[1] "ofn"        "-oTLUAD-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/LUAD-TP/15084450/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/15092520/transformed.cor.cli.txt"

nPatients in clinical file=521, in cluster file=516, common to both=515
[1]  68 515
[1] "AMP PEAK  1(1P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                          141                           374 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                          141                           374 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          371                           144 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          371                           144 
[1] "AMP PEAK  3(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                          170                           345 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                          170                           345 
[1] "AMP PEAK  4(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           328                            187 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           328                            187 
[1] "AMP PEAK  5(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          190                           325 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          190                           325 
[1] "AMP PEAK  6(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          271                           244 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          271                           244 
[1] "AMP PEAK  7(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                          214                           301 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                          214                           301 
[1] "AMP PEAK  8(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                           173                            342 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                           173                            342 
[1] "AMP PEAK  9(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           321                            194 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           321                            194 
[1] "AMP PEAK 10(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                           170                            345 
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                           170                            345 
[1] "AMP PEAK 11(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                           178                            337 
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                           178                            337 
[1] "AMP PEAK 12(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE 
                           168                            347 
  AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE 
                           168                            347 
[1] "AMP PEAK 13(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE 
                         171                          344 
  AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE 
                         171                          344 
[1] "AMP PEAK 14(14Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE 
                           228                            287 
  AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE 
                           228                            287 
[1] "AMP PEAK 15(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE 
                         226                          289 
  AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE 
                         226                          289 
[1] "AMP PEAK 16(17Q23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE 
                           249                            266 
  AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE 
                           249                            266 
[1] "AMP PEAK 17(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE 
                           103                            412 
  AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE 
                           103                            412 
[1] "AMP PEAK 18(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE 
                         136                          379 
  AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE 
                         136                          379 
[1] "AMP PEAK 19(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                            243                             272 
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                            243                             272 
[1] "AMP PEAK 20(22Q11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE 
                             88                             427 
  AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE 
                             88                             427 
[1] "AMP PEAK 21(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE 
                        157                         358 
  AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE 
                        157                         358 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           124                            391 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           124                            391 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          148                           367 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          148                           367 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           46                           469 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           46                           469 
[1] "DEL PEAK  4(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                          236                           279 
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                          236                           279 
[1] "DEL PEAK  5(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                           245                            270 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                           245                            270 
[1] "DEL PEAK  6(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                          140                           375 
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                          140                           375 
[1] "DEL PEAK  7(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                        135                         380 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                        135                         380 
[1] "DEL PEAK  8(4P16.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                          130                           385 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                          130                           385 
[1] "DEL PEAK  9(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          187                           328 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          187                           328 
[1] "DEL PEAK 10(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          176                           339 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          176                           339 
[1] "DEL PEAK 11(5Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                          207                           308 
