0.0 - 156.7 (22.3)" "0.1 - 173.8 (21.3)"
[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       59       94        2        42
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(16P13.3) MUTATED          38         2         27          2
  DEL PEAK 38(16P13.3) WILD-TYPE        57         1         36         17
                                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                             59
  STAGE IB                             58                             94
  STAGE II                              0                              2
  STAGE IIA                            23                             42
  STAGE IIB                            38                             57
  STAGE III                             2                              1
  STAGE IIIA                           27                             36
  STAGE IIIB                            2                             17
  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    33 113  33   8
  DEL PEAK 38(16P13.3) WILD-TYPE  79 181  38  16
D68V4, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  T1                           33                             79
  T2                          113                            181
  T3                           33                             38
  T4                            8                             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 38(16P13.3) MUTATED   123  49  14   0
  DEL PEAK 38(16P13.3) WILD-TYPE 194  84  26   5
D68V5, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  N0                          123                            194
  N1                           49                             84
  N2                           14                             26
  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   153   3
  DEL PEAK 38(16P13.3) WILD-TYPE 258   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED    153    3
  DEL PEAK 38(16P13.3) WILD-TYPE  258    4
   clus
vv  DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  0                          153                            258
  1                            3                              4
[1] 2 2
[1] FALSE
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED    51 136
  DEL PEAK 38(16P13.3) WILD-TYPE  79 235
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED     51  136
  DEL PEAK 38(16P13.3) WILD-TYPE   79  235
        clus
vv       DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  FEMALE                           51                             79
  MALE                            136                            235
[1] 2 2
[1] FALSE
D68V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED   146  21
  DEL PEAK 38(16P13.3) WILD-TYPE 238  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED    146   21
  DEL PEAK 38(16P13.3) WILD-TYPE  238   32
     clus
vv    DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  NO                           146                            238
  YES                           21                             32
[1] 2 2
[1] FALSE
D68V9, 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 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                                                           176
  DEL PEAK 38(16P13.3) WILD-TYPE                                                         303
D68V10, multiclass
                                                             clus
vv                                                            DEL PEAK 38(16P13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          176
                                                             clus
vv                                                            DEL PEAK 38(16P13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            303
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, continuous
D68V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(16P13.3) MUTATED   154   1   0   7
  DEL PEAK 38(16P13.3) WILD-TYPE 245  11   4  16
D68V13, multiclass
    clus
vv   DEL PEAK 38(16P13.3) MUTATED DEL PEAK 38(16P13.3) WILD-TYPE
  R0                          154                            245
  R1                            1                             11
  R2                            0                              4
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(16P13.3) MUTATED       2                        15   127
  DEL PEAK 38(16P13.3) WILD-TYPE     7                        16   222
D68V14, multiclass
                           clus
vv                          DEL PEAK 38(16P13.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           15
  WHITE                                              127
                           clus
vv                          DEL PEAK 38(16P13.3) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             16
  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"
D68V15, binary
                                cls
clus                               0   1
  DEL PEAK 38(16P13.3) MUTATED     3 119
  DEL PEAK 38(16P13.3) WILD-TYPE   5 198
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(16P13.3) MUTATED      3  119
  DEL PEAK 38(16P13.3) WILD-TYPE    5  198
                        clus
vv                       DEL PEAK 38(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          119
                        clus
vv                       DEL PEAK 38(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            198
[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  82
  DEL PEAK 39(16Q23.1) WILD-TYPE 156 132
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                           206                            288 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                            82                            132 
$`DEL PEAK 39(16Q23.1) MUTATED`
TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-33-4533 TCGA-33-6737 TCGA-34-2604 
        4.80        31.99         6.18       133.74        19.76        31.50 
TCGA-34-2609 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-56-7221 
       31.27        22.49        18.38         7.76        78.18        19.99 
TCGA-56-8201 TCGA-56-8308 TCGA-56-A4BY TCGA-60-2711 TCGA-63-A5MH TCGA-90-7766 
       13.05        17.00        17.85        41.42        66.61         9.50 
TCGA-94-7557 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HR 
        0.16        16.14        19.36         5.69        19.10        40.90 
TCGA-NK-A5CT TCGA-O2-A52W TCGA-18-3415 TCGA-18-3419 TCGA-18-5592 TCGA-21-1070 
       65.65         8.58        92.15        92.42        49.94       119.54 
TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 
       60.89       122.43        43.23        10.82        21.99         7.33 
TCGA-22-1002 TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4599 TCGA-22-4604 
        4.31        14.10        48.33        24.13        38.17        13.12 
TCGA-22-5473 TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5489 TCGA-33-4547 
       63.55         0.79        71.34        79.20        62.86        79.53 
TCGA-33-4583 TCGA-33-4586 TCGA-33-AASI TCGA-33-AASJ TCGA-33-AASL TCGA-34-2596 
      151.27        14.07        44.19       118.36        27.16         2.63 
TCGA-34-5231 TCGA-34-5236 TCGA-34-5239 TCGA-34-5927 TCGA-34-5929 TCGA-34-8455 
       65.23         9.07        60.30        44.75         4.96         4.04 
TCGA-34-A5IX TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 
       33.90        37.58        21.70       133.25       126.58       111.35 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5040 TCGA-43-3394 
       82.52       102.18         1.71         1.94        17.06        39.12 
TCGA-43-3920 TCGA-43-5670 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 
       33.11        27.91        11.77         9.73        14.20        13.32 
TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7622 
        4.44        10.65        13.91         0.39        29.95        28.34 
TCGA-52-7809 TCGA-52-7810 TCGA-56-7222 TCGA-56-7579 TCGA-56-7580 TCGA-56-7730 
        5.46        30.35        18.48        31.27        30.41         6.51 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 
       17.49        33.24        14.96        26.89        14.07         1.35 
TCGA-56-8626 TCGA-56-A49D TCGA-56-A4BX TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
        9.93        20.94        13.32         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-60-2713 TCGA-60-2714 TCGA-60-2719 
       35.24        21.11        66.54        56.91        50.33        42.64 
TCGA-60-2720 TCGA-60-2723 TCGA-60-2725 TCGA-63-6202 TCGA-63-7023 TCGA-63-A5MB 
        3.19        35.90        26.83        52.67        55.30       102.67 
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       140.09         0.49        73.22 
TCGA-77-7463 TCGA-77-7465 TCGA-77-8136 TCGA-77-8139 TCGA-77-8143 TCGA-77-8150 
       46.78        32.55        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        36.36        38.86        40.24         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        26.79         5.29 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN 
        3.09         2.01        36.59        18.08        22.59        34.13 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z TCGA-85-A512 
       30.97        19.86        19.73        27.16        16.21        15.29 
TCGA-85-A5B5 TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-8064 TCGA-92-8065 
        3.65         2.93        20.22        22.62         5.26         2.30 
TCGA-94-8035 TCGA-94-A4VJ TCGA-96-8169 TCGA-96-A4JL TCGA-98-A538 TCGA-98-A53A 
        4.01        14.14        18.31        27.68        27.16        18.15 
TCGA-98-A53I TCGA-LA-A7SW TCGA-NC-A5HG TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL 
       18.58        13.41        64.54        13.74         4.21         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N 
       49.28        43.92        14.73        26.43        83.57        33.07 
TCGA-O2-A5IB TCGA-XC-AA0X 
       11.18         0.20 

$`DEL PEAK 39(16Q23.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 
       12.20         4.47       123.19        27.19        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 
       48.82        60.66        64.93        22.06       129.01         1.55 
TCGA-34-2605 TCGA-39-5039 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-8305 
       28.96        17.88         2.93        11.61        12.03         3.45 
TCGA-56-8504 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2712 TCGA-60-2715 
       16.77        21.04         0.13         3.58         9.01        35.34 
TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 
       32.32         8.02        20.78        42.08        30.81        14.07 
TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 TCGA-98-8020 TCGA-98-A53D TCGA-NC-A5HD 
       21.04        18.38        57.07         2.76        21.21         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3411 
       76.80        39.85        16.80         0.43        75.75       117.57 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       11.34        23.54        36.07        86.96         2.79       154.32 
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-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4596 
       64.21         1.74        27.02        20.48        35.08         0.56 
TCGA-22-4601 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5474 
       34.75        32.02        19.30         9.57        11.77        14.63 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 
       44.25        86.30        11.74        18.84        30.12        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4566 TCGA-33-4582 TCGA-33-4587 TCGA-33-6738 
       16.64        97.94       173.82       103.53        54.44        63.35 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-34-2600 
        4.70         0.30        36.62         6.94       110.99        61.61 
TCGA-34-2608 TCGA-34-5232 TCGA-34-5234 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 
       32.88        81.24        74.66        50.66        16.93        39.32 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
        1.12        38.79        26.43         4.01         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        7.96         8.12         7.46         7.82         6.81         0.39 
TCGA-37-5819 TCGA-39-5021 TCGA-39-5022 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 
        3.39        68.58        55.20        24.33        60.53        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-2581 TCGA-43-6143 
       68.38        71.18        55.56        40.21        38.66        22.98 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 
       24.89        21.47         5.46         3.81        19.59        13.38 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-51-4080 TCGA-52-7811 TCGA-52-7812 
       12.16        13.02         9.83         0.39         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 TCGA-56-7582 
       28.96        12.43        18.25        21.90        14.53        19.76 
TCGA-56-7731 TCGA-56-8083 TCGA-56-8304 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 
        0.10         4.93         3.48         1.81        22.75        13.81 
TCGA-56-8625 TCGA-56-8628 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4ZK TCGA-56-A5DS 
       10.36        20.25        15.81        19.23        18.74         0.26 
TCGA-56-A62T TCGA-58-A46K TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       14.47        34.36        29.92        12.23        10.22        96.82 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2716 
       37.94        92.71        21.93        80.45        49.48        48.49 
TCGA-60-2722 TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 
       29.85        23.57        11.77        70.13        70.42        68.15 
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-A5MW TCGA-66-2737 TCGA-66-2742 
       78.28        16.37        36.16        53.88         2.01        21.07 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2756 TCGA-66-2758 TCGA-66-2765 TCGA-66-2766 
        0.99         2.01         0.99        21.01         2.01         1.02 
TCGA-66-2771 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 
       19.00         3.02         2.01        12.03         3.98        24.95 
TCGA-66-2785 TCGA-66-2788 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 
        1.97        22.98         5.03        54.08         4.01         2.73 
TCGA-68-7757 TCGA-68-A59I TCGA-70-6722 TCGA-70-6723 TCGA-77-6843 TCGA-77-6844 
        6.94        16.18        12.07        12.33        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 
       23.28        11.18        70.13       106.95         0.16         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
       86.76        55.73        37.81       156.66        12.59        53.92 
TCGA-77-8138 TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 
       17.72        11.54        27.39         6.97        66.51        60.53 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
      126.18       132.36       150.25        22.29         5.92        61.94 
TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-7696 TCGA-85-7710 TCGA-85-7843 
       27.62         9.67        41.39        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        30.64        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 
       15.39         7.76        38.14        12.59        30.28        24.36 
TCGA-85-A4QQ TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
       30.48        15.85        14.96        29.92        12.39        24.92 
TCGA-90-7769 TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-94-8490 
       11.77        10.59         2.70         3.48         4.01         5.03 
TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 
       26.63        17.69        71.01        17.46        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J 
       30.67        21.34         2.01        27.02        20.32        20.71 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HH 
       12.89        16.11        13.18        11.84         4.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HP TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V 
       57.30        25.32         3.65         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                         173.82 
  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE 
                         23.57                          21.04 
[1] "0.0 - 151.3 (23.6)" "0.1 - 173.8 (21.0)"
[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       31       60        0        29
  DEL PEAK 39(16Q23.1) WILD-TYPE       0       58       92        2        36
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(16Q23.1) MUTATED          45         1         30          7
  DEL PEAK 39(16Q23.1) WILD-TYPE        50         2         33         12
                                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                             31                             58
  STAGE IB                             60                             92
  STAGE II                              0                              2
  STAGE IIA                            29                             36
  STAGE IIB                            45                             50
  STAGE III                             1                              2
  STAGE IIIA                           30                             33
  STAGE IIIB                            7                             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
  DEL PEAK 39(16Q23.1) MUTATED    40 123  37  10
  DEL PEAK 39(16Q23.1) WILD-TYPE  72 171  34  14
D69V4, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  T1                           40                             72
  T2                          123                            171
  T3                           37                             34
  T4                           10                             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   134  54  17   3
  DEL PEAK 39(16Q23.1) WILD-TYPE 183  79  23   2
D69V5, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  N0                          134                            183
  N1                           54                             79
  N2                           17                             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   176   2
  DEL PEAK 39(16Q23.1) WILD-TYPE 235   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED    176    2
  DEL PEAK 39(16Q23.1) WILD-TYPE  235    5
   clus
vv  DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  0                          176                            235
  1                            2                              5
[1] 2 2
[1] FALSE
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED    62 148
  DEL PEAK 39(16Q23.1) WILD-TYPE  68 223
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED     62  148
  DEL PEAK 39(16Q23.1) WILD-TYPE   68  223
        clus
vv       DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  FEMALE                           62                             68
  MALE                            148                            223
[1] 2 2
[1] FALSE
D69V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(16Q23.1) MUTATED   160  28
  DEL PEAK 39(16Q23.1) WILD-TYPE 224  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED    160   28
  DEL PEAK 39(16Q23.1) WILD-TYPE  224   25
     clus
vv    DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  NO                           160                            224
  YES                           28                             25
[1] 2 2
[1] FALSE
D69V9, 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 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                                                           203
  DEL PEAK 39(16Q23.1) WILD-TYPE                                                         276
D69V10, multiclass
                                                             clus
vv                                                            DEL PEAK 39(16Q23.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          203
                                                             clus
vv                                                            DEL PEAK 39(16Q23.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   6
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            276
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, continuous
D69V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(16Q23.1) MUTATED   163   5   2   8
  DEL PEAK 39(16Q23.1) WILD-TYPE 236   7   2  15
D69V13, multiclass
    clus
vv   DEL PEAK 39(16Q23.1) MUTATED DEL PEAK 39(16Q23.1) WILD-TYPE
  R0                          163                            236
  R1                            5                              7
  R2                            2                              2
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(16Q23.1) MUTATED       3                        16   145
  DEL PEAK 39(16Q23.1) WILD-TYPE     6                        15   204
D69V14, multiclass
                           clus
vv                          DEL PEAK 39(16Q23.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           16
  WHITE                                              145
                           clus
vv                          DEL PEAK 39(16Q23.1) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             15
  WHITE                                                204
[1] 3 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     2 136
  DEL PEAK 39(16Q23.1) WILD-TYPE   6 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(16Q23.1) MUTATED      2  136
  DEL PEAK 39(16Q23.1) WILD-TYPE    6  181
                        clus
vv                       DEL PEAK 39(16Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          136
                        clus
vv                       DEL PEAK 39(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            181
[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   153 117
  DEL PEAK 40(17P11.2) WILD-TYPE 127  97
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           270                            224 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                           117                             97 
$`DEL PEAK 40(17P11.2) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3410 TCGA-18-3416 TCGA-21-A5DI TCGA-22-5472 
       12.20         4.47         4.80        31.99        32.19        64.93 
TCGA-22-A5C4 TCGA-33-4532 TCGA-34-2604 TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V 
       22.06       129.01        31.50        78.18        11.61        12.03 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2712 TCGA-60-2721 TCGA-63-A5MH 
       17.85        21.04         3.58         9.01        32.32        66.61 
TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       30.81        14.07        21.04        16.14        57.07        19.36 
TCGA-98-A539 TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3412 
        5.69        39.85        40.90        65.65        16.80        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 
       23.54        92.15        92.42        86.96         2.79       154.32 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1077 TCGA-21-1082 TCGA-21-1083 
      119.54        46.88        70.16        34.78       119.80        43.23 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5787 TCGA-22-0944 TCGA-22-1011 TCGA-22-1012 
       31.63        88.11        10.82         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-22-5477 TCGA-22-5480 
       32.02        19.30         9.57        11.77        44.25        71.34 
TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4547 
       79.20        18.84        62.86        56.32        16.64        79.53 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-A4WN TCGA-33-A5GW 
      103.53       151.27        14.07        54.44         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASD TCGA-33-AASJ TCGA-33-AASL TCGA-34-2600 
       36.62         6.94       110.99       118.36        27.16        61.61 
TCGA-34-2608 TCGA-34-5240 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX 
       32.88        50.66        38.79         4.04        26.43        33.90 
TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        4.01         0.43         7.82         6.81         0.39         3.39 
TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5029 TCGA-39-5034 TCGA-39-5035 
       37.58        21.70       126.58        24.33        36.39        68.38 
TCGA-39-5040 TCGA-43-2576 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-8115 
       17.06        40.21        27.91        22.98        19.59        13.38 
TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-6025 TCGA-46-6026 
       11.77         9.73        14.20        13.32        10.65        13.91 
TCGA-51-4080 TCGA-52-7622 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 
        0.39        28.34        27.45        28.96        12.43        18.25 
TCGA-56-7223 TCGA-56-7580 TCGA-56-7582 TCGA-56-7822 TCGA-56-8083 TCGA-56-8304 
       14.53        30.41        19.76        17.49         4.93         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       26.89        14.07         1.35        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       20.25        15.81        20.94        14.47         0.03        13.25 
TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46L TCGA-58-A46M 
       13.55        29.95        71.24        34.78        56.65        35.24 
TCGA-60-2695 TCGA-60-2703 TCGA-60-2706 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
       21.11        96.82        92.71        56.91        50.33        42.64 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
        3.19        29.85        35.90        26.83        11.77        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       70.13        70.42        55.30       102.67        70.62        58.65 
TCGA-63-A5MJ TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       59.97        16.37        36.16        53.88        34.59        16.96 
TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 
       21.07         1.02         2.01        43.99        21.01        25.05 
TCGA-66-2763 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2771 
        0.99         1.02         2.01         2.01         7.07        19.00 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
        3.02         2.01        12.03         3.98        12.00        24.95 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2793 
        1.97        25.97        22.98         4.04         5.03        10.06 
TCGA-66-2795 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 
        4.01         6.94        13.35        14.73        12.07        29.56 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7337 
       75.09        23.28       140.09         0.49        73.22       106.95 
TCGA-77-7338 TCGA-77-7465 TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 
        0.16        32.55        86.76        55.73        37.81       156.66 
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-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G3 
        6.97        66.51        54.41        60.53       132.36       150.25 
TCGA-77-A5G6 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7697 TCGA-85-7843 TCGA-85-7844 
       22.29        38.86        41.39        34.95         1.15        29.95 
TCGA-85-8070 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8479 TCGA-85-8584 
       31.56        34.52         0.76        13.22        15.39        12.59 
TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 
       30.28        30.97        19.86        30.48        16.21        15.85 
TCGA-85-A512 TCGA-85-A513 TCGA-85-A53L TCGA-90-7767 TCGA-90-A4ED TCGA-92-7341 
       15.29        29.92        12.39         2.93        20.22         3.48 
TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 
        4.01         2.30         4.01        26.63        14.14        17.69 
TCGA-96-7544 TCGA-96-8170 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A 
       71.01        17.46        30.81        30.67        27.16        18.15 
TCGA-98-A53B TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-NC-A5HF TCGA-NC-A5HG 
        2.01        18.58        12.89        16.11         4.54        64.54 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ 
       57.30         4.21         2.89        43.92        25.32        14.73 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
       83.57         3.65        33.07         3.72        43.89         0.20 

$`DEL PEAK 40(17P11.2) WILD-TYPE`
TCGA-18-3409 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 
      123.19         6.18        27.19        14.93        48.82        60.66 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 
      133.74         1.55        19.76        28.96        31.27        17.88 
TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-8118 TCGA-56-7221 TCGA-56-8201 
       22.49        18.38         7.76         2.93        19.99        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A5DR TCGA-60-2711 TCGA-60-2715 
        3.45        17.00        16.77         0.13        41.42        35.34 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 TCGA-94-7557 TCGA-94-7943 
        8.02        20.78        42.08         9.50         0.16        18.38 
TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NK-A7XE 
        2.76        21.21        19.10         0.07        76.80         0.43 
TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3417 TCGA-18-5592 TCGA-21-1072 
        8.58        75.75       117.57        36.07        49.94        99.16 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-5784 
       60.89        15.58        31.73       122.43         9.34        41.69 
TCGA-21-5786 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-4593 TCGA-22-4594 
       33.93        21.99         4.31        64.21        35.08        48.33 
TCGA-22-4601 TCGA-22-5473 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 
       34.75        63.55        14.63         0.79        86.30        11.74 
TCGA-22-5485 TCGA-33-4538 TCGA-33-4566 TCGA-33-6738 TCGA-33-AASI TCGA-34-2596 
       30.12        97.94       173.82        63.35        44.19         2.63 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5241 
       65.23        81.24        74.66         9.07        60.30        16.93 
TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-37-3792 TCGA-37-4129 
       44.75        39.32         4.96         1.12         0.39         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        8.12         7.46       133.25       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-39-5036 
       82.52       102.18         1.71         1.94        60.53        71.18 
TCGA-39-5037 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6647 TCGA-43-6770 
       55.56        38.66        39.12        33.11        24.89        21.47 
TCGA-43-6771 TCGA-43-6773 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 
        5.46         3.81        12.16        13.02         9.83         4.44 
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        21.90 
TCGA-56-7222 TCGA-56-7579 TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 
       18.48        31.27         6.51         0.10        33.24        14.96 
TCGA-56-8622 TCGA-56-8623 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
        1.81        22.75        19.23        13.32        18.74         0.26 
TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 
       16.47        85.12        34.36        29.92        12.23        10.22 
TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2716 
       37.94        21.93        80.45        49.48        66.54        48.49 
TCGA-60-2724 TCGA-63-7022 TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       23.57        68.15        45.57        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 TCGA-66-2755 
       89.29        78.28        43.10         2.01         0.99         0.92 
TCGA-66-2756 TCGA-66-2765 TCGA-66-2770 TCGA-66-2778 TCGA-66-2787 TCGA-66-2790 
        0.99         2.01        23.01        19.00        40.01        22.98 
TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-A59I 
       30.02        54.08        49.05         2.73         6.64        16.18 
TCGA-70-6723 TCGA-77-6843 TCGA-77-7138 TCGA-77-7335 TCGA-77-7463 TCGA-77-8007 
       12.33        73.12        11.18        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        36.36       126.18         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
       61.94        27.62         9.67        40.24         6.41        36.53 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
       31.30        32.91         1.38        18.94        25.15        19.04 
TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 
       24.13        26.79        30.64        10.09        22.45        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 
        5.29         3.09        32.71         2.01         7.76        36.59 
TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A4QR 
       38.14        18.08        22.59        34.13        24.36        19.73 
TCGA-85-A50M TCGA-85-A511 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7769 TCGA-90-A4EE 
       27.16        14.96         3.65        24.92        11.77        22.62 
TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 TCGA-94-8490 TCGA-96-8169 TCGA-96-A4JL 
       10.59         2.70         5.26         5.03        18.31        27.68 
TCGA-98-7454 TCGA-98-8023 TCGA-98-A53C TCGA-98-A53H TCGA-98-A53J TCGA-LA-A446 
       21.44        21.34        27.02        20.32        20.71        13.18 
TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HN TCGA-NC-A5HT 
       13.41        11.84         1.22        13.74        49.28        26.43 
TCGA-O2-A52S TCGA-O2-A5IB 
       12.72        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 
                        156.66                         173.82 
  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE 
                        21.405                         21.915 
[1] "0.0 - 156.7 (21.4)" "0.1 - 173.8 (21.9)"
[1] "hr=" "1"  
D70V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(17P11.2) MUTATED         1       50       79        1        38
  DEL PEAK 40(17P11.2) WILD-TYPE       1       39       73        1        27
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(17P11.2) MUTATED          51         1         34         11
  DEL PEAK 40(17P11.2) WILD-TYPE        44         2         29          8
                                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                             39
  STAGE IB                             79                             73
  STAGE II                              1                              1
  STAGE IIA                            38                             27
  STAGE IIB                            51                             44
  STAGE III                             1                              2
  STAGE IIIA                           34                             29
  STAGE IIIB                           11                              8
  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    63 161  38  10
  DEL PEAK 40(17P11.2) WILD-TYPE  49 133  33  14
D70V4, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  T1                           63                             49
  T2                          161                            133
  T3                           38                             33
  T4                           10                             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   170  69  25   4
  DEL PEAK 40(17P11.2) WILD-TYPE 147  64  15   1
D70V5, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  N0                          170                            147
  N1                           69                             64
  N2                           25                             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   221   5
  DEL PEAK 40(17P11.2) WILD-TYPE 190   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED    221    5
  DEL PEAK 40(17P11.2) WILD-TYPE  190    2
   clus
vv  DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  0                          221                            190
  1                            5                              2
[1] 2 2
[1] FALSE
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED    65 207
  DEL PEAK 40(17P11.2) WILD-TYPE  65 164
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED     65  207
  DEL PEAK 40(17P11.2) WILD-TYPE   65  164
        clus
vv       DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  FEMALE                           65                             65
  MALE                            207                            164
[1] 2 2
[1] FALSE
D70V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(17P11.2) MUTATED   202  26
  DEL PEAK 40(17P11.2) WILD-TYPE 182  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED    202   26
  DEL PEAK 40(17P11.2) WILD-TYPE  182   27
     clus
vv    DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  NO                           202                            182
  YES                           26                             27
[1] 2 2
[1] FALSE
D70V9, 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 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                                                           259
  DEL PEAK 40(17P11.2) WILD-TYPE                                                         220
D70V10, multiclass
                                                             clus
vv                                                            DEL PEAK 40(17P11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          259
                                                             clus
vv                                                            DEL PEAK 40(17P11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            220
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, continuous
D70V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(17P11.2) MUTATED   226   6   2  10
  DEL PEAK 40(17P11.2) WILD-TYPE 173   6   2  13
D70V13, multiclass
    clus
vv   DEL PEAK 40(17P11.2) MUTATED DEL PEAK 40(17P11.2) WILD-TYPE
  R0                          226                            173
  R1                            6                              6
  R2                            2                              2
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(17P11.2) MUTATED       5                        15   183
  DEL PEAK 40(17P11.2) WILD-TYPE     4                        16   166
D70V14, multiclass
                           clus
vv                          DEL PEAK 40(17P11.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           15
  WHITE                                              183
                           clus
vv                          DEL PEAK 40(17P11.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             16
  WHITE                                                166
[1] 3 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     4 163
  DEL PEAK 40(17P11.2) WILD-TYPE   4 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(17P11.2) MUTATED      4  163
  DEL PEAK 40(17P11.2) WILD-TYPE    4  154
                        clus
vv                       DEL PEAK 40(17P11.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          163
                        clus
vv                       DEL PEAK 40(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            154
[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  49
  DEL PEAK 41(17Q11.2) WILD-TYPE 198 165
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                           131                            363 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                            49                            165 
$`DEL PEAK 41(17Q11.2) MUTATED`
TCGA-18-3410 TCGA-18-3416 TCGA-21-A5DI TCGA-22-5472 TCGA-34-2604 TCGA-43-2578 
        4.80        31.99        32.19        64.93        31.50        22.49 
TCGA-43-A56V TCGA-56-8305 TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2721 TCGA-63-A5MH 
       12.03         3.45        21.04         3.58        32.32        66.61 
TCGA-68-8250 TCGA-77-A5GB TCGA-94-7033 TCGA-94-7557 TCGA-98-8020 TCGA-NC-A5HM 
        8.02        30.81        21.04         0.16         2.76        39.85 
TCGA-NK-A5CT TCGA-18-3414 TCGA-21-1070 TCGA-21-1082 TCGA-21-5786 TCGA-22-1011 
       65.65        23.54       119.54       119.80        33.93         1.74 
TCGA-22-1016 TCGA-22-4595 TCGA-22-4596 TCGA-22-4607 TCGA-22-5478 TCGA-22-5492 
       27.02        24.13         0.56        19.30         0.79        16.64 
TCGA-33-4583 TCGA-33-4587 TCGA-33-AASD TCGA-33-AASI TCGA-34-2600 TCGA-34-5239 
      151.27        54.44       110.99        44.19        61.61        60.30 
TCGA-34-5241 TCGA-34-8454 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3789 TCGA-37-4141 
       16.93        38.79         4.04        33.90         0.43         0.39 
TCGA-39-5029 TCGA-39-5035 TCGA-43-2581 TCGA-43-3920 TCGA-43-5670 TCGA-43-6770 
       24.33        68.38        38.66        33.11        27.91        21.47 
TCGA-43-7656 TCGA-43-A56U TCGA-46-6025 TCGA-52-7810 TCGA-52-7812 TCGA-56-5897 
       19.59        14.20        10.65        30.35        27.45        12.43 
TCGA-56-5898 TCGA-56-7223 TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 
       18.25        14.53        30.41        17.49         1.35        13.81 
TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D TCGA-56-A62T TCGA-58-8386 TCGA-58-8391 
       10.36        20.25        20.94        14.47         0.03        71.24 
TCGA-58-8393 TCGA-60-2695 TCGA-60-2706 TCGA-60-2713 TCGA-60-2714 TCGA-60-2719 
       34.78        21.11        92.71        56.91        50.33        42.64 
TCGA-60-2720 TCGA-60-2723 TCGA-60-2724 TCGA-63-6202 TCGA-63-7020 TCGA-63-A5MG 
        3.19        35.90        23.57        52.67        70.13        70.62 
TCGA-63-A5MI TCGA-66-2753 TCGA-66-2763 TCGA-66-2769 TCGA-66-2771 TCGA-66-2780 
       58.65         1.02         0.99         7.07        19.00        12.03 
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-66-2793 TCGA-66-2794 TCGA-68-8251 TCGA-68-A59J TCGA-77-8008 TCGA-77-8130 
       10.06        54.08        13.35        14.73        86.76       156.66 
TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8144 TCGA-77-8150 TCGA-77-A5G1 
       12.59        39.09        17.72        27.39        54.41       132.36 
TCGA-77-A5G6 TCGA-77-A5GH TCGA-85-7697 TCGA-85-7950 TCGA-85-8287 TCGA-85-8352 
       22.29        38.86        34.95        18.94         0.76         5.29 
TCGA-85-8479 TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A513 
       15.39        30.97        19.86        30.48        16.21        29.92 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 TCGA-94-8491 
       12.39         3.65        20.22         4.01         2.30        26.63 
TCGA-94-A5I6 TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-L3-A4E7 TCGA-NC-A5HF 
       17.69        30.81        30.67        27.16        12.89         4.54 
TCGA-NC-A5HG TCGA-NC-A5HK TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52Q 
       64.54         4.21        14.73         3.65         3.72 

$`DEL PEAK 41(17Q11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 
       12.20         4.47       123.19         6.18        27.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 
       48.82        60.66        22.06       129.01       133.74         1.55 
TCGA-33-6737 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 
       19.76        28.96        31.27        17.88        18.38         7.76 
TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 
       78.18         2.93        11.61        19.99        13.05        17.00 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       16.77        17.85         0.13        41.42         9.01        35.34 
TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7943 TCGA-94-A5I4 
       20.78        42.08         9.50        14.07        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       57.07        19.36         5.69        21.21        19.10         0.07 
TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 
       76.80        40.90        16.80         0.43         8.58        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
      117.57        11.34        92.15        36.07        92.42        86.96 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2.79       154.32        49.94        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-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 
        7.33         4.31        64.21        14.10        20.48        35.08 
TCGA-22-4594 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 
       48.33        38.17        34.75        13.12        32.02         9.57 
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        86.30        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-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 
       97.94        79.53       173.82       103.53        14.07        63.35 
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-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
        2.63        32.88        65.23        81.24        74.66         9.07 
TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 
       50.66        44.75        39.32         4.96         1.12        26.43 
TCGA-37-3783 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        4.01         0.39         7.96         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 
        6.81         3.39        37.58        21.70       133.25       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      111.35        68.58        55.20        82.52       102.18         1.71 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
        1.94        60.53        36.39        71.18        55.56        17.06 
TCGA-43-2576 TCGA-43-3394 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 
       40.21        39.12        22.98        24.89         5.46         3.81 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
       13.38        11.77         9.73        13.32        12.16        13.02 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 
        9.83         4.44        13.91         0.39         0.39        29.95 
TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-56-1622 TCGA-56-6545 TCGA-56-7222 
       28.34         5.46         8.75        28.96        21.90        18.48 
TCGA-56-7579 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 
       31.27        19.76         6.51         0.10        33.24        14.96 
TCGA-56-8083 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 
        4.93         3.48        26.89        14.07         1.81        22.75 
TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
        9.93        15.81        19.23        13.32        18.74         0.26 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K 
       13.25        13.55        29.95        16.47        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
       56.65        35.24        29.92        12.23        10.22        96.82 
TCGA-60-2704 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2716 
       37.94        21.93        80.45        49.48        66.54        48.49 
TCGA-60-2722 TCGA-60-2725 TCGA-60-2726 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       29.85        26.83        11.77        70.42        68.15        55.30 
TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
      102.67        59.97        45.57        14.99        11.34        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-66-2744 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-66-2765 
        0.92         0.99        43.99        21.01        25.05         2.01 
TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
        1.02         2.01         2.01        23.01         3.02         2.01 
TCGA-66-2778 TCGA-66-2781 TCGA-66-2787 TCGA-66-2790 TCGA-66-2791 TCGA-66-2792 
       19.00         3.98        40.01        22.98         5.03        30.02 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-A59I 
        4.01        49.05         2.73         6.64         6.94        16.18 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 
       12.07        12.33        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       140.09         0.49        73.22        70.13       106.95 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8009 TCGA-77-8128 
        0.16        46.78        32.55         6.51        55.73        37.81 
TCGA-77-8133 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 
       53.92       104.09        11.54        26.40         6.97        66.51 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G7 
       65.49        60.53        36.36       126.18       150.25         5.92 
TCGA-77-A5G8 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
       61.94        27.62         9.67        41.39        40.24         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-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
       25.15        19.04        24.13        31.56        26.79        30.64 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 
       34.52        10.09        13.22        22.45        16.77         3.09 
TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
       32.71         2.01         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A4QR 
       18.08        22.59        30.28        34.13        24.36        19.73 
TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-90-6837 TCGA-90-7767 
       27.16        15.85        14.96        15.29        24.92         2.93 
TCGA-90-7769 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
       11.77        22.62        10.59         2.70         3.48         5.26 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
        4.01         5.03        14.14        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       27.68        21.44        21.34        18.15         2.01        27.02 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW 
       20.32        18.58        20.71        16.11        13.18        13.41 
TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN 
       11.84         1.22        57.30        13.74         2.89        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52S 
       43.92        25.32        26.43        83.57        33.07        12.72 
TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       43.89        11.18         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 
                        156.66                         173.82 
  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE 
                         21.47                          21.90 
[1] "0.0 - 156.7 (21.5)" "0.1 - 173.8 (21.9)"
[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       45        0         9
  DEL PEAK 41(17Q11.2) WILD-TYPE       2       64      107        2        56
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(17Q11.2) MUTATED          20         1         22          6
  DEL PEAK 41(17Q11.2) WILD-TYPE        75         2         41         13
                                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                             64
  STAGE IB                             45                            107
  STAGE II                              0                              2
  STAGE IIA                             9                             56
  STAGE IIB                            20                             75
  STAGE III                             1                              2
  STAGE IIIA                           22                             41
  STAGE IIIB                            6                             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 41(17Q11.2) MUTATED    29  71  25   7
  DEL PEAK 41(17Q11.2) WILD-TYPE  83 223  46  17
D71V4, multiclass
    clus
vv   DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  T1                           29                             83
  T2                           71                            223
  T3                           25                             46
  T4                            7                             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 41(17Q11.2) MUTATED    92  20  14   2
  DEL PEAK 41(17Q11.2) WILD-TYPE 225 113  26   3
D71V5, multiclass
    clus
vv   DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  N0                           92                            225
  N1                           20                            113
  N2                           14                             26
  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   104   3
  DEL PEAK 41(17Q11.2) WILD-TYPE 307   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED    104    3
  DEL PEAK 41(17Q11.2) WILD-TYPE  307    4
   clus
vv  DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  0                          104                            307
  1                            3                              4
[1] 2 2
[1] FALSE
D71V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q11.2) MUTATED    37  95
  DEL PEAK 41(17Q11.2) WILD-TYPE  93 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED     37   95
  DEL PEAK 41(17Q11.2) WILD-TYPE   93  276
        clus
vv       DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  FEMALE                           37                             93
  MALE                             95                            276
[1] 2 2
[1] FALSE
D71V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(17Q11.2) MUTATED   105  11
  DEL PEAK 41(17Q11.2) WILD-TYPE 279  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED    105   11
  DEL PEAK 41(17Q11.2) WILD-TYPE  279   42
     clus
vv    DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  NO                           105                            279
  YES                           11                             42
[1] 2 2
[1] FALSE
D71V9, 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 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                                                           128
  DEL PEAK 41(17Q11.2) WILD-TYPE                                                         351
D71V10, multiclass
                                                             clus
vv                                                            DEL PEAK 41(17Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          128
                                                             clus
vv                                                            DEL PEAK 41(17Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            351
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, continuous
D71V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(17Q11.2) MUTATED   103   2   1   9
  DEL PEAK 41(17Q11.2) WILD-TYPE 296  10   3  14
D71V13, multiclass
    clus
vv   DEL PEAK 41(17Q11.2) MUTATED DEL PEAK 41(17Q11.2) WILD-TYPE
  R0                          103                            296
  R1                            2                             10
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(17Q11.2) MUTATED       3                        12    83
  DEL PEAK 41(17Q11.2) WILD-TYPE     6                        19   266
D71V14, multiclass
                           clus
vv                          DEL PEAK 41(17Q11.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                               83
                           clus
vv                          DEL PEAK 41(17Q11.2) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             19
  WHITE                                                266
[1] 3 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  85
  DEL PEAK 41(17Q11.2) WILD-TYPE   5 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(17Q11.2) MUTATED      3   85
  DEL PEAK 41(17Q11.2) WILD-TYPE    5  232
                        clus
vv                       DEL PEAK 41(17Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           85
                        clus
vv                       DEL PEAK 41(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            232
[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    64  36
  DEL PEAK 42(17Q25.3) WILD-TYPE 216 178
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                           100                            394 
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                            36                            178 
$`DEL PEAK 42(17Q25.3) MUTATED`
TCGA-21-A5DI TCGA-22-5472 TCGA-56-8305 TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 
       32.19        64.93         3.45        21.04         0.13         3.58 
TCGA-60-2721 TCGA-63-A5MH TCGA-77-A5GB TCGA-94-7557 TCGA-NK-A5CT TCGA-NK-A5D1 
       32.32        66.61        30.81         0.16        65.65        16.80 
TCGA-18-3415 TCGA-18-3421 TCGA-21-1070 TCGA-21-1075 TCGA-22-1011 TCGA-22-1016 
       92.15        86.96       119.54        70.16         1.74        27.02 
TCGA-22-5482 TCGA-33-4538 TCGA-33-4583 TCGA-33-A4WN TCGA-34-2600 TCGA-34-5241 
       11.74        97.94       151.27         4.70        61.61        16.93 
TCGA-34-5929 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-5819 
        4.96        33.90         4.01         0.43         0.39         3.39 
TCGA-39-5029 TCGA-43-2581 TCGA-43-5670 TCGA-43-A56U TCGA-46-3769 TCGA-51-4080 
       24.33        38.66        27.91        14.20         4.44         0.39 
TCGA-52-7622 TCGA-52-7810 TCGA-56-5898 TCGA-56-7580 TCGA-56-7822 TCGA-56-8503 
       28.34        30.35        18.25        30.41        17.49         1.35 
TCGA-56-8624 TCGA-56-8626 TCGA-56-8628 TCGA-58-8388 TCGA-58-8393 TCGA-60-2695 
       13.81         9.93        20.25        13.55        34.78        21.11 
TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 TCGA-63-7020 TCGA-63-7023 
       80.45        50.33        42.64         3.19        70.13        55.30 
TCGA-63-A5MG TCGA-63-A5ML TCGA-66-2780 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
       70.62        45.57        12.03        12.00        24.95         1.97 
TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 TCGA-68-A59J TCGA-77-6842 TCGA-77-6844 
       25.97         4.04        22.98        14.73        29.56        75.09 
TCGA-77-6845 TCGA-77-7337 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8138 
       23.28       106.95        37.81       156.66        12.59        17.72 
TCGA-77-8144 TCGA-77-8150 TCGA-77-A5G1 TCGA-77-A5GH TCGA-85-7697 TCGA-85-7710 
       27.39        54.41       132.36        38.86        34.95         1.38 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8070 TCGA-85-8287 TCGA-85-8288 TCGA-85-8355 
       29.95        18.94        31.56         0.76        13.22         2.01 
TCGA-85-8479 TCGA-85-A4JB TCGA-85-A4QQ TCGA-85-A50Z TCGA-92-8063 TCGA-94-8035 
       15.39        30.97        30.48        16.21         4.01         4.01 
TCGA-94-A5I6 TCGA-96-7544 TCGA-98-8021 TCGA-98-A538 TCGA-L3-A4E7 TCGA-LA-A7SW 
       17.69        71.01        30.81        27.16        12.89        13.41 
TCGA-MF-A522 TCGA-NC-A5HK TCGA-NC-A5HT TCGA-NK-A5CX 
       11.84         4.21        26.43         3.65 

$`DEL PEAK 42(17Q25.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 
       12.20         4.47       123.19         4.80        31.99         6.18 
TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-22-A5C4 TCGA-33-4532 
       27.19        14.93        48.82        60.66        22.06       129.01 
TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 
      133.74         1.55        19.76        31.50        28.96        31.27 
TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       17.88        22.49        18.38         7.76        78.18         2.93 
TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 TCGA-56-8504 
       11.61        12.03        19.99        13.05        17.00        16.77 
TCGA-56-A4BY TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-68-8250 TCGA-77-7140 
       17.85        41.42         9.01        35.34         8.02        20.78 
TCGA-77-A5GA TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 TCGA-94-A5I4 
       42.08         9.50        14.07        21.04        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH 
       57.07        19.36         2.76         5.69        21.21        19.10 
TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W 
        0.07        76.80        39.85        40.90         0.43         8.58 
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 
       75.75       117.57        11.34        23.54        36.07        92.42 
TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1071 TCGA-21-1072 TCGA-21-1076 
        2.79       154.32        49.94        46.88        99.16        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-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
       43.23        31.63        88.11        41.69        33.93        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1012 TCGA-22-4591 
       21.99         7.33         4.31        64.21        14.10        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-22-5473 
       13.12        32.02        19.30         9.57        11.77        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        86.30        71.34        79.20 
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-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A5GW 
      173.82       103.53        14.07        54.44        63.35         0.30 
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-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
        2.63        32.88        65.23        81.24        74.66         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 
       60.30        50.66        44.75        39.32         1.12        38.79 
TCGA-34-8455 TCGA-34-8456 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 
        4.04        26.43         7.96         8.12         7.46         7.82 
TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 TCGA-39-5016 
        6.81         0.39        37.58        21.70       133.25       126.58 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 
      111.35        68.58        55.20        82.52       102.18         1.71 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        60.53        36.39        68.38        71.18        55.56 
TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 
       17.06        40.21        39.12        33.11        22.98        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-A475 TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 
        9.73        13.32        12.16        13.02         9.83        10.65 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4081 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 
       13.91         0.39        29.95         5.46         8.75        27.45 
TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       28.96        12.43        21.90        18.48        14.53        31.27 
TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 
       19.76         6.51         0.10        33.24        14.96         4.93 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 
        3.48        26.89        14.07         1.81        22.75        10.36 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
       15.81        20.94        19.23        13.32        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 
       14.47         0.03        13.25        29.95        71.24        16.47 
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-60-2709 
       10.22        96.82        37.94        92.71        21.93        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
       66.54        56.91        48.49        29.85        35.90        23.57 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB 
       26.83        11.77        52.67        70.42        68.15       102.67 
TCGA-63-A5MI TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MR 
       58.65        59.97        14.99        11.34        25.28        89.29 
TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 
       78.28        16.37        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-68-8251 TCGA-68-A59I 
       49.05         2.73         6.64         6.94        13.35        16.18 
TCGA-70-6722 TCGA-70-6723 TCGA-77-6843 TCGA-77-7138 TCGA-77-7139 TCGA-77-7141 
       12.07        12.33        73.12        11.18       140.09         0.49 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
       73.22        70.13         0.16        46.78        32.55         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8133 TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 
       86.76        55.73        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        66.51        65.49        60.53        36.36 
TCGA-77-A5FZ TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF 
      126.18       150.25        22.29         5.92        61.94        27.62 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
        9.67        41.39        40.24         6.41        36.53        31.30 
TCGA-85-7699 TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8071 
       32.91         1.15        25.15        19.04        24.13        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 
       30.64        34.52        10.09        22.45        16.77         5.29 
TCGA-85-8353 TCGA-85-8354 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 
        3.09        32.71         7.76        36.59        38.14        12.59 
TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4PA 
       18.08        22.59        30.28        34.13        19.86        24.36 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
       19.73        27.16        15.85        14.96        15.29        29.92 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
       12.39         3.65        24.92         2.93        11.77        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-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL 
        5.03        26.63        14.14        18.31        17.46        27.68 
TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C 
       21.44        30.67        21.34        18.15         2.01        27.02 
TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-NC-A5HF 
       20.32        18.58        20.71        16.11        13.18         4.54 
TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HN 
       64.54         1.22        57.30        13.74         2.89        49.28 
TCGA-NC-A5HO TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q 
       43.92        25.32        14.73        83.57        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89        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 
                        156.66                         173.82 
  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE 
                        23.130                         21.585 
[1] "0.1 - 156.7 (23.1)" "0.0 - 173.8 (21.6)"
[1] "hr=" "1.2"
D72V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(17Q25.3) MUTATED         0       19       37        0         7
  DEL PEAK 42(17Q25.3) WILD-TYPE       2       70      115        2        58
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(17Q25.3) MUTATED          22         0         13          3
  DEL PEAK 42(17Q25.3) WILD-TYPE        73         3         50         16
                                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                             70
  STAGE IB                             37                            115
  STAGE II                              0                              2
  STAGE IIA                             7                             58
  STAGE IIB                            22                             73
  STAGE III                             0                              3
  STAGE IIIA                           13                             50
  STAGE IIIB                            3                             16
  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  56  20   2
  DEL PEAK 42(17Q25.3) WILD-TYPE  88 238  51  22
D72V4, multiclass
    clus
vv   DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  T1                           24                             88
  T2                           56                            238
  T3                           20                             51
  T4                            2                             22
[1] 4 2
[1] TRUE
[1] "dimension of 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    72  20   6   2
  DEL PEAK 42(17Q25.3) WILD-TYPE 245 113  34   3
D72V5, multiclass
    clus
vv   DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  N0                           72                            245
  N1                           20                            113
  N2                            6                             34
  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    86   0
  DEL PEAK 42(17Q25.3) WILD-TYPE 325   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q25.3) MUTATED     86    0
  DEL PEAK 42(17Q25.3) WILD-TYPE  325    7
   clus
vv  DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  0                           86                            325
  1                            0                              7
[1] 2 2
[1] FALSE
D72V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q25.3) MUTATED    22  80
  DEL PEAK 42(17Q25.3) WILD-TYPE 108 291
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q25.3) MUTATED     22   80
  DEL PEAK 42(17Q25.3) WILD-TYPE  108  291
        clus
vv       DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  FEMALE                           22                            108
  MALE                             80                            291
[1] 2 2
[1] FALSE
D72V8, binary
                                cls
clus                               0   1
  DEL PEAK 42(17Q25.3) MUTATED    80   7
  DEL PEAK 42(17Q25.3) WILD-TYPE 304  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q25.3) MUTATED     80    7
  DEL PEAK 42(17Q25.3) WILD-TYPE  304   46
     clus
vv    DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  NO                            80                            304
  YES                            7                             46
[1] 2 2
[1] FALSE
D72V9, 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 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                                                            97
  DEL PEAK 42(17Q25.3) WILD-TYPE                                                         382
D72V10, multiclass
                                                             clus
vv                                                            DEL PEAK 42(17Q25.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           97
                                                             clus
vv                                                            DEL PEAK 42(17Q25.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   11
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            382
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, continuous
D72V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(17Q25.3) MUTATED    82   1   1   6
  DEL PEAK 42(17Q25.3) WILD-TYPE 317  11   3  17
D72V13, multiclass
    clus
vv   DEL PEAK 42(17Q25.3) MUTATED DEL PEAK 42(17Q25.3) WILD-TYPE
  R0                           82                            317
  R1                            1                             11
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(17Q25.3) MUTATED       0                         7    72
  DEL PEAK 42(17Q25.3) WILD-TYPE     9                        24   277
D72V14, multiclass
                           clus
vv                          DEL PEAK 42(17Q25.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               72
                           clus
vv                          DEL PEAK 42(17Q25.3) WILD-TYPE
  ASIAN                                                  9
  BLACK OR AFRICAN AMERICAN                             24
  WHITE                                                277
[1] 3 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  68
  DEL PEAK 42(17Q25.3) WILD-TYPE   5 249
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(17Q25.3) MUTATED      3   68
  DEL PEAK 42(17Q25.3) WILD-TYPE    5  249
                        clus
vv                       DEL PEAK 42(17Q25.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           68
                        clus
vv                       DEL PEAK 42(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            249
[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   133  97
  DEL PEAK 43(18Q23) WILD-TYPE 147 117
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                         230                          264 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                          97                          117 
$`DEL PEAK 43(18Q23) MUTATED`
TCGA-18-3416 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 TCGA-22-5471 TCGA-33-4533 
       31.99        32.19        14.93        48.82        60.66       133.74 
TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-43-2578 TCGA-43-5668 
        1.55        19.76        31.50        28.96        22.49        18.38 
TCGA-56-7221 TCGA-56-8305 TCGA-56-A4BY TCGA-56-A5DR TCGA-63-A5MH TCGA-90-7766 
       19.99         3.45        17.85         0.13        66.61         9.50 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8020 
       21.04         0.16        18.38        16.14        19.36         2.76 
TCGA-98-A539 TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NC-A5HR 
        5.69        19.10         0.07        76.80        39.85        40.90 
TCGA-NK-A5D1 TCGA-18-3412 TCGA-18-3414 TCGA-18-3417 TCGA-18-3421 TCGA-18-4086 
       16.80        11.34        23.54        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-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
       33.93        10.82        27.02        20.48        35.08        24.13 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4613 TCGA-22-5473 TCGA-22-5491 TCGA-22-5492 
       38.17        34.75        11.77        63.55        56.32        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-6738 
       97.94        79.53       173.82       103.53       151.27        63.35 
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-34-2608 TCGA-34-5231 TCGA-34-5236 TCGA-34-5241 TCGA-34-8454 TCGA-34-8455 
       32.88        65.23         9.07        16.93        38.79         4.04 
TCGA-34-A5IX TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-37-A5EL TCGA-39-5016 
       33.90         0.39         8.12         7.82        37.58       126.58 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5036 TCGA-43-2576 TCGA-43-3394 
      102.18         1.71        24.33        71.18        40.21        39.12 
TCGA-43-5670 TCGA-43-6770 TCGA-43-7656 TCGA-43-8116 TCGA-46-3768 TCGA-46-6025 
       27.91        21.47        19.59        11.77         9.83        10.65 
TCGA-51-4079 TCGA-52-7810 TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 
        0.39        30.35        27.45        28.96        12.43        21.90 
TCGA-56-7222 TCGA-56-7223 TCGA-56-7730 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 
       18.48        14.53         6.51        17.49         3.48        26.89 
TCGA-56-8309 TCGA-56-8503 TCGA-56-8624 TCGA-56-8626 TCGA-56-8629 TCGA-56-A4BW 
       14.07         1.35        13.81         9.93        15.81        19.23 
TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8386 TCGA-58-A46K TCGA-58-A46M TCGA-60-2698 
       18.74        14.47         0.03        34.36        35.24        10.22 
TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2714 TCGA-60-2719 TCGA-60-2720 
       92.71        21.93        80.45        50.33        42.64         3.19 
TCGA-60-2726 TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5MP TCGA-63-A5MR TCGA-63-A5MS 
       11.77       102.67        59.97        25.28        89.29        78.28 
TCGA-63-A5MT TCGA-63-A5MW TCGA-66-2734 TCGA-66-2737 TCGA-66-2744 TCGA-66-2753 
       16.37        53.88        43.10         2.01         0.99         1.02 
TCGA-66-2758 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2768 TCGA-66-2771 
       21.01         0.99         2.01         1.02         2.01        19.00 
TCGA-66-2773 TCGA-66-2780 TCGA-66-2781 TCGA-66-2785 TCGA-66-2787 TCGA-66-2790 
        3.02        12.03         3.98         1.97        40.01        22.98 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 
        5.03        30.02        54.08        49.05         2.73         6.94 
TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7141 
       14.73        12.07        12.33        29.56        23.28         0.49 
TCGA-77-7142 TCGA-77-7337 TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 
       73.22       106.95       156.66        12.59        39.09        17.72 
TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 TCGA-77-8154 TCGA-77-8156 
      104.09        11.54        27.39        66.51        60.53        36.36 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-6175 TCGA-85-6560 
      132.36       150.25        22.29        61.94         9.67        41.39 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7843 
       40.24         6.41        36.53        34.95        31.30         1.15 
TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8071 TCGA-85-8072 TCGA-85-8276 
       29.95        18.94        19.04        26.79        30.64        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 
       10.09         0.76         5.29         3.09        32.71         2.01 
TCGA-85-8479 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JC TCGA-85-A4QQ 
       15.39        12.59        18.08        22.59        19.86        30.48 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 
       15.85        14.96        15.29        12.39         3.65        11.77 
TCGA-90-A4ED TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-94-8491 TCGA-94-A5I6 
       20.22         3.48         4.01         5.26        26.63        17.69 
TCGA-96-8169 TCGA-96-8170 TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       18.31        17.46        21.44        30.67        21.34        27.16 
TCGA-98-A53B TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A7SW TCGA-NC-A5HG TCGA-NC-A5HH 
        2.01        20.71        16.11        13.41        64.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ 
       57.30         4.21         2.89        49.28        25.32        14.73 
TCGA-O2-A52N TCGA-O2-A52Q 
       33.07         3.72 