  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                          207                           308 
[1] "DEL PEAK 12(6Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                          134                           381 
  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                          134                           381 
[1] "DEL PEAK 13(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                           251                            264 
  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                           251                            264 
[1] "DEL PEAK 14(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                        256                         259 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                        256                         259 
[1] "DEL PEAK 15(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          256                           259 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          256                           259 
[1] "DEL PEAK 16(8P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                           122                            393 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                           122                            393 
[1] "DEL PEAK 17(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                        284                         231 
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                        284                         231 
[1] "DEL PEAK 18(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          290                           225 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          290                           225 
[1] "DEL PEAK 19(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                           256                            259 
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                           256                            259 
[1] "DEL PEAK 20(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           126                            389 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           126                            389 
[1] "DEL PEAK 21(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                           156                            359 
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                           156                            359 
[1] "DEL PEAK 22(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                           143                            372 
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                           143                            372 
[1] "DEL PEAK 23(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                           119                            396 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                           119                            396 
[1] "DEL PEAK 24(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                         116                          399 
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                         116                          399 
[1] "DEL PEAK 25(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                           138                            377 
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                           138                            377 
[1] "DEL PEAK 26(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                          98                          417 
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                          98                          417 
[1] "DEL PEAK 27(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                            137                             378 
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                            137                             378 
[1] "DEL PEAK 28(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                            293                             222 
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                            293                             222 
[1] "DEL PEAK 29(13Q12.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                            292                             223 
  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                            292                             223 
[1] "DEL PEAK 30(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           281                            234 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           281                            234 
[1] "DEL PEAK 31(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                         242                          273 
  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                         242                          273 
[1] "DEL PEAK 32(14Q32.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE 
                            144                             371 
  DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE 
                            144                             371 
[1] "DEL PEAK 33(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                           262                            253 
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                           262                            253 
[1] "DEL PEAK 34(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                           274                            241 
  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                           274                            241 
[1] "DEL PEAK 35(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                           169                            346 
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                           169                            346 
[1] "DEL PEAK 36(17P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                           281                            234 
  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                           281                            234 
[1] "DEL PEAK 37(18Q21.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                            251                             264 
  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                            251                             264 
[1] "DEL PEAK 38(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                           282                            233 
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                           282                            233 
[1] "DEL PEAK 39(19P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                           279                            236 
  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                           279                            236 
[1] "DEL PEAK 40(19P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                           269                            246 
  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                           269                            246 
[1] "DEL PEAK 41(19Q11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE 
                         134                          381 
  DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE 
                         134                          381 
[1] "DEL PEAK 42(19Q13.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE 
                            194                             321 
  DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE 
                            194                             321 
[1] "DEL PEAK 43(20P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE 
                         131                          384 
  DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE 
                         131                          384 
[1] "DEL PEAK 44(20Q13.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE 
                             80                             435 
  DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE 
                             80                             435 
[1] "DEL PEAK 45(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           185                            330 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           185                            330 
[1] "DEL PEAK 46(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            254                             261 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            254                             261 
[1] "DEL PEAK 47(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE 
                          143                           372 
  DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE 
                          143                           372 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "COMPLETENESS_OF_RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCH_NUMBER"                          

Input Data has 23 rows and 515 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=147,	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=323,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=95,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS_OF_RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH_NUMBER':	nDistinctValues=29,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 515 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY_PERFORMANCE_SCORE"           
 [8] "HISTOLOGICAL_TYPE"                     
 [9] "RADIATIONS_RADIATION_REGIMENINDICATION"
[10] "NUMBER_PACK_YEARS_SMOKED"              
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[12] "COMPLETENESS_OF_RESECTION"             
[13] "RACE"                                  
[14] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=52, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
170 278  46  19 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
170 278  46  19 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
170 278  46  19 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
170 278  46  19 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
332  96  74   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  332    96    76 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
332  96  74   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  332    96    76 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=12, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=95, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=59, binary=FALSE, numeric=TRUE
COMPLETENESS_OF_RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P22.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P22.3) MUTATED    93  45
  AMP PEAK  1(1P22.3) WILD-TYPE 244 109
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                          138                           353 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                           45                           109 
$`AMP PEAK  1(1P22.3) MUTATED`
TCGA-05-4389 TCGA-05-4402 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 
       45.01         8.02        29.98        12.00        30.02        26.01 
TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 
       25.02        29.00        22.03         9.04         0.46         5.98 
TCGA-38-4632 TCGA-44-2659 TCGA-44-2662 TCGA-44-3917 TCGA-44-6775 TCGA-44-6778 
       44.61        44.94        42.08        38.89        23.18        61.28 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 TCGA-44-8117 TCGA-44-A47B TCGA-44-A4SS 
       16.44         7.17        18.87        12.66         9.44        13.64 
TCGA-44-A4SU TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-6742 
       13.45        12.66        14.07         8.81        29.75        14.63 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR4 TCGA-49-AARN TCGA-49-AARO 
       29.26        22.26       153.04        28.90        37.32       123.58 
TCGA-49-AARQ TCGA-50-5045 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5935 
      211.82        71.47        49.28         8.22        14.27        21.47 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6593 TCGA-50-6597 TCGA-55-1592 
       18.64        25.12        22.55        11.05        41.69        23.05 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        0.79        40.73         7.79         2.20        45.34        32.71 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7910 TCGA-55-8089 
        0.59         1.15         0.13         1.32         6.48         3.29 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8206 TCGA-55-8507 TCGA-55-8514 
        0.13        23.64        17.98         1.51         0.26         6.64 
TCGA-55-A48X TCGA-55-A48Z TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8399 
       22.65        21.40        19.99        17.95         4.57        88.64 
TCGA-62-A46O TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5781 
       47.80        56.81        55.43        38.37         2.04        51.25 
TCGA-67-6215 TCGA-67-6217 TCGA-69-7979 TCGA-69-8254 TCGA-69-A59K TCGA-73-4662 
        5.72        13.87         2.93        13.45         7.04        29.98 
TCGA-73-4668 TCGA-73-4676 TCGA-73-7498 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
       15.35         5.39        39.09       163.10        27.16        19.27 
TCGA-78-7149 TCGA-78-7155 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 
       35.93        38.50         5.88         7.07       104.19        88.14 
TCGA-78-7535 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-86-7953 TCGA-86-8054 
       31.20        10.55       214.62        77.59        19.43        24.49 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 
        4.08         0.79        15.75        15.85        23.05         1.15 
TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       13.32        13.64        10.19        13.71        12.23        27.68 
TCGA-91-8499 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7562 
        1.18         6.12        23.61         1.08        19.00         2.86 
TCGA-95-7944 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8176 TCGA-97-A4M1 
       12.39        31.69        43.79         5.95        15.39        19.76 
TCGA-99-7458 TCGA-J2-8192 TCGA-J2-A4AG TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 
       24.56        24.30        16.44        17.46        12.59        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 TCGA-NJ-A55O 
        5.29         2.43        29.46        11.05        73.91         0.43 

$`AMP PEAK  1(1P22.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        14.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03        47.05        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 
       14.96         9.01        21.99        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 
       15.02        15.02         4.96         2.04         7.40         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       11.64        14.73        26.30         4.37        43.53        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       13.15        24.36        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       21.63        63.72        32.45        14.60        19.46        12.03 
TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 
       36.07        29.00        17.59        23.64         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-49-4486 TCGA-49-4487 
       15.98        15.32        11.08        11.54        76.21        28.11 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 
       28.57        35.54        46.72        32.84        29.46        55.89 
TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       12.13        17.16        11.64        22.26        63.95        62.24 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5049 
        8.55        40.41       164.12         9.86        20.52        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 
       15.72        60.16        31.04         9.27        40.60        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
        8.45        15.12        29.03        42.35         3.91        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       27.25        34.29        30.54        13.94         9.21        38.73 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
       48.62        45.21         2.86         0.07        32.65        42.51 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6983 
       15.25         0.82        48.49         3.88         5.49        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 
       24.99        40.54       107.21        70.26         7.99         0.20 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        3.12        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.78        18.64         0.53        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
        0.16        29.72        15.19        19.66        19.73         5.06 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       15.65         1.08         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.95         0.36         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        0.10         4.80        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
        2.17        16.93        20.71         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
        0.92        15.81        20.19        39.98        42.38        14.60 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       49.25        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
       13.61        39.25        40.96        29.92        20.65        39.09 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 
       37.02        87.98        42.90        28.41        28.47         1.02 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-69-7760 
       20.05        18.84        14.04        12.66         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.12        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 
        2.30        12.56        14.01         4.24        26.73         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
       52.60        23.38        26.30         4.31         1.32         1.25 
TCGA-73-7499 TCGA-73-A9RS TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
       23.51        11.18         5.69        20.58        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 
       24.99        19.50        32.09        64.90        22.29       223.96 
TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
        8.48        26.53         8.02        53.33        10.75        39.35 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       32.68        39.75        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 
        5.88        31.13        34.39        13.87        20.55        19.89 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 
       16.70         4.57        24.33        16.08        15.65        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       13.32         3.81        17.62        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
        1.97         2.60         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JQ 
       14.27         1.45        19.82         9.76         4.18        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        1.12         1.22        18.67        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
        2.76        21.40        18.18        19.89        64.60        63.52 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       25.48         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       18.12        16.41        14.30        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       21.44        20.52        17.75        20.84        18.67        20.68 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 
       34.85        36.76         1.45         5.59        21.63        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       18.08        35.47        19.00        14.30         3.81         0.20 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.53         1.91        11.87        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       41.59        31.23        10.09        14.66        14.10        11.15 
TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.26        19.82         9.70        59.11        16.87 

  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                         0.13                          0.00 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                       214.62                        223.96 
  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE 
                        18.31                         18.64 
[1] "0.1 - 214.6 (18.3)" "0.0 - 224.0 (18.6)"
[1] "hr=" "1"  
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1P22.3) MUTATED         1       37       35        0        21
  AMP PEAK  1(1P22.3) WILD-TYPE       4       98      105        1        30
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  1(1P22.3) MUTATED          17         18          4        7
  AMP PEAK  1(1P22.3) WILD-TYPE        56         54          7       19
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                            37                            98
  STAGE IB                            35                           105
  STAGE II                             0                             1
  STAGE IIA                           21                            30
  STAGE IIB                           17                            56
  STAGE IIIA                          18                            54
  STAGE IIIB                           4                             7
  STAGE IV                             7                            19
[1] 9 2
[1] 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(1P22.3) MUTATED    48  77   9   6
  AMP PEAK  1(1P22.3) WILD-TYPE 122 201  37  13
D1V4, multiclass
    clus
vv   AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  T1                          48                           122
  T2                          77                           201
  T3                           9                            37
  T4                           6                            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  1(1P22.3) MUTATED    86  35    17
  AMP PEAK  1(1P22.3) WILD-TYPE 246  61    59
D1V5, multiclass
       clus
vv      AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  N0                             86                           246
  N1                             35                            61
  N2+N3                          17                            59
[1] 3 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(1P22.3) MUTATED    95   7