$`DEL PEAK 43(18Q23) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19         4.80         6.18        27.19 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-34-2609 TCGA-39-5039 TCGA-43-7657 
       64.93        22.06       129.01        31.27        17.88         7.76 
TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 TCGA-56-8308 
       78.18         2.93        11.61        12.03        13.05        17.00 
TCGA-56-8504 TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       16.77        21.04         3.58        41.42         9.01        35.34 
TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 
       32.32         8.02        20.78        42.08        30.81        14.07 
TCGA-96-7545 TCGA-98-A53D TCGA-NK-A5CT TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 
       57.07        21.21        65.65         0.43         8.58        75.75 
TCGA-18-3411 TCGA-18-3415 TCGA-18-3419 TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 
      117.57        92.15        92.42       154.32        49.94        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-21-1078 TCGA-21-1081 TCGA-21-1082 
       70.16        60.89        34.78        15.58         9.34       119.80 
TCGA-21-5783 TCGA-21-5784 TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
       88.11        41.69        21.99         7.33         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4594 TCGA-22-4596 TCGA-22-4604 TCGA-22-4605 
        1.74        14.10        48.33         0.56        13.12        32.02 
TCGA-22-4607 TCGA-22-4609 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 
       19.30         9.57        14.63        44.25         0.79        86.30 
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-33-4586 TCGA-33-4587 TCGA-33-A4WN TCGA-33-AAS8 TCGA-34-2596 TCGA-34-2600 
       14.07        54.44         4.70        36.62         2.63        61.61 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-5928 
       81.24        74.66        60.30        50.66        44.75        39.32 
TCGA-34-5929 TCGA-34-7107 TCGA-34-8456 TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
        4.96         1.12        26.43         4.01         0.43         7.96 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 
        7.46         6.81         0.39         3.39        21.70       133.25 
TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5030 TCGA-39-5031 
      111.35        68.58        55.20        82.52         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2581 TCGA-43-3920 
       36.39        68.38        55.56        17.06        38.66        33.11 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-A475 
       22.98        24.89         5.46         3.81        13.38         9.73 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3769 TCGA-46-6026 
       14.20        13.32        12.16        13.02         4.44        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-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 TCGA-56-7823 TCGA-56-8082 
       31.27        30.41        19.76         0.10        33.24        14.96 
TCGA-56-8083 TCGA-56-8622 TCGA-56-8623 TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D 
        4.93         1.81        22.75        10.36        20.25        20.94 
TCGA-56-A4BX TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
       13.32         0.26        13.25        13.55        29.95        71.24 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46L TCGA-58-A46N TCGA-60-2695 
       16.47        34.78        85.12        56.65        29.92        21.11 
TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 
       12.23        96.82        37.94        49.48        66.54        56.91 
TCGA-60-2716 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 
       48.49        29.85        35.90        23.57        26.83        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI 
       70.13        70.42        68.15        55.30        70.62        58.65 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MV TCGA-63-A5MY TCGA-66-2727 
       45.57        14.99        11.34        36.16        34.59        16.96 
TCGA-66-2742 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 
       21.07         2.01         0.92         0.99        43.99        25.05 
TCGA-66-2767 TCGA-66-2769 TCGA-66-2770 TCGA-66-2777 TCGA-66-2778 TCGA-66-2782 
        2.01         7.07        23.01         2.01        19.00        12.00 
TCGA-66-2783 TCGA-66-2786 TCGA-66-2788 TCGA-66-2789 TCGA-66-2793 TCGA-66-2795 
       24.95        25.97        22.98         4.04        10.06         4.01 
TCGA-68-7756 TCGA-68-8251 TCGA-68-A59I TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 
        6.64        13.35        16.18        73.12        75.09        11.18 
TCGA-77-7139 TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
      140.09        70.13         0.16        46.78        32.55         6.51 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8143 TCGA-77-8145 
       86.76        55.73        37.81        53.92        26.40         6.97 
TCGA-77-8150 TCGA-77-8153 TCGA-77-A5FZ TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH 
       54.41        65.49       126.18         5.92        27.62        38.86 
TCGA-85-7699 TCGA-85-7710 TCGA-85-8048 TCGA-85-8052 TCGA-85-8070 TCGA-85-8288 
       32.91         1.38        25.15        24.13        31.56        13.22 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-A4CL 
       22.45        16.77         7.76        36.59        38.14        30.28 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       34.13        30.97        24.36        19.73        27.16        16.21 
TCGA-85-A513 TCGA-90-6837 TCGA-90-7767 TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
       29.92        24.92         2.93        22.62        10.59         2.70 
TCGA-92-8065 TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-A4JL 
        2.30         4.01         5.03        14.14        71.01        27.68 
TCGA-98-8021 TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 
       30.81        18.15        27.02        20.32        18.58        12.89 
TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HJ TCGA-NC-A5HO TCGA-NC-A5HT 
       13.18        11.84         4.54        13.74        43.92        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       83.57         3.65        12.72        43.89        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 
                      173.82                       154.32 
  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE 
                      20.860                       22.865 
[1] "0.0 - 173.8 (20.9)" "0.1 - 154.3 (22.9)"
[1] "hr=" "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       53       80        2        36
                              vv
clus                           STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(18Q23) MUTATED          50         1         33          4
  DEL PEAK 43(18Q23) WILD-TYPE        45         2         30         15
                              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                           53
  STAGE IB                           72                           80
  STAGE II                            0                            2
  STAGE IIA                          29                           36
  STAGE IIB                          50                           45
  STAGE III                           1                            2
  STAGE IIIA                         33                           30
  STAGE IIIB                          4                           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 43(18Q23) MUTATED    47 139  40   8
  DEL PEAK 43(18Q23) WILD-TYPE  65 155  31  16
D73V4, multiclass
    clus
vv   DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  T1                         47                           65
  T2                        139                          155
  T3                         40                           31
  T4                          8                           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 43(18Q23) MUTATED   144  67  18   1
  DEL PEAK 43(18Q23) WILD-TYPE 173  66  22   4
D73V5, multiclass
    clus
vv   DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  N0                        144                          173
  N1                         67                           66
  N2                         18                           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"
D73V6, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED   193   5
  DEL PEAK 43(18Q23) WILD-TYPE 218   2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED    193    5
  DEL PEAK 43(18Q23) WILD-TYPE  218    2
   clus
vv  DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  0                        193                          218
  1                          5                            2
[1] 2 2
[1] FALSE
D73V7, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED    46 188
  DEL PEAK 43(18Q23) WILD-TYPE  84 183
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED     46  188
  DEL PEAK 43(18Q23) WILD-TYPE   84  183
        clus
vv       DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  FEMALE                         46                           84
  MALE                          188                          183
[1] 2 2
[1] FALSE
D73V8, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED   177  24
  DEL PEAK 43(18Q23) WILD-TYPE 207  29
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED    177   24
  DEL PEAK 43(18Q23) WILD-TYPE  207   29
     clus
vv    DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  NO                         177                          207
  YES                         24                           29
[1] 2 2
[1] FALSE
D73V9, continuous
                              vv
clus                           LUNG BASALOID SQUAMOUS CELL CARCINOMA
  DEL PEAK 43(18Q23) MUTATED                                       6
  DEL PEAK 43(18Q23) WILD-TYPE                                     9
                              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                                                           225
  DEL PEAK 43(18Q23) WILD-TYPE                                                         254
D73V10, multiclass
                                                             clus
vv                                                            DEL PEAK 43(18Q23) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                               3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                              0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        225
                                                             clus
vv                                                            DEL PEAK 43(18Q23) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          254
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V11, continuous
D73V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 43(18Q23) MUTATED   189   4   1  14
  DEL PEAK 43(18Q23) WILD-TYPE 210   8   3   9
D73V13, multiclass
    clus
vv   DEL PEAK 43(18Q23) MUTATED DEL PEAK 43(18Q23) WILD-TYPE
  R0                        189                          210
  R1                          4                            8
  R2                          1                            3
  RX                         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                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(18Q23) MUTATED       4                        16   162
  DEL PEAK 43(18Q23) WILD-TYPE     5                        15   187
D73V14, multiclass
                           clus
vv                          DEL PEAK 43(18Q23) MUTATED
  ASIAN                                              4
  BLACK OR AFRICAN AMERICAN                         16
  WHITE                                            162
                           clus
vv                          DEL PEAK 43(18Q23) WILD-TYPE
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                           15
  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"
D73V15, binary
                              cls
clus                             0   1
  DEL PEAK 43(18Q23) MUTATED     5 144
  DEL PEAK 43(18Q23) WILD-TYPE   3 173
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(18Q23) MUTATED      5  144
  DEL PEAK 43(18Q23) WILD-TYPE    3  173
                        clus
vv                       DEL PEAK 43(18Q23) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        144
                        clus
vv                       DEL PEAK 43(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          173
[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   136  97
  DEL PEAK 44(19P13.3) WILD-TYPE 144 117
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                           233                            261 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            97                            117 
$`DEL PEAK 44(19P13.3) MUTATED`
TCGA-18-3407 TCGA-18-3409 TCGA-21-A5DI TCGA-22-A5C4 TCGA-33-4532 TCGA-33-6737 
        4.47       123.19        32.19        22.06       129.01        19.76 
TCGA-34-2604 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-A56V TCGA-56-8305 
       31.50        22.49        18.38         7.76        12.03         3.45 
TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-68-8250 TCGA-90-7964 
       21.04         0.13         3.58        41.42         8.02        14.07 
TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-98-8020 TCGA-98-A539 TCGA-NC-A5HD 
       21.04         0.16        18.38         2.76         5.69         0.07 
TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3411 TCGA-18-3412 TCGA-18-3417 
       39.85        65.65        16.80       117.57        11.34        36.07 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1077 TCGA-21-1080 TCGA-21-1081 
       49.94       119.54        46.88        34.78       122.43         9.34 
TCGA-21-1083 TCGA-21-5783 TCGA-21-5787 TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 
       43.23        88.11        10.82        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-33-4547 
       14.63         0.79        79.20        18.84        16.64        79.53 
TCGA-33-4582 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-AASB TCGA-33-AASD 
      103.53        14.07        54.44        63.35         6.94       110.99 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2608 TCGA-34-5236 TCGA-34-5241 TCGA-34-5928 
       44.19        27.16        32.88         9.07        16.93        39.32 
TCGA-34-5929 TCGA-34-8456 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
        4.96        26.43         0.43         0.39         7.96         8.12 
TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-37-A5EL 
        7.46         7.82         6.81         0.39         3.39        37.58 
TCGA-37-A5EN TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5029 TCGA-39-5034 
       21.70       133.25       111.35        68.58        24.33        36.39 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-3394 
       68.38        71.18        55.56        17.06        40.21        39.12 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-7656 TCGA-43-8115 
       33.11        27.91        22.98        21.47        19.59        13.38 
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-56-7222 TCGA-56-7223 TCGA-56-7579 
       28.96        12.43        18.25        18.48        14.53        31.27 
TCGA-56-7730 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8624 
        6.51        17.49        33.24        14.96         4.93        13.81 
TCGA-56-8629 TCGA-56-A49D TCGA-56-A4ZK TCGA-56-A62T TCGA-58-8388 TCGA-58-8390 
       15.81        20.94        18.74        14.47        13.55        29.95 
TCGA-58-8393 TCGA-58-A46L TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2714 
       34.78        56.65        10.22        92.71        21.93        50.33 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-63-6202 TCGA-63-7020 TCGA-63-A5MB 
        3.19        29.85        35.90        52.67        70.13       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-A59I TCGA-70-6723 TCGA-77-6843 TCGA-77-6845 TCGA-77-7138 
        6.64        16.18        12.33        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        55.73       156.66        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        36.36       132.36        41.39 
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        26.79        30.64        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        15.39        12.59 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A510 TCGA-85-A53L 
       18.08        30.28        30.97        19.86        15.85        12.39 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7341 TCGA-92-8063 TCGA-92-8065 
       20.22        22.62        10.59         3.48         4.01         2.30 
TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-8169 TCGA-98-A538 TCGA-98-A53A 
        5.03        14.14        17.69        18.31        27.16        18.15 
TCGA-98-A53B TCGA-98-A53J TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HG 
        2.01        20.71        13.18        13.41        11.84        64.54 
TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HP 
       57.30        13.74         4.21         2.89        49.28        25.32 
TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-XC-AA0X 
       14.73         3.65        33.07         3.72         0.20 