  AMP PEAK  1(1P22.3) WILD-TYPE 253  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     95    7
  AMP PEAK  1(1P22.3) WILD-TYPE  253   18
   clus
vv  AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  0                          95                           253
  1                           7                            18
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED    76  65
  AMP PEAK  1(1P22.3) WILD-TYPE 199 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED     76   65
  AMP PEAK  1(1P22.3) WILD-TYPE  199  175
        clus
vv       AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  FEMALE                          76                           199
  MALE                            65                           175
[1] 2 2
[1] FALSE
D1V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  1(1P22.3) MUTATED                            6
  AMP PEAK  1(1P22.3) WILD-TYPE                         13
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  1(1P22.3) MUTATED                                  25
  AMP PEAK  1(1P22.3) WILD-TYPE                                82
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P22.3) MUTATED                                                   92
  AMP PEAK  1(1P22.3) WILD-TYPE                                                227
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  1(1P22.3) MUTATED                                            0
  AMP PEAK  1(1P22.3) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  1(1P22.3) MUTATED                                               7
  AMP PEAK  1(1P22.3) WILD-TYPE                                            12
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  1(1P22.3) MUTATED                                0
  AMP PEAK  1(1P22.3) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  1(1P22.3) MUTATED                                    2
  AMP PEAK  1(1P22.3) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  1(1P22.3) MUTATED                              0
  AMP PEAK  1(1P22.3) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  1(1P22.3) MUTATED                               5
  AMP PEAK  1(1P22.3) WILD-TYPE                            18
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  1(1P22.3) MUTATED                                 0
  AMP PEAK  1(1P22.3) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  1(1P22.3) MUTATED                                               2
  AMP PEAK  1(1P22.3) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  1(1P22.3) MUTATED                              2
  AMP PEAK  1(1P22.3) WILD-TYPE                            8
D1V9, multiclass
                                                    clus
vv                                                   AMP PEAK  1(1P22.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          92
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                7
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                5
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                2
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   AMP PEAK  1(1P22.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           227
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 12
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 18
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED     5 136
  AMP PEAK  1(1P22.3) WILD-TYPE  16 358
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED      5  136
  AMP PEAK  1(1P22.3) WILD-TYPE   16  358
     clus
vv    AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  NO                            5                            16
  YES                         136                           358
[1] 2 2
[1] FALSE
D1V11, continuous
D1V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1P22.3) MUTATED    95   5   1   8
  AMP PEAK  1(1P22.3) WILD-TYPE 248   7   3  18
D1V13, multiclass
    clus
vv   AMP PEAK  1(1P22.3) MUTATED AMP PEAK  1(1P22.3) WILD-TYPE
  R0                          95                           248
  R1                           5                             7
  R2                           1                             3
  RX                           8                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1P22.3) MUTATED                                  1     3
  AMP PEAK  1(1P22.3) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P22.3) MUTATED                          18   103
  AMP PEAK  1(1P22.3) WILD-TYPE                        33   286
D1V14, multiclass
                                  clus
vv                                 AMP PEAK  1(1P22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 18
  WHITE                                                    103
                                  clus
vv                                 AMP PEAK  1(1P22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   33
  WHITE                                                      286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V15, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P22.3) MUTATED     1 100
  AMP PEAK  1(1P22.3) WILD-TYPE   6 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P22.3) MUTATED      1  100
  AMP PEAK  1(1P22.3) WILD-TYPE    6  282
                        clus
vv                       AMP PEAK  1(1P22.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         100
                        clus
vv                       AMP PEAK  1(1P22.3) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           282
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q21.3) MUTATED   241 117
  AMP PEAK  2(1Q21.3) WILD-TYPE  96  37
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          358                           133 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          117                            37 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 
        0.00         9.96        47.05         8.02        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 TCGA-05-4430 
       14.96         9.01        12.00        30.02        26.01        25.02 
TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        15.02         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 
        2.04         0.46         5.98         8.68        97.74        49.05 
TCGA-38-4629 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2659 
       28.41        44.61        14.73        26.30        43.53        44.94 
TCGA-44-2662 TCGA-44-2668 TCGA-44-3917 TCGA-44-5644 TCGA-44-6144 TCGA-44-6147 
       42.08        25.02        38.89        28.37        23.77        27.78 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.18        63.72        32.45        61.28        16.44        14.60 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
       19.46         7.17        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS 
       12.66         3.25        15.32         9.44        11.08        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV 
       14.63        12.13        29.26        11.64        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN 
      153.04        62.24        28.90         8.55        40.41        37.32 
TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      123.58       211.82         9.86        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       15.72        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 
       40.60        78.67        21.47         8.45        18.64        25.12 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 
       22.55         3.91        11.05        41.69        10.13        25.61 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       27.25        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
       48.62         2.86        32.65         0.79        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        0.82        48.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       60.03        24.99        70.26         0.59         1.15         7.99 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7815 TCGA-55-7903 
        0.13         3.12         1.32         1.28         1.78        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        0.53         6.48         6.15         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8206 
        3.29         5.06         0.13        23.64        17.98         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8301 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        2.17        22.16         1.45         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48X TCGA-55-A48Y 
        0.30         6.64         0.49         1.58        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       21.40         1.58        19.59        15.81        20.19        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P 
       17.95         4.57        14.60        88.64        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-64-1676 
       56.71        54.35        67.96        72.30        39.25        56.81 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
       55.43        37.02        38.37        87.98        42.90        28.41 
TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 
       51.25        20.05        18.84        12.66         5.72        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 
        2.93        12.56        14.01        13.45         7.04         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       52.60        23.38        29.98        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
        1.32         5.39         1.25        39.09        23.51        11.18 
TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
      163.10         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 
       26.53        31.20         8.02        53.33        10.75        32.68 
TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
      214.62        77.59       110.50        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        13.87        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 
       15.85        23.05        21.47        14.60         1.15        30.84 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
        0.62        14.96        13.32        13.32         3.81        17.62 
TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       13.64        10.62        41.36        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        1.18         4.18         6.12        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       27.29         2.76        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8171 
       64.60        43.79        25.48         5.95         0.59        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       17.92         5.39        15.39        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       20.19        21.44        19.76        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
       20.68        24.56        34.85         1.45         5.59        23.80 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A5IP 
       18.08        16.44        19.00         3.81         0.20         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       17.46        12.59        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD 
       58.45        58.85         5.49         5.29         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.66        11.15        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O 
       71.05        62.60         0.13         1.64        29.13         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82         9.70        59.11        16.87 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-05-4397 TCGA-05-4403 TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 
       24.03        19.00        29.98        21.99        26.01        24.00 
TCGA-05-4434 TCGA-35-4122 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-4631 
       15.02         7.40       120.79        37.71        35.28        11.64 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 
        4.37        46.98        13.15        24.36        42.77         3.19 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        34.06         6.25        26.56        33.30 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-7661 
       12.59        10.78         9.93        23.15        21.63        12.03 
TCGA-44-7667 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G TCGA-49-4514 TCGA-49-6745 
       36.07         8.55        15.98        11.54        55.89        17.16 
TCGA-49-AAR2 TCGA-49-AARR TCGA-50-5055 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 
       63.95       164.12        60.16        15.12        29.03        42.35 
TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8459 TCGA-55-1594 
       25.55        12.16         6.21         0.72         7.59        38.73 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6968 TCGA-55-6975 TCGA-55-6978 TCGA-55-6985 
       45.21         0.07        42.51         3.88         5.49        40.54 
TCGA-55-6986 TCGA-55-7570 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
      107.21         0.20        23.18         1.28         1.12         0.79 
TCGA-55-7911 TCGA-55-7994 TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 TCGA-55-8205 
       17.65        19.82        19.66        19.73        15.65         1.08 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8512 TCGA-55-8513 
       15.42         0.76         0.95         0.36         0.10         4.80 
TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A491 TCGA-55-A493 
       17.62         1.61         2.17        16.93        20.58         0.92 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 
       39.98        42.38        49.25        13.61        40.96        29.92 
TCGA-64-1677 TCGA-64-1678 TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 
       20.65        39.09         2.04        28.47         1.02        14.04 
TCGA-67-6216 TCGA-69-7974 TCGA-69-7978 TCGA-69-8255 TCGA-69-8453 TCGA-78-7145 
        4.64         6.05         2.30         4.24        26.73        27.16 
TCGA-78-7155 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8660 TCGA-83-5908 
       38.50        39.35        10.55        39.75        10.55        27.09 
TCGA-86-7714 TCGA-86-8073 TCGA-86-8668 TCGA-86-8671 TCGA-86-A4P8 TCGA-91-6830 
       20.55        24.33        13.91        27.58        26.47         1.97 
TCGA-91-6848 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JQ TCGA-95-7948 
        7.36         1.45        19.82         9.76        17.29        15.65 
TCGA-97-7552 TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 TCGA-97-A4M2 TCGA-99-8028 
       63.52         0.72        18.12        16.41        20.52        36.76 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A8F4 
       21.63        24.30        35.47        14.30        14.53        11.87 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TI 
       49.35        37.35        86.04        41.59        31.23        14.10 
TCGA-NJ-A55A 