$`DEL PEAK 44(19P13.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-18-5595 TCGA-22-1000 
       12.20         4.80        31.99         6.18        27.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-33-4533 TCGA-33-4589 TCGA-34-2605 
       48.82        60.66        64.93       133.74         1.55        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 
       31.27        17.88        78.18         2.93        11.61        19.99 
TCGA-56-8201 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-60-2712 TCGA-60-2715 
       13.05        17.00        16.77        17.85         9.01        35.34 
TCGA-60-2721 TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 
       32.32        66.61        20.78        42.08        30.81         9.50 
TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE 
       16.14        57.07        19.36        21.21        19.10        76.80 
TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3414 TCGA-18-3415 
       40.90         0.43         8.58        75.75        23.54        92.15 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1072 TCGA-21-1075 
       92.42        86.96         2.79       154.32        99.16        70.16 
TCGA-21-1076 TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 
       60.89        15.58        31.73       119.80        31.63        41.69 
TCGA-21-5786 TCGA-22-0944 TCGA-22-1011 TCGA-22-1016 TCGA-22-4593 TCGA-22-4595 
       33.93         7.33         1.74        27.02        35.08        24.13 
TCGA-22-4596 TCGA-22-4599 TCGA-22-4604 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 
        0.56        38.17        13.12         9.57        11.77        63.55 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
       44.25        86.30        71.34        11.74        30.12        62.86 
TCGA-22-5491 TCGA-33-4538 TCGA-33-4566 TCGA-33-4583 TCGA-33-A4WN TCGA-33-A5GW 
       56.32        97.94       173.82       151.27         4.70         0.30 
TCGA-33-AAS8 TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-5231 TCGA-34-5232 
       36.62       118.36         2.63        61.61        65.23        81.24 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5927 TCGA-34-7107 TCGA-34-8454 
       74.66        60.30        50.66        44.75         1.12        38.79 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-39-5016 TCGA-39-5022 TCGA-39-5024 
        4.04        33.90         4.01       126.58        55.20        82.52 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 TCGA-39-5031 TCGA-43-2581 TCGA-43-6647 
      102.18         1.71         1.94        60.53        38.66        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 
        5.46         3.81        11.77         9.73        14.20        13.32 
TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6026 TCGA-51-4080 
       12.16        13.02         9.83         4.44        13.91         0.39 
TCGA-52-7622 TCGA-52-7812 TCGA-56-6545 TCGA-56-7580 TCGA-56-7582 TCGA-56-7731 
       28.34        27.45        21.90        30.41        19.76         0.10 
TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
        3.48        26.89        14.07         1.35         1.81        22.75 
TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A5DS 
       10.36         9.93        20.25        19.23        13.32         0.26 
TCGA-58-8386 TCGA-58-8387 TCGA-58-8391 TCGA-58-8392 TCGA-58-A46J TCGA-58-A46K 
        0.03        13.25        71.24        16.47        85.12        34.36 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 
       35.24        29.92        21.11        12.23        96.82        37.94 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 TCGA-60-2719 
       80.45        49.48        66.54        56.91        48.49        42.64 
TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 
       23.57        26.83        11.77        70.42        68.15        55.30 
TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MW 
       70.62        59.97        45.57        14.99        11.34        53.88 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2757 TCGA-66-2763 
        2.01        21.07         0.99         0.92        43.99         0.99 
TCGA-66-2765 TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2778 TCGA-66-2787 
        2.01         2.01        23.01         3.02        19.00        40.01 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7757 
        5.03        30.02        54.08        49.05         2.73         6.94 
TCGA-68-8251 TCGA-68-A59J TCGA-70-6722 TCGA-77-6842 TCGA-77-6844 TCGA-77-7139 
       13.35        14.73        12.07        29.56        75.09       140.09 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 TCGA-77-8007 
        0.49        73.22        70.13       106.95        32.55         6.51 
TCGA-77-8128 TCGA-77-8131 TCGA-77-8133 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 
       37.81        12.59        53.92       104.09        11.54        26.40 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G3 
       66.51        54.41        65.49        60.53       126.18       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       22.29         5.92        61.94        27.62        38.86         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 
       40.24         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        36.59 
TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CN TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       38.14        22.59        34.13        24.36        30.48        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 
       27.16        16.21        14.96        15.29        29.92         3.65 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-92-7340 TCGA-92-8064 TCGA-94-8035 
       24.92         2.93        11.77         2.70         5.26         4.01 
TCGA-94-8491 TCGA-96-7544 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       26.63        71.01        17.46        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 
       30.67        21.34        27.02        20.32        18.58        12.89 
TCGA-L3-A524 TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HO TCGA-NC-A5HT TCGA-NK-A5CR 
       16.11         4.54         1.22        43.92        26.43        83.57 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       12.72        43.89        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 
                        156.66                         173.82 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                         19.76                          24.89 
[1] "0.1 - 156.7 (19.8)" "0.0 - 173.8 (24.9)"
[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       39       74        0        34
  DEL PEAK 44(19P13.3) WILD-TYPE       1       50       78        2        31
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(19P13.3) MUTATED          40         1         36          8
  DEL PEAK 44(19P13.3) WILD-TYPE        55         2         27         11
                                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                             39                             50
  STAGE IB                             74                             78
  STAGE II                              0                              2
  STAGE IIA                            34                             31
  STAGE IIB                            40                             55
  STAGE III                             1                              2
  STAGE IIIA                           36                             27
  STAGE IIIB                            8                             11
  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    51 142  33  10
  DEL PEAK 44(19P13.3) WILD-TYPE  61 152  38  14
D74V4, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  T1                           51                             61
  T2                          142                            152
  T3                           33                             38
  T4                           10                             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   156  53  24   2
  DEL PEAK 44(19P13.3) WILD-TYPE 161  80  16   3
D74V5, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  N0                          156                            161
  N1                           53                             80
  N2                           24                             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   194   3
  DEL PEAK 44(19P13.3) WILD-TYPE 217   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED    194    3
  DEL PEAK 44(19P13.3) WILD-TYPE  217    4
   clus
vv  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  0                          194                            217
  1                            3                              4
[1] 2 2
[1] FALSE
D74V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED    56 180
  DEL PEAK 44(19P13.3) WILD-TYPE  74 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     56  180
  DEL PEAK 44(19P13.3) WILD-TYPE   74  191
        clus
vv       DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  FEMALE                           56                             74
  MALE                            180                            191
[1] 2 2
[1] FALSE
D74V8, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED   174  27
  DEL PEAK 44(19P13.3) WILD-TYPE 210  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED    174   27
  DEL PEAK 44(19P13.3) WILD-TYPE  210   26
     clus
vv    DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  NO                           174                            210
  YES                           27                             26
[1] 2 2
[1] FALSE
D74V9, 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 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                                                           225
  DEL PEAK 44(19P13.3) WILD-TYPE                                                         254
D74V10, multiclass
                                                             clus
vv                                                            DEL PEAK 44(19P13.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          225
                                                             clus
vv                                                            DEL PEAK 44(19P13.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            254
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, continuous
D74V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(19P13.3) MUTATED   183   6   1  11
  DEL PEAK 44(19P13.3) WILD-TYPE 216   6   3  12
D74V13, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  R0                          183                            216
  R1                            6                              6
  R2                            1                              3
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(19P13.3) MUTATED       3                        20   160
  DEL PEAK 44(19P13.3) WILD-TYPE     6                        11   189
D74V14, multiclass
                           clus
vv                          DEL PEAK 44(19P13.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           20
  WHITE                                              160
                           clus
vv                          DEL PEAK 44(19P13.3) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                189
[1] 3 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     3 155
  DEL PEAK 44(19P13.3) WILD-TYPE   5 162
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      3  155
  DEL PEAK 44(19P13.3) WILD-TYPE    5  162
                        clus
vv                       DEL PEAK 44(19P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          155
                        clus
vv                       DEL PEAK 44(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            162
[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    90  57
  DEL PEAK 45(19Q13.32) WILD-TYPE 190 157
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                            147                             347 
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                             57                             157 
$`DEL PEAK 45(19Q13.32) MUTATED`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-22-1017 TCGA-33-4532 
       12.20       123.19         4.80        31.99        48.82       129.01 
TCGA-43-7657 TCGA-43-A474 TCGA-56-7221 TCGA-56-8305 TCGA-56-8308 TCGA-60-2696 
        7.76        11.61        19.99         3.45        17.00         3.58 
TCGA-77-A5GA TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK 
       42.08         0.16        18.38        16.14        57.07        19.36 
TCGA-98-A539 TCGA-NC-A5HD TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-18-3411 TCGA-18-3412 
        5.69         0.07        40.90        16.80       117.57        11.34 
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-22-4594 TCGA-22-4595 TCGA-22-4607 TCGA-22-4613 TCGA-22-5478 TCGA-33-4538 
       48.33        24.13        19.30        11.77         0.79        97.94 
TCGA-33-4586 TCGA-33-AASB TCGA-33-AASI TCGA-34-2600 TCGA-34-5241 TCGA-34-5927 
       14.07         6.94        44.19        61.61        16.93        44.75 
TCGA-34-5929 TCGA-34-7107 TCGA-37-4129 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
        4.96         1.12         7.96         7.82         6.81         0.39 
TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 TCGA-39-5036 TCGA-43-3394 TCGA-43-6770 
       37.58        21.70       126.58        71.18        39.12        21.47 
TCGA-43-8116 TCGA-46-3769 TCGA-46-6026 TCGA-51-4081 TCGA-52-7809 TCGA-52-7810 
       11.77         4.44        13.91        29.95         5.46        30.35 
TCGA-56-5897 TCGA-56-7222 TCGA-56-7579 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       12.43        18.48        31.27        17.49        33.24        14.96 
TCGA-56-8622 TCGA-56-A4BX TCGA-56-A62T TCGA-58-8386 TCGA-58-8392 TCGA-58-A46L 
        1.81        13.32        14.47         0.03        16.47        56.65 
TCGA-60-2695 TCGA-60-2698 TCGA-60-2706 TCGA-60-2707 TCGA-60-2714 TCGA-60-2719 
       21.11        10.22        92.71        21.93        50.33        42.64 
TCGA-60-2726 TCGA-63-7023 TCGA-63-A5ML TCGA-63-A5MP TCGA-63-A5MS TCGA-66-2727 
       11.77        55.30        45.57        25.28        78.28        16.96 
TCGA-66-2753 TCGA-66-2766 TCGA-66-2777 TCGA-66-2781 TCGA-66-2783 TCGA-66-2792 
        1.02         1.02         2.01         3.98        24.95        30.02 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 TCGA-70-6723 TCGA-77-6845 
       54.08        49.05         2.73         6.64        12.33        23.28 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7463 TCGA-77-8128 TCGA-77-8143 
        0.49        73.22         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        66.51        65.49        60.53        36.36        61.94 
TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7843 TCGA-85-7950 
       41.39        40.24        36.53        34.95         1.15        18.94 
TCGA-85-8048 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8287 TCGA-85-8351 
       25.15        31.56        26.79        30.64         0.76        16.77 
TCGA-85-8353 TCGA-85-8355 TCGA-85-8584 TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4JC 
        3.09         2.01        12.59        18.08        30.28        19.86 
TCGA-85-A4QR TCGA-85-A512 TCGA-85-A53L TCGA-90-A4ED TCGA-92-7341 TCGA-94-8490 
       19.73        15.29        12.39        20.22         3.48         5.03 
TCGA-98-8021 TCGA-98-A53J TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 
       30.81        20.71        16.11        13.18        13.41        11.84 
TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
       64.54        57.30        13.74         4.21         2.89        49.28 
TCGA-NC-A5HP TCGA-O2-A52Q TCGA-XC-AA0X 
       25.32         3.72         0.20 

$`DEL PEAK 45(19Q13.32) WILD-TYPE`
TCGA-18-3407 TCGA-18-4083 TCGA-18-5595 TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 
        4.47         6.18        27.19        32.19        14.93        60.66 
TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 
       64.93        22.06       133.74         1.55        19.76        31.50 
TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7658 
       28.96        31.27        17.88        22.49        18.38        78.18 
TCGA-43-8118 TCGA-43-A56V TCGA-56-8201 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ 
        2.93        12.03        13.05        16.77        17.85        21.04 
TCGA-56-A5DR TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
        0.13        41.42         9.01        35.34        32.32        66.61 
TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GB TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 
        8.02        20.78        30.81         9.50        14.07        21.04 
TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5CT 
        2.76        21.21        19.10        76.80        39.85        65.65 
TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 
        0.43         8.58        75.75        23.54        92.15        36.07 
TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 
       92.42        86.96         2.79       154.32       119.54        46.88 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 
       99.16        70.16        15.58        31.73         9.34       119.80 
TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 
       43.23        31.63        88.11        41.69        33.93        10.82 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
       21.99         4.31         1.74        14.10        27.02        20.48 
TCGA-22-4593 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
       35.08         0.56        38.17        34.75        13.12        32.02 
TCGA-22-4609 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 
        9.57        63.55        14.63        44.25        86.30        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-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 
       16.64        79.53       173.82       103.53       151.27        54.44 
TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ 
       63.35         4.70         0.30        36.62       110.99       118.36 
TCGA-33-AASL TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
       27.16         2.63        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5928 TCGA-34-8454 TCGA-34-8455 
        9.07        60.30        50.66        39.32        38.79         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 
       26.43        33.90         4.01         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       133.25       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 
       36.39        68.38        55.56        17.06        40.21        38.66 
TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 
       33.11        27.91        22.98        24.89         5.46         3.81 
TCGA-43-7656 TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       19.59        13.38         9.73        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 
       13.02         9.83        10.65         0.39         0.39        28.34 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7223 
        8.75        27.45        28.96        18.25        21.90        14.53 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 TCGA-56-8083 TCGA-56-8304 
       30.41        19.76         6.51         0.10         4.93         3.48 
TCGA-56-8307 TCGA-56-8309 TCGA-56-8503 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 
       26.89        14.07         1.35        22.75        13.81        10.36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZK 
        9.93        20.25        15.81        20.94        19.23        18.74 
TCGA-56-A5DS TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 TCGA-58-8393 
        0.26        13.25        13.55        29.95        71.24        34.78 
TCGA-58-A46J TCGA-58-A46K TCGA-58-A46M TCGA-58-A46N TCGA-60-2697 TCGA-60-2703 
       85.12        34.36        35.24        29.92        12.23        96.82 
TCGA-60-2704 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2716 
       37.94        80.45        49.48        66.54        56.91        48.49 
TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-63-6202 
        3.19        29.85        35.90        23.57        26.83        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       70.13        70.42        68.15       102.67        70.62        58.65 
TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MT TCGA-63-A5MV 
       59.97        14.99        11.34        89.29        16.37        36.16 
TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 
       53.88        34.59        43.10         2.01        21.07         0.99 
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-66-2767 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-66-2778 TCGA-66-2780 TCGA-66-2782 TCGA-66-2785 
       19.00         3.02        19.00        12.03        12.00         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-66-2793 TCGA-66-2795 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J 
       10.06         4.01         6.94        13.35        16.18        14.73 
TCGA-70-6722 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-7138 TCGA-77-7139 
       12.07        29.56        73.12        75.09        11.18       140.09 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
       70.13       106.95        32.55         6.51        86.76        55.73 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
      156.66        12.59        53.92        39.09        17.72       104.09 
TCGA-77-8140 TCGA-77-8145 TCGA-77-8150 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       11.54         6.97        54.41       126.18       132.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 TCGA-85-6798 
       22.29         5.92        27.62        38.86         9.67         6.41 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 
       31.30        32.91         1.38        29.95        19.04        24.13 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8354 
       34.52        10.09        13.22        22.45         5.29        32.71 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8580 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4CN 
       15.39         7.76        36.59        38.14        22.59        34.13 
TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 
       30.97        24.36        30.48        27.16        16.21        15.85 
TCGA-85-A511 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 
       14.96        29.92         3.65        24.92         2.93        11.77 
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-94-8035 TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        4.01        26.63        14.14        17.69        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       17.46        27.68        21.44        30.67        21.34        27.16 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 
       18.15         2.01        27.02        20.32        18.58        12.89 
TCGA-NC-A5HF TCGA-NC-A5HH TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
        4.54         1.22        43.92        14.73        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
        3.65        33.07        12.72        43.89        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 
                         129.01                          173.82 
  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE 
                          19.36                           22.75 
[1] "0.0 - 129.0 (19.4)" "0.1 - 173.8 (22.8)"
[1] "hr=" "1"  
D75V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(19Q13.32) MUTATED         0       25       48        1        25
  DEL PEAK 45(19Q13.32) WILD-TYPE       2       64      104        1        40
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(19Q13.32) MUTATED          26         1         16          4
  DEL PEAK 45(19Q13.32) WILD-TYPE        69         2         47         15
                                 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                              25                              64
  STAGE IB                              48                             104
  STAGE II                               1                               1
  STAGE IIA                             25                              40
  STAGE IIB                             26                              69
  STAGE III                              1                               2
  STAGE IIIA                            16                              47
  STAGE IIIB                             4                              15
  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    32  88  23   6
  DEL PEAK 45(19Q13.32) WILD-TYPE  80 206  48  18
D75V4, multiclass
    clus
vv   DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  T1                            32                              80
  T2                            88                             206
  T3                            23                              48
  T4                             6                              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    99  34  12   1
  DEL PEAK 45(19Q13.32) WILD-TYPE 218  99  28   4
D75V5, multiclass
    clus
vv   DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  N0                            99                             218
  N1                            34                              99
  N2                            12                              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   126   2
  DEL PEAK 45(19Q13.32) WILD-TYPE 285   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.32) MUTATED    126    2
  DEL PEAK 45(19Q13.32) WILD-TYPE  285    5
   clus
vv  DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  0                           126                             285
  1                             2                               5
[1] 2 2
[1] FALSE
D75V7, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.32) MUTATED    31 118
  DEL PEAK 45(19Q13.32) WILD-TYPE  99 253
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.32) MUTATED     31  118
  DEL PEAK 45(19Q13.32) WILD-TYPE   99  253
        clus
vv       DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  FEMALE                            31                              99
  MALE                             118                             253
[1] 2 2
[1] FALSE
D75V8, binary
                                 cls
clus                                0   1
  DEL PEAK 45(19Q13.32) MUTATED   108  22
  DEL PEAK 45(19Q13.32) WILD-TYPE 276  31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.32) MUTATED    108   22
  DEL PEAK 45(19Q13.32) WILD-TYPE  276   31
     clus
vv    DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  NO                            108                             276
  YES                            22                              31
[1] 2 2
[1] FALSE
D75V9, 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 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                                                           139
  DEL PEAK 45(19Q13.32) WILD-TYPE                                                         340
D75V10, multiclass
                                                             clus
vv                                                            DEL PEAK 45(19Q13.32) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           139
                                                             clus
vv                                                            DEL PEAK 45(19Q13.32) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                     7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             340
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, continuous
D75V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 45(19Q13.32) MUTATED   111   4   2  10
  DEL PEAK 45(19Q13.32) WILD-TYPE 288   8   2  13
D75V13, multiclass
    clus
vv   DEL PEAK 45(19Q13.32) MUTATED DEL PEAK 45(19Q13.32) WILD-TYPE
  R0                           111                             288
  R1                             4                               8
  R2                             2                               2
  RX                            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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(19Q13.32) MUTATED       2                        11   105
  DEL PEAK 45(19Q13.32) WILD-TYPE     7                        20   244
D75V14, multiclass
                           clus
vv                          DEL PEAK 45(19Q13.32) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               105
                           clus
vv                          DEL PEAK 45(19Q13.32) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              20
  WHITE                                                 244
[1] 3 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  94
  DEL PEAK 45(19Q13.32) WILD-TYPE   6 223
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(19Q13.32) MUTATED      2   94
  DEL PEAK 45(19Q13.32) WILD-TYPE    6  223
                        clus
vv                       DEL PEAK 45(19Q13.32) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            94
                        clus
vv                       DEL PEAK 45(19Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             223
[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   134 107
  DEL PEAK 46(21Q11.2) WILD-TYPE 146 107
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           241                            253 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           107                            107 
$`DEL PEAK 46(21Q11.2) MUTATED`
TCGA-18-3416 TCGA-22-1017 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 TCGA-33-6737 
       31.99        48.82        22.06       129.01         1.55        19.76 
TCGA-34-2604 TCGA-39-5039 TCGA-43-5668 TCGA-43-A56V TCGA-56-8305 TCGA-56-A4ZJ 
       31.50        17.88        18.38        12.03         3.45        21.04 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-77-7140 
       41.42         9.01        35.34        32.32         8.02        20.78 
TCGA-90-7766 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-A539 
        9.50         0.16        18.38        16.14        19.36         5.69 
TCGA-NC-A5HD TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3408 
        0.07        39.85        65.65        16.80         8.58        75.75 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-4721 TCGA-21-1070 TCGA-21-1072 
       11.34        23.54        92.15       154.32       119.54        99.16 
TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
       70.16        60.89        31.73        43.23        33.93        10.82 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1002 TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 
       21.99         7.33         4.31        14.10        27.02        20.48 
TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 
       35.08        48.33        38.17        11.77        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        86.30        71.34        79.20        11.74 
TCGA-22-5483 TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 TCGA-33-4587 
       18.84        56.32        97.94        79.53        14.07        54.44 
TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-5231 
       36.62         6.94        44.19        27.16         2.63        65.23 
TCGA-34-5234 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 
       74.66        44.75        39.32         1.12         4.04        26.43 
TCGA-37-3792 TCGA-37-4130 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5016 
        0.39         8.12         3.39        37.58        21.70       126.58 
TCGA-39-5019 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 
      111.35        24.33        60.53        36.39        71.18        55.56 
TCGA-43-3920 TCGA-43-6771 TCGA-43-7656 TCGA-46-3766 TCGA-46-3768 TCGA-46-3769 
       33.11         5.46        19.59        12.16         9.83         4.44 
TCGA-46-6026 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 
       13.91         0.39        29.95        28.34         5.46        30.35 
TCGA-56-5897 TCGA-56-5898 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       12.43        18.25        18.48        14.53        31.27        30.41 
TCGA-56-7582 TCGA-56-7822 TCGA-56-8082 TCGA-56-8083 TCGA-56-8503 TCGA-56-8629 
       19.76        17.49        14.96         4.93         1.35        15.81 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 
       20.94        13.32        14.47         0.03        13.25        13.55 
TCGA-58-8390 TCGA-58-8392 TCGA-60-2703 TCGA-60-2707 TCGA-60-2719 TCGA-60-2723 
       29.95        16.47        96.82        21.93        42.64        35.90 
TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 
       26.83        11.77        52.67        70.13        70.42        55.30 
TCGA-63-A5MB TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS 
      102.67        59.97        45.57        11.34        25.28        78.28 
TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 
       36.16        53.88        34.59        43.10        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-66-2766 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 
        0.99         2.01         1.02        19.00         2.01        12.03 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-66-2788 TCGA-66-2791 TCGA-66-2792 
        3.98        12.00        25.97        22.98         5.03        30.02 
TCGA-66-2793 TCGA-66-2795 TCGA-68-7755 TCGA-68-7756 TCGA-68-8251 TCGA-70-6723 
       10.06         4.01         2.73         6.64        13.35        12.33 
TCGA-77-6842 TCGA-77-7138 TCGA-77-7335 TCGA-77-7463 TCGA-77-7465 TCGA-77-8008 
       29.56        11.18        70.13        46.78        32.55        86.76 
TCGA-77-8128 TCGA-77-8136 TCGA-77-8140 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       37.81        39.09        11.54         6.97        66.51        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5GF 
       65.49        60.53        36.36       150.25        22.29        27.62 
TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7843 
       38.86        41.39         6.41        36.53        31.30         1.15 
TCGA-85-8048 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8350 
       25.15        31.56        26.79        34.52         0.76        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8664 
       16.77         5.29        32.71         2.01         7.76        18.08 
TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50Z 
       22.59        30.28        34.13        19.86        19.73        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
       15.85        14.96        12.39         3.65         2.93        11.77 
TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 TCGA-94-8490 TCGA-94-8491 
       20.22        22.62         3.48         5.26         5.03        26.63 
TCGA-94-A5I6 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53I 
       17.69        30.81        30.67        21.34        27.16        18.58 
TCGA-98-A53J TCGA-L3-A524 TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HP 
       20.71        16.11         1.22        13.74         4.21        25.32 
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-A52V 
       43.89 