        0.26 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.00                          0.07 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       223.96                        164.12 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        18.41                         19.00 
[1] "0.0 - 224.0 (18.4)" "0.1 - 164.1 (19.0)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(1Q21.3) MUTATED         4       99       99        1        39
  AMP PEAK  2(1Q21.3) WILD-TYPE       1       36       41        0        12
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED          46         51         11       20
  AMP PEAK  2(1Q21.3) WILD-TYPE        27         21          0        6
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  STAGE I                              4                             1
  STAGE IA                            99                            36
  STAGE IB                            99                            41
  STAGE II                             1                             0
  STAGE IIA                           39                            12
  STAGE IIB                           46                            27
  STAGE IIIA                          51                            21
  STAGE IIIB                          11                             0
  STAGE IV                            20                             6
[1] 9 2
[1] 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(1Q21.3) MUTATED   120 202  31  16
  AMP PEAK  2(1Q21.3) WILD-TYPE  50  76  15   3
D2V4, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1                         120                            50
  T2                         202                            76
  T3                          31                            15
  T4                          16                             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  2(1Q21.3) MUTATED   235  71    56
  AMP PEAK  2(1Q21.3) WILD-TYPE  97  25    20
D2V5, multiclass
       clus
vv      AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                            235                            97
  N1                             71                            25
  N2+N3                          56                            20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED   254  19
  AMP PEAK  2(1Q21.3) WILD-TYPE  94   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    254   19
  AMP PEAK  2(1Q21.3) WILD-TYPE   94    6
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                         254                            94
  1                          19                             6
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED   190 181
  AMP PEAK  2(1Q21.3) WILD-TYPE  85  59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    190  181
  AMP PEAK  2(1Q21.3) WILD-TYPE   85   59
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                         190                            85
  MALE                           181                            59
[1] 2 2
[1] FALSE
D2V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED                           16
  AMP PEAK  2(1Q21.3) WILD-TYPE                          3
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  2(1Q21.3) MUTATED                                  83
  AMP PEAK  2(1Q21.3) WILD-TYPE                                24
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  2(1Q21.3) MUTATED                                                  223
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                 96
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  2(1Q21.3) MUTATED                                            1
  AMP PEAK  2(1Q21.3) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  2(1Q21.3) MUTATED                                              16
  AMP PEAK  2(1Q21.3) WILD-TYPE                                             3
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED                                2
  AMP PEAK  2(1Q21.3) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED                                    2
  AMP PEAK  2(1Q21.3) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED                              0
  AMP PEAK  2(1Q21.3) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED                              19
  AMP PEAK  2(1Q21.3) WILD-TYPE                             4
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED                                 1
  AMP PEAK  2(1Q21.3) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED                                               3
  AMP PEAK  2(1Q21.3) WILD-TYPE                                             2
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED                              5
  AMP PEAK  2(1Q21.3) WILD-TYPE                            5
D2V9, multiclass
                                                    clus
vv                                                   AMP PEAK  2(1Q21.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         223
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               16
  LUNG CLEAR CELL ADENOCARCINOMA                                               2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                               19
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                3
  MUCINOUS (COLLOID) CARCINOMA                                                 5
                                                    clus
vv                                                   AMP PEAK  2(1Q21.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            96
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  3
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                  4
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  2
  MUCINOUS (COLLOID) CARCINOMA                                                   5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED    17 354
  AMP PEAK  2(1Q21.3) WILD-TYPE   4 140
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     17  354
  AMP PEAK  2(1Q21.3) WILD-TYPE    4  140
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                           17                             4
  YES                         354                           140
[1] 2 2
[1] FALSE
D2V11, continuous
D2V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1Q21.3) MUTATED   242   9   2  22
  AMP PEAK  2(1Q21.3) WILD-TYPE 101   3   2   4
D2V13, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  R0                         242                           101
  R1                           9                             3
  R2                           2                             2
  RX                          22                             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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(1Q21.3) MUTATED                                  1     6
  AMP PEAK  2(1Q21.3) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q21.3) MUTATED                          38   279
  AMP PEAK  2(1Q21.3) WILD-TYPE                        13   110
D2V14, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 38
  WHITE                                                    279
                                  clus
vv                                 AMP PEAK  2(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                      110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     5 272
  AMP PEAK  2(1Q21.3) WILD-TYPE   2 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      5  272
  AMP PEAK  2(1Q21.3) WILD-TYPE    2  110
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         272
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           110