$`DEL PEAK 46(21Q11.2) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-18-5595 
       12.20         4.47       123.19         4.80         6.18        27.19 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-5471 TCGA-22-5472 TCGA-33-4533 TCGA-34-2605 
       32.19        14.93        60.66        64.93       133.74        28.96 
TCGA-34-2609 TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 
       31.27        22.49         7.76        78.18         2.93        11.61 
TCGA-56-7221 TCGA-56-8201 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A5DR 
       19.99        13.05        17.00        16.77        17.85         0.13 
TCGA-60-2696 TCGA-63-A5MH TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 
        3.58        66.61        42.08        30.81        14.07        21.04 
TCGA-96-7545 TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HE TCGA-NC-A5HR 
       57.07         2.76        21.21        19.10        76.80        40.90 
TCGA-NK-A7XE TCGA-18-3411 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 
        0.43       117.57        36.07        92.42        86.96         2.79 
TCGA-18-5592 TCGA-21-1071 TCGA-21-1077 TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 
       49.94        46.88        34.78        15.58       122.43         9.34 
TCGA-21-1082 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-22-1005 TCGA-22-1011 
      119.80        31.63        88.11        41.69        64.21         1.74 
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-22-4609 TCGA-22-5485 TCGA-22-5489 TCGA-22-5492 TCGA-33-4566 TCGA-33-4582 
        9.57        30.12        62.86        16.64       173.82       103.53 
TCGA-33-4583 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASJ 
      151.27        63.35         4.70         0.30       110.99       118.36 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5232 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       61.61        32.88        81.24         9.07        60.30        50.66 
TCGA-34-5241 TCGA-34-5929 TCGA-34-8454 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 
       16.93         4.96        38.79        33.90         4.01         0.43 
TCGA-37-4129 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 
        7.96         7.46         7.82         6.81         0.39       133.25 
TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5030 
       68.58        55.20        82.52       102.18         1.71         1.94 
TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 
       68.38        17.06        40.21        38.66        39.12        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-8115 TCGA-43-8116 
       22.98        24.89        21.47         3.81        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3767 TCGA-46-6025 TCGA-51-4079 
        9.73        14.20        13.32        13.02        10.65         0.39 
TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 TCGA-56-6545 TCGA-56-7730 TCGA-56-7731 
        8.75        27.45        28.96        21.90         6.51         0.10 
TCGA-56-7823 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 
       33.24         3.48        26.89        14.07         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A4BW TCGA-56-A4ZK 
       13.81        10.36         9.93        20.25        19.23        18.74 
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-60-2697 TCGA-60-2698 TCGA-60-2704 
       35.24        29.92        21.11        12.23        10.22        37.94 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 
       92.71        80.45        49.48        66.54        56.91        50.33 
TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2724 TCGA-63-7022 TCGA-63-A5MG 
       48.49         3.19        29.85        23.57        68.15        70.62 
TCGA-63-A5MI TCGA-63-A5MM TCGA-63-A5MR TCGA-63-A5MT TCGA-66-2727 TCGA-66-2737 
       58.65        14.99        89.29        16.37        16.96         2.01 
TCGA-66-2756 TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 
        0.99         2.01         2.01         7.07        23.01         3.02 
TCGA-66-2778 TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2789 TCGA-66-2790 
       19.00        24.95         1.97        40.01         4.04        22.98 
TCGA-66-2794 TCGA-66-2800 TCGA-68-7757 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
       54.08        49.05         6.94        16.18        14.73        12.07 
TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
       73.12        75.09        23.28       140.09         0.49        73.22 
TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8009 TCGA-77-8130 TCGA-77-8131 
      106.95         0.16         6.51        55.73       156.66        12.59 
TCGA-77-8133 TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 TCGA-77-8144 TCGA-77-A5FZ 
       53.92        17.72       104.09        26.40        27.39       126.18 
TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-85-6175 TCGA-85-6561 TCGA-85-7697 
      132.36         5.92        61.94         9.67        40.24        34.95 
TCGA-85-7699 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8049 TCGA-85-8052 
       32.91         1.38        29.95        18.94        19.04        24.13 
TCGA-85-8072 TCGA-85-8277 TCGA-85-8288 TCGA-85-8353 TCGA-85-8479 TCGA-85-8580 
       30.64        10.09        13.22         3.09        15.39        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M 
       38.14        12.59        30.97        24.36        30.48        27.16 
TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 
       15.29        29.92        24.92        10.59         2.70         4.01 
TCGA-92-8065 TCGA-94-8035 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 
        2.30         4.01        14.14        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H 
       27.68        21.44        18.15         2.01        27.02        20.32 
TCGA-L3-A4E7 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HF TCGA-NC-A5HG 
       12.89        13.18        13.41        11.84         4.54        64.54 
TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO TCGA-NC-A5HT TCGA-O2-A5IB 
       57.30         2.89        49.28        43.92        26.43        11.18 
TCGA-XC-AA0X 
        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                         173.82 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                         21.07                          22.75 
[1] "0.0 - 154.3 (21.1)" "0.1 - 173.8 (22.8)"
[1] "hr=" "1.2"
D76V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(21Q11.2) MUTATED         2       43       69        2        39
  DEL PEAK 46(21Q11.2) WILD-TYPE       0       46       83        0        26
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(21Q11.2) MUTATED          44         2         28          7
  DEL PEAK 46(21Q11.2) WILD-TYPE        51         1         35         12
                                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                             46
  STAGE IB                             69                             83
  STAGE II                              2                              0
  STAGE IIA                            39                             26
  STAGE IIB                            44                             51
  STAGE III                             2                              1
  STAGE IIIA                           28                             35
  STAGE IIIB                            7                             12
  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    54 145  34  11
  DEL PEAK 46(21Q11.2) WILD-TYPE  58 149  37  13
D76V4, multiclass
    clus
vv   DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  T1                           54                             58
  T2                          145                            149
  T3                           34                             37
  T4                           11                             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   154  68  19   1
  DEL PEAK 46(21Q11.2) WILD-TYPE 163  65  21   4
D76V5, multiclass
    clus
vv   DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  N0                          154                            163
  N1                           68                             65
  N2                           19                             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   204   5
  DEL PEAK 46(21Q11.2) WILD-TYPE 207   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED    204    5
  DEL PEAK 46(21Q11.2) WILD-TYPE  207    2
   clus
vv  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  0                          204                            207
  1                            5                              2
[1] 2 2
[1] FALSE
D76V7, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED    51 193
  DEL PEAK 46(21Q11.2) WILD-TYPE  79 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED     51  193
  DEL PEAK 46(21Q11.2) WILD-TYPE   79  178
        clus
vv       DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  FEMALE                           51                             79
  MALE                            193                            178
[1] 2 2
[1] FALSE
D76V8, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED   190  23
  DEL PEAK 46(21Q11.2) WILD-TYPE 194  30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED    190   23
  DEL PEAK 46(21Q11.2) WILD-TYPE  194   30
     clus
vv    DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  NO                           190                            194
  YES                           23                             30
[1] 2 2
[1] FALSE
D76V9, 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 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                                                           235
  DEL PEAK 46(21Q11.2) WILD-TYPE                                                         244
D76V10, multiclass
                                                             clus
vv                                                            DEL PEAK 46(21Q11.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          235
                                                             clus
vv                                                            DEL PEAK 46(21Q11.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   4
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            244
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, continuous
D76V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 46(21Q11.2) MUTATED   196   5   1   9
  DEL PEAK 46(21Q11.2) WILD-TYPE 203   7   3  14
D76V13, multiclass
    clus
vv   DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  R0                          196                            203
  R1                            5                              7
  R2                            1                              3
  RX                            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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(21Q11.2) MUTATED       3                        14   166
  DEL PEAK 46(21Q11.2) WILD-TYPE     6                        17   183
D76V14, multiclass
                           clus
vv                          DEL PEAK 46(21Q11.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              166
                           clus
vv                          DEL PEAK 46(21Q11.2) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             17
  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"
D76V15, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED     6 148
  DEL PEAK 46(21Q11.2) WILD-TYPE   2 169
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED      6  148
  DEL PEAK 46(21Q11.2) WILD-TYPE    2  169
                        clus
vv                       DEL PEAK 46(21Q11.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          148
                        clus
vv                       DEL PEAK 46(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            169
[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   159 117
  DEL PEAK 47(21Q22.3) WILD-TYPE 121  97
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                           276                            218 
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                           117                             97 
$`DEL PEAK 47(21Q22.3) MUTATED`
TCGA-18-3416 TCGA-18-4083 TCGA-22-1017 TCGA-22-5471 TCGA-33-4532 TCGA-33-4589 
       31.99         6.18        48.82        60.66       129.01         1.55 
TCGA-34-2604 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 
       31.50        28.96        17.88        22.49        18.38         7.76 
TCGA-43-8118 TCGA-43-A56V TCGA-56-8201 TCGA-56-8305 TCGA-56-A4ZJ TCGA-60-2711 
        2.93        12.03        13.05         3.45        21.04        41.42 
TCGA-60-2712 TCGA-60-2715 TCGA-60-2721 TCGA-68-8250 TCGA-90-7766 TCGA-94-7033 
        9.01        35.34        32.32         8.02         9.50        21.04 
TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-A539 TCGA-NC-A5HD 
        0.16        18.38        16.14        19.36         5.69         0.07 
TCGA-NC-A5HE TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3408 
       76.80        39.85        65.65        16.80         8.58        75.75 
TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-4086 
      117.57        11.34        23.54        92.15        36.07         2.79 
TCGA-18-4721 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1079 
      154.32       119.54        99.16        70.16        60.89        31.73 
TCGA-21-1083 TCGA-21-5783 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 
       43.23        88.11        33.93        10.82         7.33         4.31 
TCGA-22-1012 TCGA-22-1016 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4599 
       14.10        27.02        20.48        35.08        48.33        38.17 
TCGA-22-4604 TCGA-22-4609 TCGA-22-4613 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
       13.12         9.57        11.77        63.55        14.63        44.25 
TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 TCGA-22-5491 
        0.79        86.30        71.34        11.74        18.84        56.32 
TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4586 TCGA-33-AAS8 
       16.64        97.94        79.53       103.53        14.07        36.62 
TCGA-33-AASI TCGA-33-AASL TCGA-34-2608 TCGA-34-5236 TCGA-34-5241 TCGA-34-5927 
       44.19        27.16        32.88         9.07        16.93        44.75 
TCGA-34-5928 TCGA-34-7107 TCGA-34-8455 TCGA-34-8456 TCGA-37-3789 TCGA-37-3792 
       39.32         1.12         4.04        26.43         0.43         0.39 
TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN 
        8.12         7.82         6.81         3.39        37.58        21.70 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5027 TCGA-39-5029 TCGA-39-5031 TCGA-39-5034 
      126.58       111.35       102.18        24.33        60.53        36.39 
TCGA-39-5036 TCGA-39-5037 TCGA-43-2576 TCGA-43-3920 TCGA-43-6647 TCGA-43-6771 
       71.18        55.56        40.21        33.11        24.89         5.46 
TCGA-43-7656 TCGA-43-8116 TCGA-46-3766 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 
       19.59        11.77        12.16         4.44        10.65        13.91 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-56-1622 
        0.39        29.95        28.34         5.46        30.35        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 
       12.43        18.25        21.90        18.48        14.53        31.27 
TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7822 TCGA-56-7823 TCGA-56-8082 
       30.41        19.76         6.51        17.49        33.24        14.96 
TCGA-56-8083 TCGA-56-8503 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX 
        4.93         1.35        15.81        20.94        19.23        13.32 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 
       14.47         0.03        13.25        13.55        29.95        16.47 
TCGA-58-A46K TCGA-60-2698 TCGA-60-2703 TCGA-60-2707 TCGA-60-2708 TCGA-60-2713 
       34.36        10.22        96.82        21.93        80.45        56.91 
TCGA-60-2719 TCGA-60-2722 TCGA-60-2723 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
       42.64        29.85        35.90        26.83        11.77        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MI TCGA-63-A5ML 
       70.13        70.42        55.30       102.67        58.65        45.57 
TCGA-63-A5MN TCGA-63-A5MP TCGA-63-A5MS TCGA-63-A5MV TCGA-63-A5MW TCGA-63-A5MY 
       11.34        25.28        78.28        36.16        53.88        34.59 
TCGA-66-2727 TCGA-66-2734 TCGA-66-2742 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
       16.96        43.10        21.07         1.02         2.01         0.92 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
       21.01        25.05         0.99         2.01         1.02         2.01 
TCGA-66-2769 TCGA-66-2771 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 
        7.07        19.00         2.01        12.03         3.98        12.00 
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-68-8251 TCGA-70-6723 TCGA-77-6842 TCGA-77-7141 TCGA-77-7335 TCGA-77-7463 
       13.35        12.33        29.56         0.49        70.13        46.78 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 
       86.76        55.73        37.81         6.97        66.51        54.41 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
       65.49        60.53        36.36       150.25        22.29         5.92 
TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
       27.62        38.86        40.24         6.41        36.53        31.30 
TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 
        1.15        25.15        19.04        31.56        26.79        34.52 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 
        0.76        22.45        16.77         5.29        32.71         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       15.39         7.76        18.08        22.59        30.28        34.13 
TCGA-85-A4JC TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L 
       19.86        19.73        16.21        15.85        14.96        12.39 
TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-92-7341 TCGA-92-8064 
        3.65        11.77        20.22        22.62         3.48         5.26 
TCGA-94-8491 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
       26.63        14.14        17.69        30.81        30.67        21.34 
TCGA-98-A538 TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 
       27.16        18.58        20.71        12.89        16.11        13.18 
TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ 
        1.22        13.74         4.21        49.28        25.32        14.73 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB 
       83.57         3.65         3.72        12.72        43.89        11.18 

$`DEL PEAK 47(21Q22.3) WILD-TYPE`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-21-A5DI 
       12.20         4.47       123.19         4.80        27.19        32.19 
TCGA-22-1000 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-6737 TCGA-34-2609 
       14.93        64.93        22.06       133.74        19.76        31.27 
TCGA-43-7658 TCGA-43-A474 TCGA-56-7221 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY 
       78.18        11.61        19.99        17.00        16.77        17.85 
TCGA-56-A5DR TCGA-60-2696 TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
        0.13         3.58        66.61        20.78        42.08        30.81 
TCGA-90-7964 TCGA-96-7545 TCGA-98-8020 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HR 
       14.07        57.07         2.76        21.21        19.10        40.90 
TCGA-NK-A7XE TCGA-18-3419 TCGA-18-3421 TCGA-18-5592 TCGA-21-1071 TCGA-21-1077 
        0.43        92.42        86.96        49.94        46.88        34.78 
TCGA-21-1078 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 
       15.58       122.43         9.34       119.80        31.63        41.69 
TCGA-22-0940 TCGA-22-1005 TCGA-22-1011 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 
       21.99        64.21         1.74        24.13         0.56        34.75 
TCGA-22-4605 TCGA-22-4607 TCGA-22-5481 TCGA-22-5485 TCGA-22-5489 TCGA-33-4566 
       32.02        19.30        79.20        30.12        62.86       173.82 
TCGA-33-4583 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASB 
      151.27        54.44        63.35         4.70         0.30         6.94 
TCGA-33-AASD TCGA-33-AASJ TCGA-34-2596 TCGA-34-2600 TCGA-34-5231 TCGA-34-5232 
      110.99       118.36         2.63        61.61        65.23        81.24 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5929 TCGA-34-8454 TCGA-34-A5IX 
       74.66        60.30        50.66         4.96        38.79        33.90 
TCGA-37-3783 TCGA-37-4129 TCGA-37-4132 TCGA-37-4141 TCGA-39-5011 TCGA-39-5021 
        4.01         7.96         7.46         0.39       133.25        68.58 
TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5035 TCGA-39-5040 
       55.20        82.52         1.71         1.94        68.38        17.06 
TCGA-43-2581 TCGA-43-3394 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 TCGA-43-6773 
       38.66        39.12        27.91        22.98        21.47         3.81 
TCGA-43-8115 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3767 TCGA-46-3768 
       13.38         9.73        14.20        13.32        13.02         9.83 
TCGA-51-4079 TCGA-52-7811 TCGA-52-7812 TCGA-56-7731 TCGA-56-8304 TCGA-56-8307 
        0.39         8.75        27.45         0.10         3.48        26.89 
TCGA-56-8309 TCGA-56-8622 TCGA-56-8623 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 
       14.07         1.81        22.75        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
       20.25        18.74         0.26        71.24        34.78        85.12 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2704 
       56.65        35.24        29.92        21.11        12.23        37.94 
TCGA-60-2706 TCGA-60-2709 TCGA-60-2710 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 
       92.71        49.48        66.54        50.33        48.49         3.19 
TCGA-60-2724 TCGA-63-7022 TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MR 
       23.57        68.15        70.62        59.97        14.99        89.29 
TCGA-63-A5MT TCGA-66-2737 TCGA-66-2744 TCGA-66-2756 TCGA-66-2757 TCGA-66-2768 
       16.37         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-70-6722 TCGA-77-6843 TCGA-77-6844 
        6.94        16.18        14.73        12.07        73.12        75.09 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7142 TCGA-77-7337 TCGA-77-7338 
       23.28        11.18       140.09        73.22       106.95         0.16 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       32.55         6.51       156.66        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-85-6175 TCGA-85-6560 TCGA-85-7697 TCGA-85-7699 
      132.36        61.94         9.67        41.39        34.95        32.91 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8072 TCGA-85-8277 
        1.38        29.95        18.94        24.13        30.64        10.09 
TCGA-85-8288 TCGA-85-8353 TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-A4JB 
       13.22         3.09        36.59        38.14        12.59        30.97 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A512 TCGA-85-A513 TCGA-90-6837 
       24.36        30.48        27.16        15.29        29.92        24.92 
TCGA-90-7767 TCGA-90-A59Q TCGA-92-7340 TCGA-92-8063 TCGA-92-8065 TCGA-94-8035 
        2.93        10.59         2.70         4.01         2.30         4.01 
TCGA-94-8490 TCGA-96-7544 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
        5.03        71.01        18.31        17.46        27.68        21.44 
TCGA-98-A53A TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-LA-A7SW TCGA-MF-A522 
       18.15         2.01        27.02        20.32        13.41        11.84 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HT 
        4.54        64.54        57.30         2.89        43.92        26.43 
TCGA-O2-A52N TCGA-XC-AA0X 
       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                         173.82 
  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE 
                        20.975                         23.425 
[1] "0.0 - 154.3 (21.0)" "0.1 - 173.8 (23.4)"
[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       86        2        40
  DEL PEAK 47(21Q22.3) WILD-TYPE       1       38       66        0        25
                                vv
clus                             STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(21Q22.3) MUTATED          46         3         32         11
  DEL PEAK 47(21Q22.3) WILD-TYPE        49         0         31          8
                                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                             38
  STAGE IB                             86                             66
  STAGE II                              2                              0
  STAGE IIA                            40                             25
  STAGE IIB                            46                             49
  STAGE III                             3                              0
  STAGE IIIA                           32                             31
  STAGE IIIB                           11                              8
  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    61 170  35  15
  DEL PEAK 47(21Q22.3) WILD-TYPE  51 124  36   9
D77V4, multiclass
    clus
vv   DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  T1                           61                             51
  T2                          170                            124
  T3                           35                             36
  T4                           15                              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   181  72  23   2
  DEL PEAK 47(21Q22.3) WILD-TYPE 136  61  17   3
D77V5, multiclass
    clus
vv   DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  N0                          181                            136
  N1                           72                             61
  N2                           23                             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   236   6
  DEL PEAK 47(21Q22.3) WILD-TYPE 175   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q22.3) MUTATED    236    6
  DEL PEAK 47(21Q22.3) WILD-TYPE  175    1
   clus
vv  DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  0                          236                            175
  1                            6                              1
[1] 2 2
[1] FALSE
D77V7, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q22.3) MUTATED    58 223
  DEL PEAK 47(21Q22.3) WILD-TYPE  72 148
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q22.3) MUTATED     58  223
  DEL PEAK 47(21Q22.3) WILD-TYPE   72  148
        clus
vv       DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  FEMALE                           58                             72
  MALE                            223                            148
[1] 2 2
[1] FALSE
D77V8, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q22.3) MUTATED   214  29
  DEL PEAK 47(21Q22.3) WILD-TYPE 170  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q22.3) MUTATED    214   29
  DEL PEAK 47(21Q22.3) WILD-TYPE  170   24
     clus
vv    DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  NO                           214                            170
  YES                           29                             24
[1] 2 2
[1] FALSE
D77V9, 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 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                                                           271
  DEL PEAK 47(21Q22.3) WILD-TYPE                                                         208
D77V10, multiclass
                                                             clus
vv                                                            DEL PEAK 47(21Q22.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                 3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          271
                                                             clus
vv                                                            DEL PEAK 47(21Q22.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                   3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                  1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            208
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, continuous
D77V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 47(21Q22.3) MUTATED   222   7   2  12
  DEL PEAK 47(21Q22.3) WILD-TYPE 177   5   2  11
D77V13, multiclass
    clus
vv   DEL PEAK 47(21Q22.3) MUTATED DEL PEAK 47(21Q22.3) WILD-TYPE
  R0                          222                            177
  R1                            7                              5
  R2                            2                              2
  RX                           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                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 47(21Q22.3) MUTATED       3                        14   194
  DEL PEAK 47(21Q22.3) WILD-TYPE     6                        17   155
D77V14, multiclass
                           clus
vv                          DEL PEAK 47(21Q22.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              194
                           clus
vv                          DEL PEAK 47(21Q22.3) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             17
  WHITE                                                155
[1] 3 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     6 172
  DEL PEAK 47(21Q22.3) WILD-TYPE   2 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q22.3) MUTATED      6  172
  DEL PEAK 47(21Q22.3) WILD-TYPE    2  145
                        clus
vv                       DEL PEAK 47(21Q22.3) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          172
                        clus
vv                       DEL PEAK 47(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            145
[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    51  43
  DEL PEAK 48(22Q11.21) WILD-TYPE 229 171
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                             94                             400 
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                             43                             171 
$`DEL PEAK 48(22Q11.21) MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI TCGA-22-5471 TCGA-22-A5C4 
        4.47        31.99         6.18        32.19        60.66        22.06 
TCGA-33-6737 TCGA-43-2578 TCGA-43-A56V TCGA-68-8250 TCGA-NC-A5HE TCGA-NC-A5HM 
       19.76        22.49        12.03         8.02        76.80        39.85 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3417 TCGA-21-1071 TCGA-21-1080 
       65.65        16.80         8.58        36.07        46.88       122.43 
TCGA-21-5787 TCGA-22-0940 TCGA-22-1016 TCGA-22-4594 TCGA-22-4601 TCGA-22-5480 
       10.82        21.99        27.02        48.33        34.75        71.34 
TCGA-33-4583 TCGA-33-4587 TCGA-33-AAS8 TCGA-33-AASB TCGA-33-AASL TCGA-37-3792 
      151.27        54.44        36.62         6.94        27.16         0.39 
TCGA-37-4129 TCGA-37-4132 TCGA-37-A5EL TCGA-39-5011 TCGA-39-5016 TCGA-39-5035 
        7.96         7.46        37.58       133.25       126.58        68.38 
TCGA-39-5040 TCGA-43-2581 TCGA-43-6771 TCGA-43-7656 TCGA-46-3765 TCGA-52-7812 
       17.06        38.66         5.46        19.59        13.32        27.45 
TCGA-56-7222 TCGA-56-7823 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-58-A46M 
       18.48        33.24         3.48        26.89        14.07        35.24 
TCGA-60-2698 TCGA-63-6202 TCGA-63-A5MN TCGA-63-A5MP TCGA-66-2727 TCGA-66-2753 
       10.22        52.67        11.34        25.28        16.96         1.02 
TCGA-66-2754 TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2771 
        2.01        43.99        21.01        25.05         1.02        19.00 
TCGA-66-2778 TCGA-66-2782 TCGA-66-2785 TCGA-66-2790 TCGA-66-2793 TCGA-66-2795 
       19.00        12.00         1.97        22.98        10.06         4.01 
TCGA-68-A59I TCGA-77-6843 TCGA-77-7138 TCGA-77-8139 TCGA-77-8150 TCGA-85-6560 
       16.18        73.12        11.18       104.09        54.41        41.39 
TCGA-85-8049 TCGA-85-8072 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
       19.04        30.64        12.59        18.08        22.59        30.28 
TCGA-85-A53L TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 
       12.39        20.22        22.62        10.59         4.01         2.30 
TCGA-94-8035 TCGA-98-7454 TCGA-98-8023 TCGA-98-A53B TCGA-MF-A522 TCGA-NC-A5HJ 
        4.01        21.44        21.34         2.01        11.84        13.74 
TCGA-NC-A5HL TCGA-NC-A5HO TCGA-NC-A5HQ TCGA-NK-A5CX 
        2.89        43.92        14.73         3.65 

$`DEL PEAK 48(22Q11.21) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-5595 TCGA-22-1000 TCGA-22-1017 
       12.20       123.19         4.80        27.19        14.93        48.82 
TCGA-22-5472 TCGA-33-4532 TCGA-33-4533 TCGA-33-4589 TCGA-34-2604 TCGA-34-2605 
       64.93       129.01       133.74         1.55        31.50        28.96 
TCGA-34-2609 TCGA-39-5039 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 
       31.27        17.88        18.38         7.76        78.18         2.93 
TCGA-43-A474 TCGA-56-7221 TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
       11.61        19.99        13.05         3.45        17.00        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 
       17.85        21.04         0.13         3.58        41.42         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB 
       35.34        32.32        66.61        20.78        42.08        30.81 
TCGA-90-7766 TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 
        9.50        14.07        21.04         0.16        18.38        16.14 
TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH 
       57.07        19.36         2.76         5.69        21.21        19.10 
TCGA-NC-A5HD TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 
        0.07        40.90         0.43        75.75       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        92.42        86.96         2.79       154.32 
TCGA-18-5592 TCGA-21-1070 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
       49.94       119.54        99.16        70.16        60.89        34.78 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 TCGA-21-5782 
       15.58        31.73         9.34       119.80        43.23        31.63 
TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 
       88.11        41.69        33.93         7.33         4.31        64.21 
TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 TCGA-22-4596 
        1.74        14.10        20.48        35.08        24.13         0.56 
TCGA-22-4599 TCGA-22-4604 TCGA-22-4605 TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 
       38.17        13.12        32.02        19.30         9.57        11.77 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 
       63.55        14.63        44.25         0.79        86.30        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-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 
       97.94        79.53       173.82       103.53        14.07        63.35 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AASD TCGA-33-AASI TCGA-33-AASJ TCGA-34-2596 
        4.70         0.30       110.99        44.19       118.36         2.63 
TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 
       61.61        32.88        65.23        81.24        74.66         9.07 
TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 
       60.30        50.66        16.93        44.75        39.32         4.96 
TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 
        1.12        38.79         4.04        26.43        33.90         4.01 
TCGA-37-3789 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
        0.43         8.12         7.82         6.81         0.39         3.39 
TCGA-37-A5EN TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5027 
       21.70       111.35        68.58        55.20        82.52       102.18 
TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5036 
        1.71        24.33         1.94        60.53        36.39        71.18 
TCGA-39-5037 TCGA-43-2576 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 TCGA-43-6143 
       55.56        40.21        39.12        33.11        27.91        22.98 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 
       24.89        21.47         3.81        13.38        11.77         9.73 
TCGA-43-A56U TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 
       14.20        12.16        13.02         9.83         4.44        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        12.43        18.25        21.90 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       14.53        31.27        30.41        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-8082 TCGA-56-8083 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
       17.49        14.96         4.93         1.35         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
       13.81        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       19.23        13.32        18.74         0.26        14.47         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-A46N TCGA-60-2695 TCGA-60-2697 
       85.12        34.36        56.65        29.92        21.11        12.23 
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-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       66.54        56.91        50.33        48.49        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 
       29.85        35.90        23.57        26.83        11.77        70.13 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       70.42        68.15        55.30       102.67        70.62        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-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-66-2755 TCGA-66-2756 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 
        0.99         0.92         0.99         0.99         2.01         2.01 
TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2780 
        2.01         7.07        23.01         3.02         2.01        12.03 
TCGA-66-2781 TCGA-66-2783 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
        3.98        24.95        25.97        40.01        22.98         4.04 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2800 TCGA-68-7755 TCGA-68-7756 
        5.03        30.02        54.08        49.05         2.73         6.64 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 
        6.94        13.35        14.73        12.07        12.33        29.56 
TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 TCGA-77-7335 
       75.09        23.28       140.09         0.49        73.22        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        32.55         6.51        86.76 
TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 
       55.73        37.81       156.66        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        66.51 
TCGA-77-8153 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 
       65.49        60.53        36.36       126.18       132.36       150.25 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       22.29         5.92        61.94        27.62        38.86         9.67 
TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 
       40.24         6.41        36.53        34.95        31.30        32.91 
TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 TCGA-85-8052 
        1.38         1.15        29.95        18.94        25.15        24.13 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 
       31.56        26.79        34.52        10.09         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-A4CN TCGA-85-A4JB 
       15.39         7.76        36.59        38.14        34.13        30.97 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M TCGA-85-A50Z 
       19.86        24.36        30.48        19.73        27.16        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 TCGA-90-6837 
       15.85        14.96        15.29        29.92         3.65        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 TCGA-94-8490 
        2.93        11.77         2.70         3.48         5.26         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        71.01        18.31        17.46 
TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-98-A538 TCGA-98-A53A TCGA-98-A53C 
       27.68        30.81        30.67        27.16        18.15        27.02 
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-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI TCGA-NC-A5HK 
       13.41         4.54        64.54         1.22        57.30         4.21 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR TCGA-O2-A52N TCGA-O2-A52Q 
       49.28        25.32        26.43        83.57        33.07         3.72 
TCGA-O2-A52S TCGA-O2-A52V TCGA-O2-A5IB TCGA-XC-AA0X 
       12.72        43.89        11.18         0.20 

  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                           0.39                            0.03 
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                         151.27                          173.82 
  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE 
                          19.99                           22.60 
[1] "0.4 - 151.3 (20.0)" "0.0 - 173.8 (22.6)"
[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       18       22        0        15
  DEL PEAK 48(22Q11.21) WILD-TYPE       1       71      130        2        50
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(22Q11.21) MUTATED          17         0         16          3
  DEL PEAK 48(22Q11.21) WILD-TYPE        78         3         47         16
                                 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                              18                              71
  STAGE IB                              22                             130
  STAGE II                               0                               2
  STAGE IIA                             15                              50
  STAGE IIB                             17                              78
  STAGE III                              0                               3
  STAGE IIIA                            16                              47
  STAGE IIIB                             3                              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 48(22Q11.21) MUTATED    22  55  15   3
  DEL PEAK 48(22Q11.21) WILD-TYPE  90 239  56  21
D78V4, multiclass
    clus
vv   DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  T1                            22                              90
  T2                            55                             239
  T3                            15                              56
  T4                             3                              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 48(22Q11.21) MUTATED    57  26  11   1
  DEL PEAK 48(22Q11.21) WILD-TYPE 260 107  29   4
D78V5, multiclass
    clus
vv   DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  N0                            57                             260
  N1                            26                             107
  N2                            11                              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"
D78V6, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q11.21) MUTATED    74   2
  DEL PEAK 48(22Q11.21) WILD-TYPE 337   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q11.21) MUTATED     74    2
  DEL PEAK 48(22Q11.21) WILD-TYPE  337    5
   clus
vv  DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  0                            74                             337
  1                             2                               5
[1] 2 2
[1] FALSE
D78V7, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q11.21) MUTATED    24  71
  DEL PEAK 48(22Q11.21) WILD-TYPE 106 300
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q11.21) MUTATED     24   71
  DEL PEAK 48(22Q11.21) WILD-TYPE  106  300
        clus
vv       DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  FEMALE                            24                             106
  MALE                              71                             300
[1] 2 2
[1] FALSE
D78V8, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q11.21) MUTATED    67  15
  DEL PEAK 48(22Q11.21) WILD-TYPE 317  38
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q11.21) MUTATED     67   15
  DEL PEAK 48(22Q11.21) WILD-TYPE  317   38
     clus
vv    DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  NO                             67                             317
  YES                            15                              38
[1] 2 2
[1] FALSE
D78V9, 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 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                                                            91
  DEL PEAK 48(22Q11.21) WILD-TYPE                                                         388
D78V10, multiclass
                                                             clus
vv                                                            DEL PEAK 48(22Q11.21) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            91
                                                             clus
vv                                                            DEL PEAK 48(22Q11.21) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             388
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
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 328  11   2  19
D78V13, multiclass
    clus
vv   DEL PEAK 48(22Q11.21) MUTATED DEL PEAK 48(22Q11.21) WILD-TYPE
  R0                            71                             328
  R1                             1                              11
  R2                             2                               2
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 48(22Q11.21) MUTATED       2                         8    62
  DEL PEAK 48(22Q11.21) WILD-TYPE     7                        23   287
D78V14, multiclass
                           clus
vv                          DEL PEAK 48(22Q11.21) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                62
                           clus
vv                          DEL PEAK 48(22Q11.21) WILD-TYPE
  ASIAN                                                   7
  BLACK OR AFRICAN AMERICAN                              23
  WHITE                                                 287
[1] 3 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  56
  DEL PEAK 48(22Q11.21) WILD-TYPE   7 261
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q11.21) MUTATED      1   56
  DEL PEAK 48(22Q11.21) WILD-TYPE    7  261
                        clus
vv                       DEL PEAK 48(22Q11.21) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            56
                        clus
vv                       DEL PEAK 48(22Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             261
[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    69  55
  DEL PEAK 49(22Q13.32) WILD-TYPE 211 159
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                            124                             370 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                             55                             159 
$`DEL PEAK 49(22Q13.32) MUTATED`
TCGA-18-3407 TCGA-18-4083 TCGA-21-A5DI TCGA-33-4532 TCGA-33-6737 TCGA-43-2578 
        4.47         6.18        32.19       129.01        19.76        22.49 
TCGA-43-5668 TCGA-43-7658 TCGA-56-8201 TCGA-56-A5DR TCGA-68-8250 TCGA-NC-A5HE 
       18.38        78.18        13.05         0.13         8.02        76.80 
TCGA-NC-A5HM TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-O2-A52W TCGA-18-3417 TCGA-21-1070 
       39.85        65.65        16.80         8.58        36.07       119.54 
TCGA-21-1071 TCGA-21-1080 TCGA-21-5783 TCGA-21-5787 TCGA-22-0940 TCGA-22-1005 
       46.88       122.43        88.11        10.82        21.99        64.21 
TCGA-22-1016 TCGA-22-4607 TCGA-22-4613 TCGA-22-5483 TCGA-22-5492 TCGA-33-4566 
       27.02        19.30        11.77        18.84        16.64       173.82 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4587 TCGA-33-AAS8 TCGA-34-5928 TCGA-34-8454 
      103.53       151.27        54.44        36.62        39.32        38.79 
TCGA-34-8456 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4141 
       26.43         0.39         7.96         8.12         7.46         0.39 
TCGA-37-A5EL TCGA-39-5011 TCGA-39-5016 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 
       37.58       133.25       126.58        68.38        17.06        40.21 
TCGA-43-2581 TCGA-43-6143 TCGA-43-6771 TCGA-46-3769 TCGA-52-7809 TCGA-52-7812 
       38.66        22.98         5.46         4.44         5.46        27.45 
TCGA-56-7222 TCGA-56-8082 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 TCGA-56-A62T 
       18.48        14.96         3.48        26.89        14.07        14.47 
TCGA-60-2695 TCGA-63-6202 TCGA-63-A5MJ TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       21.11        52.67        59.97        14.99        11.34        25.28 
TCGA-63-A5MT TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2753 TCGA-66-2754 
       16.37        53.88        34.59        16.96         1.02         2.01 
TCGA-66-2757 TCGA-66-2759 TCGA-66-2771 TCGA-66-2778 TCGA-66-2782 TCGA-66-2789 
       43.99        25.05        19.00        19.00        12.00         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2800 TCGA-68-A59I TCGA-70-6723 
       22.98         5.03        10.06        49.05        16.18        12.33 
TCGA-77-7138 TCGA-77-7142 TCGA-77-7337 TCGA-77-7465 TCGA-77-8128 TCGA-77-8139 
       11.18        73.22       106.95        32.55        37.81       104.09 
TCGA-77-8144 TCGA-77-8150 TCGA-77-8153 TCGA-77-A5G6 TCGA-85-6560 TCGA-85-7697 
       27.39        54.41        65.49        22.29        41.39        34.95 
TCGA-85-7843 TCGA-85-8048 TCGA-85-8049 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 
        1.15        25.15        19.04        32.71         2.01        15.39 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A510 TCGA-85-A53L 
       38.14        12.59        18.08        22.59        15.85        12.39 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-8491 
       20.22        22.62        10.59         4.01         2.30        26.63 
TCGA-98-7454 TCGA-98-A53B TCGA-MF-A522 TCGA-NC-A5HJ TCGA-NC-A5HL TCGA-NC-A5HO 
       21.44         2.01        11.84        13.74         2.89        43.92 
TCGA-NC-A5HQ TCGA-NK-A5CX TCGA-O2-A52Q TCGA-O2-A5IB 
       14.73         3.65         3.72        11.18 

$`DEL PEAK 49(22Q13.32) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-5595 TCGA-22-1000 
       12.20       123.19         4.80        31.99        27.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 
       48.82        60.66        64.93        22.06       133.74         1.55 
TCGA-34-2604 TCGA-34-2605 TCGA-34-2609 TCGA-39-5039 TCGA-43-7657 TCGA-43-8118 
       31.50        28.96        31.27        17.88         7.76         2.93 
TCGA-43-A474 TCGA-43-A56V TCGA-56-7221 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
       11.61        12.03        19.99         3.45        17.00        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 TCGA-60-2715 
       17.85        21.04         3.58        41.42         9.01        35.34 
TCGA-60-2721 TCGA-63-A5MH TCGA-77-7140 TCGA-77-A5GA TCGA-77-A5GB TCGA-90-7766 
       32.32        66.61        20.78        42.08        30.81         9.50 
TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 
       14.07        21.04         0.16        18.38        16.14        57.07 
TCGA-96-A4JK TCGA-98-8020 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       19.36         2.76         5.69        21.21        19.10         0.07 
TCGA-NC-A5HR TCGA-NK-A7XE TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3414 
       40.90         0.43        75.75       117.57        11.34        23.54 
TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 
       92.15        92.42        86.96         2.79       154.32        49.94 
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-21-1082 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-22-0944 TCGA-22-1002 TCGA-22-1011 TCGA-22-1012 TCGA-22-4591 TCGA-22-4593 
        7.33         4.31         1.74        14.10        20.48        35.08 
TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
       48.33        24.13         0.56        38.17        34.75        13.12 
TCGA-22-4605 TCGA-22-4609 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 
       32.02         9.57        63.55        14.63        44.25         0.79 
TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 
       86.30        71.34        79.20        11.74        30.12        62.86 
TCGA-22-5491 TCGA-33-4538 TCGA-33-4547 TCGA-33-4586 TCGA-33-6738 TCGA-33-A4WN 
       56.32        97.94        79.53        14.07        63.35         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-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 
        2.63        61.61        32.88        65.23        81.24        74.66 
TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5929 
        9.07        60.30        50.66        16.93        44.75         4.96 
TCGA-34-7107 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4133 
        1.12         4.04        33.90         4.01         0.43         7.82 
TCGA-37-4135 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 
        6.81         3.39        21.70       111.35        68.58        55.20 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
       82.52       102.18         1.71        24.33         1.94        60.53 
TCGA-39-5034 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       36.39        71.18        55.56        39.12        33.11        27.91 
TCGA-43-6647 TCGA-43-6770 TCGA-43-6773 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
       24.89        21.47         3.81        19.59        13.38        11.77 
TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 
        9.73        14.20        13.32        12.16        13.02         9.83 
TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-52-7622 
       10.65        13.91         0.39         0.39        29.95        28.34 
TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 
       30.35         8.75        28.96        12.43        18.25        21.90 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-7730 TCGA-56-7731 
       14.53        31.27        30.41        19.76         6.51         0.10 
TCGA-56-7822 TCGA-56-7823 TCGA-56-8083 TCGA-56-8503 TCGA-56-8622 TCGA-56-8623 
       17.49        33.24         4.93         1.35         1.81        22.75 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
       13.81        10.36         9.93        20.25        15.81        20.94 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 
       19.23        13.32        18.74         0.26         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-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-60-2708 TCGA-60-2709 
       96.82        37.94        92.71        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       66.54        56.91        50.33        48.49        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 
       29.85        35.90        23.57        26.83        11.77        70.13 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MI 
       70.42        68.15        55.30       102.67        70.62        58.65 
TCGA-63-A5ML TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MV TCGA-66-2734 TCGA-66-2737 
       45.57        89.29        78.28        36.16        43.10         2.01 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2763 
       21.07         0.99         0.92         0.99        21.01         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-66-2773 TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 
        3.02         2.01        12.03         3.98        24.95         1.97 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
       25.97        40.01        22.98        30.02        54.08         4.01 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59J TCGA-70-6722 
        2.73         6.64         6.94        13.35        14.73        12.07 
TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
       29.56        73.12        75.09        23.28       140.09         0.49 
TCGA-77-7335 TCGA-77-7338 TCGA-77-7463 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
       70.13         0.16        46.78         6.51        86.76        55.73 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8136 TCGA-77-8138 TCGA-77-8140 
      156.66        12.59        53.92        39.09        17.72        11.54 
TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5FZ 
       26.40         6.97        66.51        60.53        36.36       126.18 
TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH 
      132.36       150.25         5.92        61.94        27.62        38.86 
TCGA-85-6175 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7699 
        9.67        40.24         6.41        36.53        31.30        32.91 
TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 
        1.38        29.95        18.94        24.13        31.56        26.79 
TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 
       30.64        34.52        10.09         0.76        13.22        22.45 
TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8481 TCGA-85-8580 TCGA-85-A4CL 
       16.77         5.29         3.09         7.76        36.59        30.28 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
       34.13        30.97        19.86        24.36        30.48        19.73 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 TCGA-85-A5B5 
       27.16        16.21        14.96        15.29        29.92         3.65 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
       24.92         2.93        11.77         2.70         3.48         5.26 
TCGA-94-8035 TCGA-94-8490 TCGA-94-A4VJ TCGA-94-A5I6 TCGA-96-7544 TCGA-96-8169 
        4.01         5.03        14.14        17.69        71.01        18.31 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       17.46        27.68        30.81        30.67        21.34        27.16 
TCGA-98-A53A TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
       18.15        27.02        20.32        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH 
       16.11        13.18        13.41         4.54        64.54         1.22 
TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HT TCGA-NK-A5CR 
       57.30         4.21        49.28        25.32        26.43        83.57 
TCGA-O2-A52N TCGA-O2-A52S TCGA-O2-A52V TCGA-XC-AA0X 
       33.07        12.72        43.89         0.20 

  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                           0.13                            0.03 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                         173.82                          156.66 
  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE 
                         19.990                          22.255 
[1] "0.1 - 173.8 (20.0)" "0.0 - 156.7 (22.3)"
[1] "hr=" "1"  
D79V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 49(22Q13.32) MUTATED         1       24       31        0        21
  DEL PEAK 49(22Q13.32) WILD-TYPE       1       65      121        2        44
                                 vv
clus                              STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 49(22Q13.32) MUTATED          21         2         18          5
  DEL PEAK 49(22Q13.32) WILD-TYPE        74         1         45         14
                                 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                              24                              65
  STAGE IB                              31                             121
  STAGE II                               0                               2
  STAGE IIA                             21                              44
  STAGE IIB                             21                              74
  STAGE III                              2                               1
  STAGE IIIA                            18                              45
  STAGE IIIB                             5                              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 49(22Q13.32) MUTATED    29  74  21   3
  DEL PEAK 49(22Q13.32) WILD-TYPE  83 220  50  21
D79V4, multiclass
    clus
vv   DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  T1                            29                              83
  T2                            74                             220
  T3                            21                              50
  T4                             3                              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 49(22Q13.32) MUTATED    78  34  12   3
  DEL PEAK 49(22Q13.32) WILD-TYPE 239  99  28   2
D79V5, multiclass
    clus
vv   DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  N0                            78                             239
  N1                            34                              99
  N2                            12                              28
  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   103   2
  DEL PEAK 49(22Q13.32) WILD-TYPE 308   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED    103    2
  DEL PEAK 49(22Q13.32) WILD-TYPE  308    5
   clus
vv  DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  0                           103                             308
  1                             2                               5
[1] 2 2
[1] FALSE
D79V7, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.32) MUTATED    36  91
  DEL PEAK 49(22Q13.32) WILD-TYPE  94 280
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED     36   91
  DEL PEAK 49(22Q13.32) WILD-TYPE   94  280
        clus
vv       DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  FEMALE                            36                              94
  MALE                              91                             280
[1] 2 2
[1] FALSE
D79V8, binary
                                 cls
clus                                0   1
  DEL PEAK 49(22Q13.32) MUTATED    90  19
  DEL PEAK 49(22Q13.32) WILD-TYPE 294  34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED     90   19
  DEL PEAK 49(22Q13.32) WILD-TYPE  294   34
     clus
vv    DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  NO                             90                             294
  YES                            19                              34
[1] 2 2
[1] FALSE
D79V9, 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 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                                                           118
  DEL PEAK 49(22Q13.32) WILD-TYPE                                                         361
D79V10, multiclass
                                                             clus
vv                                                            DEL PEAK 49(22Q13.32) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           118
                                                             clus
vv                                                            DEL PEAK 49(22Q13.32) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                    10
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                    3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                   0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             361
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V11, continuous
D79V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 49(22Q13.32) MUTATED    96   4   1   6
  DEL PEAK 49(22Q13.32) WILD-TYPE 303   8   3  17
D79V13, multiclass
    clus
vv   DEL PEAK 49(22Q13.32) MUTATED DEL PEAK 49(22Q13.32) WILD-TYPE
  R0                            96                             303
  R1                             4                               8
  R2                             1                               3
  RX                             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                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 49(22Q13.32) MUTATED       3                         8    85
  DEL PEAK 49(22Q13.32) WILD-TYPE     6                        23   264
D79V14, multiclass
                           clus
vv                          DEL PEAK 49(22Q13.32) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                85
                           clus
vv                          DEL PEAK 49(22Q13.32) WILD-TYPE
  ASIAN                                                   6
  BLACK OR AFRICAN AMERICAN                              23
  WHITE                                                 264
[1] 3 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  76
  DEL PEAK 49(22Q13.32) WILD-TYPE   7 241
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 49(22Q13.32) MUTATED      1   76
  DEL PEAK 49(22Q13.32) WILD-TYPE    7  241
                        clus
vv                       DEL PEAK 49(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            76
                        clus
vv                       DEL PEAK 49(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   7
  NOT HISPANIC OR LATINO                             241
[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    83  69
  DEL PEAK 50(XP22.2) WILD-TYPE 197 145
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                          152                           342 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                           69                           145 
$`DEL PEAK 50(XP22.2) MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-18-5595 TCGA-22-1017 TCGA-22-A5C4 TCGA-33-4532 
        4.47        31.99        27.19        48.82        22.06       129.01 
TCGA-34-2605 TCGA-34-2609 TCGA-43-5668 TCGA-43-8118 TCGA-43-A474 TCGA-56-7221 
       28.96        31.27        18.38         2.93        11.61        19.99 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 
        0.13         3.58        41.42        20.78        42.08         9.50 
TCGA-90-7964 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-A4JK TCGA-98-8020 TCGA-J1-A4AH 
       14.07         0.16        16.14        19.36         2.76        19.10 
TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3408 TCGA-18-3412 TCGA-18-3417 TCGA-18-4086 
       65.65        16.80        75.75        11.34        36.07         2.79 
TCGA-18-5592 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-22-0940 TCGA-22-0944 
       49.94       122.43       119.80        43.23        21.99         7.33 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4607 TCGA-22-5473 TCGA-22-5477 TCGA-22-5480 
       20.48        35.08        19.30        63.55        44.25        71.34 
TCGA-22-5483 TCGA-22-5485 TCGA-33-4566 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASJ 
       18.84        30.12       173.82         0.30        36.62       118.36 
TCGA-34-2600 TCGA-34-5236 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       61.61         9.07        44.75         4.96         1.12        38.79 
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-43-5670 TCGA-43-6770 TCGA-43-7656 TCGA-46-3769 
      102.18         1.71        27.91        21.47        19.59         4.44 
TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-7730 TCGA-56-7823 
       13.91         0.39         0.39        29.95         6.51        33.24 
TCGA-56-8082 TCGA-56-8083 TCGA-56-8624 TCGA-56-8629 TCGA-56-A62T TCGA-58-8390 
       14.96         4.93        13.81        15.81        14.47        29.95 
TCGA-58-8392 TCGA-60-2698 TCGA-60-2703 TCGA-60-2707 TCGA-60-2710 TCGA-60-2713 
       16.47        10.22        96.82        21.93        66.54        56.91 
TCGA-63-7023 TCGA-63-A5MG TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MV 
       55.30        70.62        58.65        25.28        16.37        36.16 
TCGA-63-A5MY TCGA-66-2753 TCGA-66-2757 TCGA-66-2758 TCGA-66-2763 TCGA-66-2769 
       34.59         1.02        43.99        21.01         0.99         7.07 
TCGA-66-2773 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-66-2790 TCGA-66-2792 
        3.02         3.98        12.00        25.97        22.98        30.02 
TCGA-66-2800 TCGA-68-7756 TCGA-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 
       49.05         6.64        12.33        29.56        23.28        11.18 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-8009 TCGA-77-8130 TCGA-77-8140 
        0.49        73.22         0.16        55.73       156.66        11.54 
TCGA-77-8144 TCGA-77-8150 TCGA-77-8154 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6175 
       27.39        54.41        60.53       150.25        27.62         9.67 
TCGA-85-6561 TCGA-85-7698 TCGA-85-7699 TCGA-85-8070 TCGA-85-8071 TCGA-85-8288 
       40.24        31.30        32.91        31.56        26.79        13.22 
TCGA-85-8352 TCGA-85-8354 TCGA-85-8580 TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50M 
        5.29        32.71        36.59        34.13        19.73        27.16 
TCGA-85-A512 TCGA-92-8063 TCGA-94-8035 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 
       15.29         4.01         4.01        26.63        17.69        71.01 
TCGA-96-A4JL TCGA-98-A53A TCGA-98-A53B TCGA-98-A53J TCGA-L3-A4E7 TCGA-LA-A446 
       27.68        18.15         2.01        20.71        12.89        13.18 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL TCGA-NC-A5HN TCGA-NC-A5HO 
        4.54        64.54        57.30         2.89        49.28        43.92 
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-18-4083 TCGA-21-A5DI TCGA-22-1000 
       12.20       123.19         4.80         6.18        32.19        14.93 
TCGA-22-5471 TCGA-22-5472 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 
       60.66        64.93       133.74         1.55        19.76        31.50 
TCGA-39-5039 TCGA-43-2578 TCGA-43-7657 TCGA-43-7658 TCGA-43-A56V TCGA-56-8201 
       17.88        22.49         7.76        78.18        12.03        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2712 
        3.45        17.00        16.77        17.85        21.04         9.01 
TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 TCGA-77-A5GB TCGA-94-7033 
       35.34        32.32        66.61         8.02        30.81        21.04 
TCGA-94-7943 TCGA-96-7545 TCGA-98-A539 TCGA-98-A53D TCGA-NC-A5HD TCGA-NC-A5HE 
       18.38        57.07         5.69        21.21         0.07        76.80 
TCGA-NC-A5HM TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3414 
       39.85        40.90         0.43         8.58       117.57        23.54 
TCGA-18-3415 TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 
       92.15        92.42        86.96       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-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4594 
        4.31        64.21         1.74        14.10        27.02        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-22-4613 TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 
        9.57        11.77        14.63         0.79        86.30        79.20 
TCGA-22-5482 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 
       11.74        62.86        56.32        16.64        97.94        79.53 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN 
      103.53       151.27        14.07        54.44        63.35         4.70 
TCGA-33-AASB TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL TCGA-34-2596 TCGA-34-2608 
        6.94       110.99        44.19        27.16         2.63        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       65.23        81.24        74.66        60.30        50.66        16.93 
TCGA-34-5928 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-4129 
       39.32         4.04        33.90         4.01         0.43         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-A5EL TCGA-37-A5EN TCGA-39-5011 
        8.12         7.46         7.82        37.58        21.70       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 
      126.58       111.35        55.20        82.52        24.33         1.94 
TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5040 
       60.53        36.39        68.38        71.18        55.56        17.06 
TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-6143 TCGA-43-6647 
       40.21        38.66        39.12        33.11        22.98        24.89 
TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U 
        5.46         3.81        13.38        11.77         9.73        14.20 
TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 TCGA-52-7622 
       13.32        12.16        13.02         9.83        10.65        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        12.43 
TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 
       18.25        21.90        18.48        14.53        31.27        30.41 
TCGA-56-7582 TCGA-56-7731 TCGA-56-7822 TCGA-56-8304 TCGA-56-8307 TCGA-56-8309 
       19.76         0.10        17.49         3.48        26.89        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-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-58-8386 
       20.94        19.23        13.32        18.74         0.26         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K 
       13.25        13.55        71.24        34.78        85.12        34.36 
TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2704 
       56.65        35.24        29.92        21.11        12.23        37.94 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       92.71        80.45        49.48        50.33        48.49        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-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MJ 
       52.67        70.13        70.42        68.15       102.67        59.97 
TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MW 
       45.57        14.99        11.34        89.29        78.28        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-66-2759 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 
        0.92         0.99        25.05         2.01         1.02         2.01 
TCGA-66-2768 TCGA-66-2770 TCGA-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 
        2.01        23.01        19.00         2.01        19.00        12.03 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 
       24.95         1.97        40.01        22.98         4.04         5.03 
TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-68-7755 TCGA-68-7757 TCGA-68-8251 
       10.06        54.08         4.01         2.73         6.94        13.35 
TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 TCGA-77-7139 
       16.18        14.73        12.07        73.12        75.09       140.09 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 
       70.13       106.95        46.78        32.55         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-77-8143 TCGA-77-8145 TCGA-77-8148 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5FZ 
       26.40         6.97        66.51        65.49        36.36       126.18 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 
      132.36        22.29         5.92        61.94        38.86        41.39 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 
        6.41        36.53        34.95         1.38         1.15        29.95 
TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 
       18.94        25.15        19.04        24.13        30.64        34.52 
TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 
       10.09         0.76        22.45        16.77         3.09         2.01 
TCGA-85-8479 TCGA-85-8481 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 
       15.39         7.76        38.14        12.59        18.08        22.59 
TCGA-85-A4CL TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z 
       30.28        30.97        19.86        24.36        30.48        16.21 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 
       15.85        14.96        29.92        12.39         3.65        24.92 
TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 
        2.93        11.77        20.22        22.62        10.59         2.70 
TCGA-92-7341 TCGA-92-8064 TCGA-92-8065 TCGA-94-8490 TCGA-94-A4VJ TCGA-96-8169 
        3.48         5.26         2.30         5.03        14.14        18.31 
TCGA-96-8170 TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 
       17.46        21.44        30.81        30.67        21.34        27.16 
TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 
       27.02        20.32        18.58        16.11        13.41        11.84 
TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HK TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT 
        1.22        13.74         4.21        25.32        14.73        26.43 
TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
       83.57         3.65        33.07         3.72        43.89         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 
                       173.82                        154.32 
  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE 
                         21.7                          21.8 
[1] "0.1 - 173.8 (21.7)" "0.0 - 154.3 (21.8)"
[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       20       49        1        33
  DEL PEAK 50(XP22.2) WILD-TYPE       2       69      103        1        32
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 50(XP22.2) MUTATED          28         2         14          5
  DEL PEAK 50(XP22.2) WILD-TYPE        67         1         49         14
                               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                            20                            69
  STAGE IB                            49                           103
  STAGE II                             1                             1
  STAGE IIA                           33                            32
  STAGE IIB                           28                            67
  STAGE III                            2                             1
  STAGE IIIA                          14                            49
  STAGE IIIB                           5                            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 50(XP22.2) MUTATED    30  97  18  10
  DEL PEAK 50(XP22.2) WILD-TYPE  82 197  53  14
D80V4, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  T1                          30                            82
  T2                          97                           197
  T3                          18                            53
  T4                          10                            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 50(XP22.2) MUTATED    99  48   7   0
  DEL PEAK 50(XP22.2) WILD-TYPE 218  85  33   5
D80V5, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  N0                          99                           218
  N1                          48                            85
  N2                           7                            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"
D80V6, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED   129   1
  DEL PEAK 50(XP22.2) WILD-TYPE 282   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED    129    1
  DEL PEAK 50(XP22.2) WILD-TYPE  282    6
   clus
vv  DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  0                         129                           282
  1                           1                             6
[1] 2 2
[1] FALSE
D80V7, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED    35 120
  DEL PEAK 50(XP22.2) WILD-TYPE  95 251
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED     35  120
  DEL PEAK 50(XP22.2) WILD-TYPE   95  251
        clus
vv       DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  FEMALE                          35                            95
  MALE                           120                           251
[1] 2 2
[1] FALSE
D80V8, binary
                               cls
clus                              0   1
  DEL PEAK 50(XP22.2) MUTATED   123  15
  DEL PEAK 50(XP22.2) WILD-TYPE 261  38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED    123   15
  DEL PEAK 50(XP22.2) WILD-TYPE  261   38
     clus
vv    DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  NO                          123                           261
  YES                          15                            38
[1] 2 2
[1] FALSE
D80V9, 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 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                                                           151
  DEL PEAK 50(XP22.2) WILD-TYPE                                                         328
D80V10, multiclass
                                                             clus
vv                                                            DEL PEAK 50(XP22.2) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         151
                                                             clus
vv                                                            DEL PEAK 50(XP22.2) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V11, continuous
D80V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 50(XP22.2) MUTATED   121   5   1   9
  DEL PEAK 50(XP22.2) WILD-TYPE 278   7   3  14
D80V13, multiclass
    clus
vv   DEL PEAK 50(XP22.2) MUTATED DEL PEAK 50(XP22.2) WILD-TYPE
  R0                         121                           278
  R1                           5                             7
  R2                           1                             3
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 50(XP22.2) MUTATED       4                        11   102
  DEL PEAK 50(XP22.2) WILD-TYPE     5                        20   247
D80V14, multiclass
                           clus
vv                          DEL PEAK 50(XP22.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             102
                           clus
vv                          DEL PEAK 50(XP22.2) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               247
[1] 3 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  95
  DEL PEAK 50(XP22.2) WILD-TYPE   7 222
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 50(XP22.2) MUTATED      1   95
  DEL PEAK 50(XP22.2) WILD-TYPE    7  222
                        clus
vv                       DEL PEAK 50(XP22.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          95
                        clus
vv                       DEL PEAK 50(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           222
[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    79  69
  DEL PEAK 51(XP21.1) WILD-TYPE 201 145
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                          148                           346 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                           69                           145 
$`DEL PEAK 51(XP21.1) MUTATED`
TCGA-18-3407 TCGA-18-3416 TCGA-18-5595 TCGA-33-4532 TCGA-34-2605 TCGA-34-2609 
        4.47        31.99        27.19       129.01        28.96        31.27 
TCGA-43-8118 TCGA-56-7221 TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 TCGA-60-2712 
        2.93        19.99         0.13         3.58        41.42         9.01 
TCGA-77-7140 TCGA-77-A5GA TCGA-90-7766 TCGA-94-7557 TCGA-94-A5I4 TCGA-96-A4JK 
       20.78        42.08         9.50         0.16        16.14        19.36 
TCGA-98-8020 TCGA-NK-A5CT TCGA-18-3408 TCGA-18-3412 TCGA-18-3417 TCGA-18-3421 
        2.76        65.65        75.75        11.34        36.07        86.96 
TCGA-18-4086 TCGA-18-5592 TCGA-21-1072 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
        2.79        49.94        99.16       122.43       119.80        43.23 
TCGA-22-0940 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4607 TCGA-22-5473 
       21.99        20.48        35.08        48.33        19.30        63.55 
TCGA-22-5477 TCGA-22-5480 TCGA-22-5483 TCGA-22-5485 TCGA-33-4566 TCGA-33-A5GW 
       44.25        71.34        18.84        30.12       173.82         0.30 
TCGA-33-AAS8 TCGA-33-AASJ TCGA-33-AASL TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 
       36.62       118.36        27.16        44.75         4.96         1.12 
TCGA-34-8454 TCGA-34-8456 TCGA-37-4135 TCGA-37-4141 TCGA-39-5021 TCGA-39-5027 
       38.79        26.43         6.81         0.39        68.58       102.18 
TCGA-39-5028 TCGA-43-6770 TCGA-43-7656 TCGA-43-8116 TCGA-46-3769 TCGA-51-4079 
        1.71        21.47        19.59        11.77         4.44         0.39 
TCGA-51-4080 TCGA-51-4081 TCGA-52-7810 TCGA-56-7222 TCGA-56-7223 TCGA-56-7730 
        0.39        29.95        30.35        18.48        14.53         6.51 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8624 TCGA-56-8629 TCGA-56-A4BW 
       33.24        14.96         4.93        13.81        15.81        19.23 
TCGA-58-8390 TCGA-58-8391 TCGA-58-8392 TCGA-60-2698 TCGA-60-2707 TCGA-60-2710 
       29.95        71.24        16.47        10.22        21.93        66.54 
TCGA-60-2713 TCGA-63-7023 TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MY 
       56.91        55.30        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-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 
        6.64        12.33        29.56        23.28        11.18         0.49 
TCGA-77-7142 TCGA-77-7338 TCGA-77-8009 TCGA-77-8130 TCGA-77-8140 TCGA-77-8144 
       73.22         0.16        55.73       156.66        11.54        27.39 
TCGA-77-8150 TCGA-77-8154 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6175 
       54.41        60.53        36.36       150.25        27.62         9.67 
TCGA-85-6561 TCGA-85-7698 TCGA-85-7699 TCGA-85-7843 TCGA-85-8070 TCGA-85-8071 
       40.24        31.30        32.91         1.15        31.56        26.79 
TCGA-85-8288 TCGA-85-8352 TCGA-85-8354 TCGA-85-8355 TCGA-85-8580 TCGA-85-A4CL 
       13.22         5.29        32.71         2.01        36.59        30.28 
TCGA-85-A4CN TCGA-85-A4QR TCGA-85-A50M TCGA-85-A512 TCGA-92-8063 TCGA-94-8035 
       34.13        19.73        27.16        15.29         4.01         4.01 
TCGA-94-8490 TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-98-A53A TCGA-98-A53B 
        5.03        26.63        17.69        71.01        18.15         2.01 
TCGA-98-A53J TCGA-LA-A446 TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HL 
       20.71        13.18         4.54        64.54        57.30         2.89 
TCGA-NC-A5HN TCGA-NC-A5HO TCGA-O2-A52S TCGA-O2-A5IB 
       49.28        43.92        12.72        11.18 

$`DEL PEAK 51(XP21.1) WILD-TYPE`
TCGA-18-3406 TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1000 
       12.20       123.19         4.80         6.18        32.19        14.93 
TCGA-22-1017 TCGA-22-5471 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4533 TCGA-33-4589 
       48.82        60.66        64.93        22.06       133.74         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 
       19.76        31.50        17.88        22.49        18.38         7.76 
TCGA-43-7658 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 
       78.18        11.61        12.03        13.05         3.45        17.00 
TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH 
       16.77        17.85        21.04        35.34        32.32        66.61 
TCGA-68-8250 TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-94-7943 TCGA-96-7545 
        8.02        30.81        14.07        21.04        18.38        57.07 
TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        5.69        21.21        19.10         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 TCGA-18-3414 
       40.90        16.80         0.43         8.58       117.57        23.54 
TCGA-18-3415 TCGA-18-3419 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 
       92.15        92.42       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-22-0944 TCGA-22-1002 
       88.11        41.69        33.93        10.82         7.33         4.31 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4595 TCGA-22-4596 
       64.21         1.74        14.10        27.02        24.13         0.56 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-4613 
       38.17        34.75        13.12        32.02         9.57        11.77 
TCGA-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5481 TCGA-22-5482 TCGA-22-5489 
       14.63         0.79        86.30        79.20        11.74        62.86 
TCGA-22-5491 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4582 TCGA-33-4583 
       56.32        16.64        97.94        79.53       103.53       151.27 
TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASD 
       14.07        54.44        63.35         4.70         6.94       110.99 
TCGA-33-AASI TCGA-34-2596 TCGA-34-2600 TCGA-34-2608 TCGA-34-5231 TCGA-34-5232 
       44.19         2.63        61.61        32.88        65.23        81.24 
TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 TCGA-34-5928 
       74.66         9.07        60.30        50.66        16.93        39.32 
TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
        4.04        33.90         4.01         0.43         0.39         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EL TCGA-37-A5EN 
        8.12         7.46         7.82         3.39        37.58        21.70 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 
      133.25       126.58       111.35        55.20        82.52        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        60.53        36.39        68.38        71.18        55.56 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       17.06        40.21        38.66        39.12        33.11        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-A475 
       22.98        24.89         5.46         3.81        13.38         9.73 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6025 
       14.20        13.32        12.16        13.02         9.83        10.65 
TCGA-46-6026 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
       13.91        28.34         5.46         8.75        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
       12.43        18.25        21.90        31.27        30.41        19.76 
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-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D 
        1.81        22.75        10.36         9.93        20.25        20.94 
TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 
       13.32        18.74         0.26        14.47         0.03        13.25 
TCGA-58-8388 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
       13.55        34.78        85.12        34.36        56.65        35.24 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2703 TCGA-60-2704 TCGA-60-2706 
       29.92        21.11        12.23        96.82        37.94        92.71 
TCGA-60-2708 TCGA-60-2709 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 
       80.45        49.48        50.33        48.49        42.64         3.19 
TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 TCGA-60-2725 TCGA-60-2726 TCGA-63-6202 
       29.85        35.90        23.57        26.83        11.77        52.67 
TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG TCGA-63-A5MJ 
       70.13        70.42        68.15       102.67        70.62        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-66-2754 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-66-2769 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-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 
       19.00        24.95         1.97        40.01        22.98         4.04 
TCGA-66-2790 TCGA-66-2791 TCGA-66-2793 TCGA-66-2794 TCGA-68-7755 TCGA-68-7757 
       22.98         5.03        10.06        54.08         2.73         6.94 
TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 TCGA-77-6844 
       13.35        16.18        14.73        12.07        73.12        75.09 
TCGA-77-7139 TCGA-77-7335 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
      140.09        70.13       106.95        46.78        32.55         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-A5FZ 
      104.09        26.40         6.97        66.51        65.49       126.18 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 
      132.36        22.29         5.92        61.94        38.86        41.39 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 
        6.41        36.53        34.95         1.38        29.95        18.94 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 
       25.15        19.04        24.13        30.64        34.52        10.09 
TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 TCGA-85-8353 TCGA-85-8479 TCGA-85-8481 
        0.76        22.45        16.77         3.09        15.39         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4JB TCGA-85-A4JC 
       38.14        12.59        18.08        22.59        30.97        19.86 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 
       24.36        30.48        16.21        15.85        14.96        29.92 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED 
       12.39         3.65        24.92         2.93        11.77        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-A4VJ TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 
       14.14        18.31        17.46        27.68        21.44        30.81 
TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I 
       30.67        21.34        27.16        27.02        20.32        18.58 
TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HH TCGA-NC-A5HJ 
       12.89        16.11        13.41        11.84         1.22        13.74 
TCGA-NC-A5HK TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR TCGA-NK-A5CX 
        4.21        25.32        14.73        26.43        83.57         3.65 
TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
       33.07         3.72        43.89         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 
                       173.82                        154.32 
  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE 
                        21.96                         21.57 
[1] "0.1 - 173.8 (22.0)" "0.0 - 154.3 (21.6)"
[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       22       49        1        26
  DEL PEAK 51(XP21.1) WILD-TYPE       2       67      103        1        39
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 51(XP21.1) MUTATED          27         2         16          5
  DEL PEAK 51(XP21.1) WILD-TYPE        68         1         47         14
                               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                            22                            67
  STAGE IB                            49                           103
  STAGE II                             1                             1
  STAGE IIA                           26                            39
  STAGE IIB                           27                            68
  STAGE III                            2                             1
  STAGE IIIA                          16                            47
  STAGE IIIB                           5                            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 51(XP21.1) MUTATED    31  89  21  10
  DEL PEAK 51(XP21.1) WILD-TYPE  81 205  50  14
D81V4, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  T1                          31                            81
  T2                          89                           205
  T3                          21                            50
  T4                          10                            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 51(XP21.1) MUTATED    95  47   8   0
  DEL PEAK 51(XP21.1) WILD-TYPE 222  86  32   5
D81V5, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  N0                          95                           222
  N1                          47                            86
  N2                           8                            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"
D81V6, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED   126   1
  DEL PEAK 51(XP21.1) WILD-TYPE 285   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED    126    1
  DEL PEAK 51(XP21.1) WILD-TYPE  285    6
   clus
vv  DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  0                         126                           285
  1                           1                             6
[1] 2 2
[1] FALSE
D81V7, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED    38 113
  DEL PEAK 51(XP21.1) WILD-TYPE  92 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED     38  113
  DEL PEAK 51(XP21.1) WILD-TYPE   92  258
        clus
vv       DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  FEMALE                          38                            92
  MALE                           113                           258
[1] 2 2
[1] FALSE
D81V8, binary
                               cls
clus                              0   1
  DEL PEAK 51(XP21.1) MUTATED   120  15
  DEL PEAK 51(XP21.1) WILD-TYPE 264  38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED    120   15
  DEL PEAK 51(XP21.1) WILD-TYPE  264   38
     clus
vv    DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  NO                          120                           264
  YES                          15                            38
[1] 2 2
[1] FALSE
D81V9, 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 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                                                           148
  DEL PEAK 51(XP21.1) WILD-TYPE                                                         331
D81V10, multiclass
                                                             clus
vv                                                            DEL PEAK 51(XP21.1) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         148
                                                             clus
vv                                                            DEL PEAK 51(XP21.1) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  13
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           331
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V11, continuous
D81V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 51(XP21.1) MUTATED   121   3   0   9
  DEL PEAK 51(XP21.1) WILD-TYPE 278   9   4  14
D81V13, multiclass
    clus
vv   DEL PEAK 51(XP21.1) MUTATED DEL PEAK 51(XP21.1) WILD-TYPE
  R0                         121                           278
  R1                           3                             9
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 51(XP21.1) MUTATED       3                        11    99
  DEL PEAK 51(XP21.1) WILD-TYPE     6                        20   250
D81V14, multiclass
                           clus
vv                          DEL PEAK 51(XP21.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                              99
                           clus
vv                          DEL PEAK 51(XP21.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               250
[1] 3 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  91
  DEL PEAK 51(XP21.1) WILD-TYPE   7 226
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 51(XP21.1) MUTATED      1   91
  DEL PEAK 51(XP21.1) WILD-TYPE    7  226
                        clus
vv                       DEL PEAK 51(XP21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          91
                        clus
vv                       DEL PEAK 51(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           226
[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  71
  DEL PEAK 52(XP11.3) WILD-TYPE 204 143
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                          147                           347 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                           71                           143 
$`DEL PEAK 52(XP11.3) MUTATED`
TCGA-18-3406 TCGA-18-3407 TCGA-18-3416 TCGA-18-5595 TCGA-22-A5C4 TCGA-33-4532 
       12.20         4.47        31.99        27.19        22.06       129.01 
TCGA-34-2605 TCGA-43-8118 TCGA-56-7221 TCGA-56-A5DR TCGA-60-2696 TCGA-60-2711 
       28.96         2.93        19.99         0.13         3.58        41.42 
TCGA-60-2712 TCGA-77-A5GA TCGA-90-7766 TCGA-96-A4JK TCGA-98-8020 TCGA-NC-A5HM 
        9.01        42.08         9.50        19.36         2.76        39.85 
TCGA-NK-A5CT TCGA-18-3408 TCGA-18-3412 TCGA-18-3415 TCGA-18-3417 TCGA-18-4086 
       65.65        75.75        11.34        92.15        36.07         2.79 
TCGA-18-5592 TCGA-21-1072 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 TCGA-22-0940 
       49.94        99.16       122.43       119.80        43.23        21.99 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 TCGA-22-4607 TCGA-22-4613 TCGA-22-5473 
       20.48        35.08        48.33        19.30        11.77        63.55 
TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5485 TCGA-22-5491 
       44.25        71.34        79.20        18.84        30.12        56.32 
TCGA-33-4566 TCGA-33-4582 TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASJ 
      173.82       103.53         0.30        36.62       110.99       118.36 
TCGA-33-AASL TCGA-34-2600 TCGA-34-5927 TCGA-34-5929 TCGA-34-7107 TCGA-34-8454 
       27.16        61.61        44.75         4.96         1.12        38.79 
TCGA-34-8456 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-39-5016 TCGA-39-5027 
       26.43         6.81         0.39        37.58       126.58       102.18 
TCGA-39-5028 TCGA-43-6770 TCGA-43-7656 TCGA-43-8116 TCGA-46-3769 TCGA-46-6025 
        1.71        21.47        19.59        11.77         4.44        10.65 
TCGA-51-4079 TCGA-51-4080 TCGA-56-7222 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 
        0.39         0.39        18.48        14.53        19.76         6.51 
TCGA-56-7823 TCGA-56-8082 TCGA-56-8083 TCGA-56-8624 TCGA-56-A4BW TCGA-58-8390 
       33.24        14.96         4.93        13.81        19.23        29.95 
TCGA-58-8391 TCGA-58-8392 TCGA-58-A46M TCGA-60-2707 TCGA-60-2710 TCGA-60-2713 
       71.24        16.47        35.24        21.93        66.54        56.91 
TCGA-63-7023 TCGA-63-A5MI TCGA-63-A5MP TCGA-63-A5MT TCGA-63-A5MY TCGA-66-2753 
       55.30        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-70-6723 TCGA-77-6842 TCGA-77-6845 TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 
       12.33        29.56        23.28        11.18         0.49        73.22 
TCGA-77-8009 TCGA-77-8133 TCGA-77-8140 TCGA-77-8144 TCGA-77-8154 TCGA-77-8156 
       55.73        53.92        11.54        27.39        60.53        36.36 
TCGA-77-A5G3 TCGA-77-A5GF TCGA-85-6175 TCGA-85-6561 TCGA-85-7698 TCGA-85-7699 
      150.25        27.62         9.67        40.24        31.30        32.91 
TCGA-85-8071 TCGA-85-8288 TCGA-85-8352 TCGA-85-8354 TCGA-85-8580 TCGA-85-A4CN 
       26.79        13.22         5.29        32.71        36.59        34.13 
TCGA-85-A4QR TCGA-85-A50M TCGA-85-A512 TCGA-92-8063 TCGA-94-8035 TCGA-94-8490 
       19.73        27.16        15.29         4.01         4.01         5.03 
TCGA-94-8491 TCGA-94-A5I6 TCGA-96-7544 TCGA-98-A53A TCGA-98-A53J TCGA-LA-A446 
       26.63        17.69        71.01        18.15        20.71        13.18 
TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HI TCGA-NC-A5HK TCGA-NC-A5HL TCGA-NC-A5HN 
        4.54        64.54        57.30         4.21         2.89        49.28 
TCGA-NC-A5HO TCGA-O2-A52S TCGA-O2-A5IB 
       43.92        12.72        11.18 

$`DEL PEAK 52(XP11.3) WILD-TYPE`
TCGA-18-3409 TCGA-18-3410 TCGA-18-4083 TCGA-21-A5DI TCGA-22-1000 TCGA-22-1017 
      123.19         4.80         6.18        32.19        14.93        48.82 
TCGA-22-5471 TCGA-22-5472 TCGA-33-4533 TCGA-33-4589 TCGA-33-6737 TCGA-34-2604 
       60.66        64.93       133.74         1.55        19.76        31.50 
TCGA-34-2609 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 TCGA-43-7657 TCGA-43-7658 
       31.27        17.88        22.49        18.38         7.76        78.18 
TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 
       11.61        12.03        13.05         3.45        17.00        16.77 
TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2715 TCGA-60-2721 TCGA-63-A5MH TCGA-68-8250 
       17.85        21.04        35.34        32.32        66.61         8.02 
TCGA-77-7140 TCGA-77-A5GB TCGA-90-7964 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
       20.78        30.81        14.07        21.04         0.16        18.38 
TCGA-94-A5I4 TCGA-96-7545 TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD 
       16.14        57.07         5.69        21.21        19.10         0.07 
TCGA-NC-A5HE TCGA-NC-A5HR TCGA-NK-A5D1 TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3411 
       76.80        40.90        16.80         0.43         8.58       117.57 
TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 TCGA-21-1071 
       23.54        92.42        86.96       154.32       119.54        46.88 
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-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0944 
       31.63        88.11        41.69        33.93        10.82         7.33 
TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 TCGA-22-1016 TCGA-22-4595 
        4.31        64.21         1.74        14.10        27.02        24.13 
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-22-5474 TCGA-22-5478 TCGA-22-5479 TCGA-22-5482 TCGA-22-5489 TCGA-22-5492 
       14.63         0.79        86.30        11.74        62.86        16.64 
TCGA-33-4538 TCGA-33-4547 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-6738 
       97.94        79.53       151.27        14.07        54.44        63.35 
TCGA-33-A4WN TCGA-33-AASB TCGA-33-AASI TCGA-34-2596 TCGA-34-2608 TCGA-34-5231 
        4.70         6.94        44.19         2.63        32.88        65.23 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 TCGA-34-5241 
       81.24        74.66         9.07        60.30        50.66        16.93 
TCGA-34-5928 TCGA-34-8455 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 
       39.32         4.04        33.90         4.01         0.43         0.39 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EN 
        7.96         8.12         7.46         7.82         3.39        21.70 
TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5029 
      133.25       111.35        68.58        55.20        82.52        24.33 
TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 
        1.94        60.53        36.39        68.38        71.18        55.56 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5670 
       17.06        40.21        38.66        39.12        33.11        27.91 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6771 TCGA-43-6773 TCGA-43-8115 TCGA-43-A475 
       22.98        24.89         5.46         3.81        13.38         9.73 
TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 TCGA-46-3768 TCGA-46-6026 
       14.20        13.32        12.16        13.02         9.83        13.91 
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-56-7579 TCGA-56-7580 
       28.96        12.43        18.25        21.90        31.27        30.41 
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-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
        1.81        22.75        10.36         9.93        20.25        15.81 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS TCGA-56-A62T TCGA-58-8386 
       20.94        13.32        18.74         0.26        14.47         0.03 
TCGA-58-8387 TCGA-58-8388 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L 
       13.25        13.55        34.78        85.12        34.36        56.65 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 TCGA-60-2704 
       29.92        21.11        12.23        10.22        96.82        37.94 
TCGA-60-2706 TCGA-60-2708 TCGA-60-2709 TCGA-60-2714 TCGA-60-2716 TCGA-60-2719 
       92.71        80.45        49.48        50.33        48.49        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-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB TCGA-63-A5MG 
       52.67        70.13        70.42        68.15       102.67        70.62 
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-A5MV TCGA-63-A5MW TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 TCGA-66-2742 
       36.16        53.88        16.96        43.10         2.01        21.07 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 
        0.99         2.01         0.92         0.99        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-66-2771 TCGA-66-2777 TCGA-66-2778 TCGA-66-2781 TCGA-66-2783 TCGA-66-2785 
       19.00         2.01        19.00         3.98        24.95         1.97 
TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2791 TCGA-66-2795 TCGA-68-7755 
       40.01        22.98         4.04         5.03         4.01         2.73 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 TCGA-77-6843 
        6.94        13.35        16.18        14.73        12.07        73.12 
TCGA-77-6844 TCGA-77-7139 TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 
       75.09       140.09        70.13       106.95         0.16        46.78 
TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
       32.55         6.51        86.76        37.81       156.66        12.59 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8143 TCGA-77-8145 TCGA-77-8148 
       39.09        17.72       104.09        26.40         6.97        66.51 
TCGA-77-8150 TCGA-77-8153 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5G7 
       54.41        65.49       126.18       132.36        22.29         5.92 
TCGA-77-A5G8 TCGA-77-A5GH TCGA-85-6560 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
       61.94        38.86        41.39         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        30.64        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        15.39         7.76 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4JB 
       38.14        12.59        18.08        22.59        30.28        30.97 
TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 
       19.86        24.36        30.48        16.21        15.85        14.96 
TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 
       29.92        12.39         3.65        24.92         2.93        11.77 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 TCGA-92-8064 
       20.22        22.62        10.59         2.70         3.48         5.26 
TCGA-92-8065 TCGA-94-A4VJ TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 
        2.30        14.14        18.31        17.46        27.68        21.44 
TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 TCGA-98-A538 TCGA-98-A53B TCGA-98-A53C 
       30.81        30.67        21.34        27.16         2.01        27.02 
TCGA-98-A53H TCGA-98-A53I TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A7SW TCGA-MF-A522 
       20.32        18.58        12.89        16.11        13.41        11.84 
TCGA-NC-A5HH TCGA-NC-A5HJ TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NC-A5HT TCGA-NK-A5CR 
        1.22        13.74        25.32        14.73        26.43        83.57 
TCGA-NK-A5CX TCGA-O2-A52N TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
        3.65        33.07         3.72        43.89         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 
                       173.82                        156.66 
  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE 
                        25.97                         21.04 
[1] "0.1 - 173.8 (26.0)" "0.0 - 156.7 (21.0)"
[1] "hr=" "1.1"
D82V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 52(XP11.3) MUTATED         0       26       44        1        26
  DEL PEAK 52(XP11.3) WILD-TYPE       2       63      108        1        39
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 52(XP11.3) MUTATED          26         2         15          6
  DEL PEAK 52(XP11.3) WILD-TYPE        69         1         48         13
                               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                            26                            63
  STAGE IB                            44                           108
  STAGE II                             1                             1
  STAGE IIA                           26                            39
  STAGE IIB                           26                            69
  STAGE III                            2                             1
  STAGE IIIA                          15                            48
  STAGE IIIB                           6                            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
  DEL PEAK 52(XP11.3) MUTATED    36  81  21  11
  DEL PEAK 52(XP11.3) WILD-TYPE  76 213  50  13
D82V4, multiclass
    clus
vv   DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  T1                          36                            76
  T2                          81                           213
  T3                          21                            50
  T4                          11                            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 52(XP11.3) MUTATED    95  44   9   0
  DEL PEAK 52(XP11.3) WILD-TYPE 222  89  31   5
D82V5, multiclass
    clus
vv   DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  N0                          95                           222
  N1                          44                            89
  N2                           9                            31
  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   125   1
  DEL PEAK 52(XP11.3) WILD-TYPE 286   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED    125    1
  DEL PEAK 52(XP11.3) WILD-TYPE  286    6
   clus
vv  DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  0                         125                           286
  1                           1                             6
[1] 2 2
[1] FALSE
D82V7, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP11.3) MUTATED    39 110
  DEL PEAK 52(XP11.3) WILD-TYPE  91 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED     39  110
  DEL PEAK 52(XP11.3) WILD-TYPE   91  261
        clus
vv       DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  FEMALE                          39                            91
  MALE                           110                           261
[1] 2 2
[1] FALSE
D82V8, binary
                               cls
clus                              0   1
  DEL PEAK 52(XP11.3) MUTATED   117  17
  DEL PEAK 52(XP11.3) WILD-TYPE 267  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED    117   17
  DEL PEAK 52(XP11.3) WILD-TYPE  267   36
     clus
vv    DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  NO                          117                           267
  YES                          17                            36
[1] 2 2
[1] FALSE
D82V9, 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 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                                                           145
  DEL PEAK 52(XP11.3) WILD-TYPE                                                         334
D82V10, multiclass
                                                             clus
vv                                                            DEL PEAK 52(XP11.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 3
  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 52(XP11.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                  12
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           334
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V11, continuous
D82V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 52(XP11.3) MUTATED   123   2   0   7
  DEL PEAK 52(XP11.3) WILD-TYPE 276  10   4  16
D82V13, multiclass
    clus
vv   DEL PEAK 52(XP11.3) MUTATED DEL PEAK 52(XP11.3) WILD-TYPE
  R0                         123                           276
  R1                           2                            10
  R2                           0                             4
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 52(XP11.3) MUTATED       3                        10    99
  DEL PEAK 52(XP11.3) WILD-TYPE     6                        21   250
D82V14, multiclass
                           clus
vv                          DEL PEAK 52(XP11.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              99
                           clus
vv                          DEL PEAK 52(XP11.3) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               250
[1] 3 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  87
  DEL PEAK 52(XP11.3) WILD-TYPE   7 230
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 52(XP11.3) MUTATED      1   87
  DEL PEAK 52(XP11.3) WILD-TYPE    7  230
                        clus
vv                       DEL PEAK 52(XP11.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          87
                        clus
vv                       DEL PEAK 52(XP11.3) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           230
[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    64  49
  DEL PEAK 53(XQ22.3) WILD-TYPE 216 165
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                          113                           381 
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                           49                           165 
$`DEL PEAK 53(XQ22.3) MUTATED`
TCGA-18-3406 TCGA-18-5595 TCGA-22-5471 TCGA-33-4533 TCGA-34-2609 TCGA-56-7221 
       12.20        27.19        60.66       133.74        31.27        19.99 
TCGA-56-A5DR TCGA-60-2696 TCGA-60-2712 TCGA-60-2721 TCGA-77-A5GA TCGA-90-7766 
        0.13         3.58         9.01        32.32        42.08         9.50 
TCGA-94-7557 TCGA-NK-A5CT TCGA-NK-A5D1 TCGA-18-3419 TCGA-18-4086 TCGA-18-5592 
        0.16        65.65        16.80        92.42         2.79        49.94 
TCGA-21-1072 TCGA-21-1080 TCGA-21-1082 TCGA-22-0940 TCGA-22-4607 TCGA-22-4613 
       99.16       122.43       119.80        21.99        19.30        11.77 
TCGA-22-5473 TCGA-22-5481 TCGA-22-5485 TCGA-22-5491 TCGA-33-4582 TCGA-33-4587 
       63.55        79.20        30.12        56.32       103.53        54.44 
TCGA-33-A4WN TCGA-33-A5GW TCGA-33-AAS8 TCGA-33-AASD TCGA-33-AASI TCGA-33-AASL 
        4.70         0.30        36.62       110.99        44.19        27.16 
TCGA-34-2600 TCGA-34-5929 TCGA-37-4135 TCGA-37-4141 TCGA-37-A5EL TCGA-39-5027 
       61.61         4.96         6.81         0.39        37.58       102.18 
TCGA-43-7656 TCGA-51-4080 TCGA-52-7810 TCGA-56-7222 TCGA-56-7223 TCGA-56-7823 
       19.59         0.39        30.35        18.48        14.53        33.24 
TCGA-56-8083 TCGA-56-8307 TCGA-56-A4BW TCGA-58-8388 TCGA-58-8390 TCGA-58-8392 
        4.93        26.89        19.23        13.55        29.95        16.47 
TCGA-60-2695 TCGA-60-2713 TCGA-60-2719 TCGA-60-2724 TCGA-60-2726 TCGA-63-7023 
       21.11        56.91        42.64        23.57        11.77        55.30 
TCGA-63-A5MI TCGA-63-A5MW TCGA-63-A5MY TCGA-66-2727 TCGA-66-2742 TCGA-66-2753 
       58.65        53.88        34.59        16.96        21.07         1.02 
TCGA-66-2754 TCGA-66-2757 TCGA-66-2763 TCGA-66-2766 TCGA-66-2780 TCGA-66-2781 
        2.01        43.99         0.99         1.02        12.03         3.98 
TCGA-66-2782 TCGA-66-2786 TCGA-66-2790 TCGA-66-2795 TCGA-68-7755 TCGA-77-6844 
       12.00        25.97        22.98         4.01         2.73        75.09 
TCGA-77-7138 TCGA-77-7142 TCGA-77-7335 TCGA-77-7337 TCGA-77-8136 TCGA-77-8139 
       11.18        73.22        70.13       106.95        39.09       104.09 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8153 TCGA-77-8154 TCGA-77-A5G3 TCGA-85-7699 
       11.54        27.39        65.49        60.53       150.25        32.91 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8288 TCGA-85-8479 TCGA-85-A512 
       31.56        26.79        30.64        13.22        15.39        15.29 
TCGA-94-8035 TCGA-94-8490 TCGA-94-8491 TCGA-94-A4VJ TCGA-96-7544 TCGA-98-8022 
        4.01         5.03        26.63        14.14        71.01        30.67 
TCGA-98-A538 TCGA-98-A53A TCGA-NC-A5HF TCGA-NC-A5HG TCGA-NC-A5HH TCGA-NC-A5HI 
       27.16        18.15         4.54        64.54         1.22        57.30 
TCGA-NC-A5HK TCGA-NC-A5HO TCGA-NC-A5HT TCGA-O2-A52S TCGA-O2-A5IB 
        4.21        43.92        26.43        12.72        11.18 

$`DEL PEAK 53(XQ22.3) WILD-TYPE`
TCGA-18-3407 TCGA-18-3409 TCGA-18-3410 TCGA-18-3416 TCGA-18-4083 TCGA-21-A5DI 
        4.47       123.19         4.80        31.99         6.18        32.19 
TCGA-22-1000 TCGA-22-1017 TCGA-22-5472 TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4589 
       14.93        48.82        64.93        22.06       129.01         1.55 
TCGA-33-6737 TCGA-34-2604 TCGA-34-2605 TCGA-39-5039 TCGA-43-2578 TCGA-43-5668 
       19.76        31.50        28.96        17.88        22.49        18.38 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8118 TCGA-43-A474 TCGA-43-A56V TCGA-56-8201 
        7.76        78.18         2.93        11.61        12.03        13.05 
TCGA-56-8305 TCGA-56-8308 TCGA-56-8504 TCGA-56-A4BY TCGA-56-A4ZJ TCGA-60-2711 
        3.45        17.00        16.77        17.85        21.04        41.42 
TCGA-60-2715 TCGA-63-A5MH TCGA-68-8250 TCGA-77-7140 TCGA-77-A5GB TCGA-90-7964 
       35.34        66.61         8.02        20.78        30.81        14.07 
TCGA-94-7033 TCGA-94-7943 TCGA-94-A5I4 TCGA-96-7545 TCGA-96-A4JK TCGA-98-8020 
       21.04        18.38        16.14        57.07        19.36         2.76 
TCGA-98-A539 TCGA-98-A53D TCGA-J1-A4AH TCGA-NC-A5HD TCGA-NC-A5HE TCGA-NC-A5HM 
        5.69        21.21        19.10         0.07        76.80        39.85 
TCGA-NC-A5HR TCGA-NK-A7XE TCGA-O2-A52W TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 
       40.90         0.43         8.58        75.75       117.57        11.34 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3417 TCGA-18-3421 TCGA-18-4721 TCGA-21-1070 
       23.54        92.15        36.07        86.96       154.32       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-21-1081 TCGA-21-1083 TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 
        9.34        43.23        31.63        88.11        41.69        33.93 
TCGA-21-5787 TCGA-22-0944 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 TCGA-22-1012 
       10.82         7.33         4.31        64.21         1.74        14.10 
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-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 TCGA-22-4609 TCGA-22-5474 
       38.17        34.75        13.12        32.02         9.57        14.63 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5482 TCGA-22-5483 
       44.25         0.79        86.30        71.34        11.74        18.84 
TCGA-22-5489 TCGA-22-5492 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 TCGA-33-4583 
       62.86        16.64        97.94        79.53       173.82       151.27 
TCGA-33-4586 TCGA-33-6738 TCGA-33-AASB TCGA-33-AASJ TCGA-34-2596 TCGA-34-2608 
       14.07        63.35         6.94       118.36         2.63        32.88 
TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 TCGA-34-5240 
       65.23        81.24        74.66         9.07        60.30        50.66 
TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-7107 TCGA-34-8454 TCGA-34-8455 
       16.93        44.75        39.32         1.12        38.79         4.04 
TCGA-34-8456 TCGA-34-A5IX TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
       26.43        33.90         4.01         0.43         0.39         7.96 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-5819 TCGA-37-A5EN TCGA-39-5011 
        8.12         7.46         7.82         3.39        21.70       133.25 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
      126.58       111.35        68.58        55.20        82.52         1.71 
TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 
       24.33         1.94        60.53        36.39        68.38        71.18 
TCGA-39-5037 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 
       55.56        17.06        40.21        38.66        39.12        33.11 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 
       27.91        22.98        24.89        21.47         5.46         3.81 
TCGA-43-8115 TCGA-43-8116 TCGA-43-A475 TCGA-43-A56U TCGA-46-3765 TCGA-46-3766 
       13.38        11.77         9.73        14.20        13.32        12.16 
TCGA-46-3767 TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 
       13.02         9.83         4.44        10.65        13.91         0.39 
TCGA-51-4081 TCGA-52-7622 TCGA-52-7809 TCGA-52-7811 TCGA-52-7812 TCGA-56-1622 
       29.95        28.34         5.46         8.75        27.45        28.96 
TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
       12.43        18.25        21.90        31.27        30.41        19.76 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8082 TCGA-56-8304 TCGA-56-8309 
        6.51         0.10        17.49        14.96         3.48        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        13.81        10.36         9.93 
TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DS 
       20.25        15.81        20.94        13.32        18.74         0.26 
TCGA-56-A62T TCGA-58-8386 TCGA-58-8387 TCGA-58-8391 TCGA-58-8393 TCGA-58-A46J 
       14.47         0.03        13.25        71.24        34.78        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-60-2708 TCGA-60-2709 
       96.82        37.94        92.71        21.93        80.45        49.48 
TCGA-60-2710 TCGA-60-2714 TCGA-60-2716 TCGA-60-2720 TCGA-60-2722 TCGA-60-2723 
       66.54        50.33        48.49         3.19        29.85        35.90 
TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 TCGA-63-7021 TCGA-63-7022 TCGA-63-A5MB 
       26.83        52.67        70.13        70.42        68.15       102.67 
TCGA-63-A5MG TCGA-63-A5MJ TCGA-63-A5ML TCGA-63-A5MM TCGA-63-A5MN TCGA-63-A5MP 
       70.62        59.97        45.57        14.99        11.34        25.28 
TCGA-63-A5MR TCGA-63-A5MS TCGA-63-A5MT TCGA-63-A5MV TCGA-66-2734 TCGA-66-2737 
       89.29        78.28        16.37        36.16        43.10         2.01 
TCGA-66-2744 TCGA-66-2755 TCGA-66-2756 TCGA-66-2758 TCGA-66-2759 TCGA-66-2765 
        0.99         0.92         0.99        21.01        25.05         2.01 
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-66-2783 TCGA-66-2785 TCGA-66-2787 TCGA-66-2788 
        2.01        19.00        24.95         1.97        40.01        22.98 
TCGA-66-2789 TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2800 
        4.04         5.03        30.02        10.06        54.08        49.05 
TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-68-A59J TCGA-70-6722 
        6.64         6.94        13.35        16.18        14.73        12.07 
TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 
       12.33        29.56        73.12        23.28       140.09         0.49 
TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 TCGA-77-8008 TCGA-77-8009 
        0.16        46.78        32.55         6.51        86.76        55.73 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 TCGA-77-8138 TCGA-77-8143 
       37.81       156.66        12.59        53.92        17.72        26.40 
TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 
        6.97        66.51        54.41        36.36       126.18       132.36 
TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6175 
       22.29         5.92        61.94        27.62        38.86         9.67 
TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 
       41.39        40.24         6.41        36.53        34.95        31.30 
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-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8350 TCGA-85-8351 
       24.13        34.52        10.09         0.76        22.45        16.77 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 
        5.29         3.09        32.71         2.01         7.76        36.59 
TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4CN 
       38.14        12.59        18.08        22.59        30.28        34.13 
TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50M 
       30.97        19.86        24.36        30.48        19.73        27.16 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-85-A5B5 
       16.21        15.85        14.96        29.92        12.39         3.65 
TCGA-90-6837 TCGA-90-7767 TCGA-90-7769 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q 
       24.92         2.93        11.77        20.22        22.62        10.59 
TCGA-92-7340 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-A5I6 
        2.70         3.48         4.01         5.26         2.30        17.69 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8023 
       18.31        17.46        27.68        21.44        30.81        21.34 
TCGA-98-A53B TCGA-98-A53C TCGA-98-A53H TCGA-98-A53I TCGA-98-A53J TCGA-L3-A4E7 
        2.01        27.02        20.32        18.58        20.71        12.89 
TCGA-L3-A524 TCGA-LA-A446 TCGA-LA-A7SW TCGA-MF-A522 TCGA-NC-A5HJ TCGA-NC-A5HL 
       16.11        13.18        13.41        11.84        13.74         2.89 
TCGA-NC-A5HN TCGA-NC-A5HP TCGA-NC-A5HQ TCGA-NK-A5CR TCGA-NK-A5CX TCGA-O2-A52N 
       49.28        25.32        14.73        83.57         3.65        33.07 
TCGA-O2-A52Q TCGA-O2-A52V TCGA-XC-AA0X 
        3.72        43.89         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 
                       150.25                        173.82 
  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE 
                        26.63                         21.04 
[1] "0.1 - 150.2 (26.6)" "0.0 - 173.8 (21.0)"
[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       23       37        0        14
  DEL PEAK 53(XQ22.3) WILD-TYPE       2       66      115        2        51
                               vv
clus                            STAGE IIB STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 53(XQ22.3) MUTATED          21         2         11          4
  DEL PEAK 53(XQ22.3) WILD-TYPE        74         1         52         15
                               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                            23                            66
  STAGE IB                            37                           115
  STAGE II                             0                             2
  STAGE IIA                           14                            51
  STAGE IIB                           21                            74
  STAGE III                            2                             1
  STAGE IIIA                          11                            52
  STAGE IIIB                           4                            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 53(XQ22.3) MUTATED    32  58  18   6
  DEL PEAK 53(XQ22.3) WILD-TYPE  80 236  53  18
D83V4, multiclass
    clus
vv   DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  T1                          32                            80
  T2                          58                           236
  T3                          18                            53
  T4                           6                            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 53(XQ22.3) MUTATED    75  33   6   0
  DEL PEAK 53(XQ22.3) WILD-TYPE 242 100  34   5
D83V5, multiclass
    clus
vv   DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  N0                          75                           242
  N1                          33                           100
  N2                           6                            34
  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    95   1
  DEL PEAK 53(XQ22.3) WILD-TYPE 316   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ22.3) MUTATED     95    1
  DEL PEAK 53(XQ22.3) WILD-TYPE  316    6
   clus
vv  DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  0                          95                           316
  1                           1                             6
[1] 2 2
[1] FALSE
D83V7, binary
                               cls
clus                              0   1
  DEL PEAK 53(XQ22.3) MUTATED    35  79
  DEL PEAK 53(XQ22.3) WILD-TYPE  95 292
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ22.3) MUTATED     35   79
  DEL PEAK 53(XQ22.3) WILD-TYPE   95  292
        clus
vv       DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  FEMALE                          35                            95
  MALE                            79                           292
[1] 2 2
[1] FALSE
D83V8, binary
                               cls
clus                              0   1
  DEL PEAK 53(XQ22.3) MUTATED    85  11
  DEL PEAK 53(XQ22.3) WILD-TYPE 299  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ22.3) MUTATED     85   11
  DEL PEAK 53(XQ22.3) WILD-TYPE  299   42
     clus
vv    DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  NO                           85                           299
  YES                          11                            42
[1] 2 2
[1] FALSE
D83V9, 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 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                                                           106
  DEL PEAK 53(XQ22.3) WILD-TYPE                                                         373
D83V10, multiclass
                                                             clus
vv                                                            DEL PEAK 53(XQ22.3) MUTATED
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                 6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                               1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         106
                                                             clus
vv                                                            DEL PEAK 53(XQ22.3) WILD-TYPE
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                                                   9
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                                                  5
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                                                 0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           373
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D83V11, continuous
D83V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 53(XQ22.3) MUTATED    95   0   1   2
  DEL PEAK 53(XQ22.3) WILD-TYPE 304  12   3  21
D83V13, multiclass
    clus
vv   DEL PEAK 53(XQ22.3) MUTATED DEL PEAK 53(XQ22.3) WILD-TYPE
  R0                          95                           304
  R1                           0                            12
  R2                           1                             3
  RX                           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                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 53(XQ22.3) MUTATED       0                        10    73
  DEL PEAK 53(XQ22.3) WILD-TYPE     9                        21   276
D83V14, multiclass
                           clus
vv                          DEL PEAK 53(XQ22.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              73
                           clus
vv                          DEL PEAK 53(XQ22.3) WILD-TYPE
  ASIAN                                                 9
  BLACK OR AFRICAN AMERICAN                            21
  WHITE                                               276
[1] 3 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  64
  DEL PEAK 53(XQ22.3) WILD-TYPE   8 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 53(XQ22.3) MUTATED      0   64
  DEL PEAK 53(XQ22.3) WILD-TYPE    8  253
                        clus
vv                       DEL PEAK 53(XQ22.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          64
                        clus
vv                       DEL PEAK 53(XQ22.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           253
[1] 2 2
[1] FALSE