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(3Q26.2) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(3Q26.2) MUTATED   108  57
  AMP PEAK  3(3Q26.2) WILD-TYPE 229  97
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                          165                           326 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                           57                            97 
$`AMP PEAK  3(3Q26.2) MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
        3.98        19.96        45.01         0.00        24.03        47.05 
TCGA-05-4402 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4430 
        8.02        14.96        29.98        30.02        26.01        25.02 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 TCGA-05-5429 TCGA-35-4122 TCGA-35-5375 
       15.02        15.02        29.00         9.04         7.40         8.68 
TCGA-38-4626 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-44-2662 TCGA-44-2668 
      120.79        49.05        35.28        11.64        42.08        25.02 
TCGA-44-3918 TCGA-44-5643 TCGA-44-6145 TCGA-44-6147 TCGA-44-6775 TCGA-44-6779 
       34.06        33.30        10.78        27.78        23.18        16.44 
TCGA-44-7660 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-A47B TCGA-49-4487 
       19.46        18.87        29.00        23.64         9.44        28.11 
TCGA-49-4488 TCGA-49-4507 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAR0 
       28.57         8.81        12.13        29.26        22.26       153.04 
TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARQ TCGA-50-5055 TCGA-50-5072 TCGA-50-5931 
        8.55        37.32       211.82        60.16         8.22        14.27 
TCGA-50-5941 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-53-7624 
       18.64        22.55         3.91        25.55         6.21        34.29 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 
        9.21        38.73        45.21         2.86        32.65        42.51 
TCGA-55-6969 TCGA-55-6972 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7284 
       40.73        48.49        24.99        40.54        70.26         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 
        0.13        23.18         1.28         1.78         0.53         6.48 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8094 TCGA-55-8205 TCGA-55-8208 
       19.82         0.16        29.72         0.13         1.08        22.16 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8614 TCGA-55-8620 TCGA-55-A490 TCGA-55-A491 
        0.26         0.49        17.62         2.17         1.58        20.58 
TCGA-55-A493 TCGA-55-A4DF TCGA-62-8394 TCGA-62-A46O TCGA-62-A46P TCGA-62-A470 
        0.92        20.19         4.57        47.80        19.53        39.25 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
       56.81        20.65        55.43        51.25        28.47        20.05 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-A59K 
        6.64         6.12         2.30         2.93        12.56         7.04 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 
        2.01        23.38        26.30        15.35         5.39        23.51 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7154 
       11.18       163.10        27.16         5.69        19.27        19.50 
TCGA-78-7155 TCGA-78-7220 TCGA-78-7539 TCGA-78-7540 TCGA-78-8662 TCGA-83-5908 
       38.50        26.53        10.75        39.35       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 TCGA-86-8055 
       12.36         5.88        31.13        34.39        19.43         4.08 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8358 TCGA-86-8669 TCGA-86-8673 
        0.79        15.75        15.65        21.47        30.84        14.96 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 
       10.62        41.36         1.97         2.60        12.23         7.36 
TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JQ 
       16.18        14.27         1.18         6.12        23.61        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-8494 
        1.12         1.22         2.86        18.67        15.68         2.76 
TCGA-97-7553 TCGA-97-8176 TCGA-97-A4LX TCGA-J2-A4AD TCGA-L9-A443 TCGA-L9-A444 
       43.79        15.39        20.19        18.08         3.81         0.20 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-MP-A4TK 
       11.87        38.63        86.14        11.05        11.15        19.13 
TCGA-NJ-A4YF TCGA-O1-A52J TCGA-S2-AA1A 
       71.05        59.11        16.87 

$`AMP PEAK  3(3Q26.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 
       50.07        14.01        37.02         9.96        19.00        20.05 
TCGA-05-4415 TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4432 
        2.99         9.01        12.00        21.99        26.01        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 
       24.00         4.96        22.03         2.04         0.46         5.98 
TCGA-38-4625 TCGA-38-4627 TCGA-38-4629 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       97.74        37.71        28.41        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
        4.37        43.53        46.98        13.15        44.94        24.36 
TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 
       42.77         3.19        37.15        38.24        38.89         6.25 
TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 TCGA-44-6148 
       26.56        28.37        12.59        23.77         9.93        23.15 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7661 
       21.63        63.72        32.45        61.28        14.60        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
        7.17        36.07        17.59        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       76.21        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 
       29.46        29.75        55.89        14.63        17.16        11.64 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO 
       22.26        63.95        62.24        28.90        40.41       123.58 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      164.12         9.86        20.52        71.47        70.55        15.72 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       31.04        49.28         9.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6593 
        8.45        15.12        29.03        25.12        42.35        11.05 
TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-6543 
       27.25        30.54        13.94        23.05        48.62         0.07 
TCGA-55-6712 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
        0.79        15.25         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6986 TCGA-55-7281 
        2.20        45.34        32.71        60.03       107.21         0.59 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 
        1.15         0.20         3.12         1.32         1.28         1.12 
TCGA-55-7728 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-8087 TCGA-55-8089 
        0.79        18.64        17.65         6.15        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       19.66        19.73         5.06        23.64        15.65        17.98 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        1.51         2.17        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.36        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.58         1.61        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 
       21.40        19.59        15.81        19.99        17.95        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46R TCGA-62-A46S 
       42.38        14.60        88.64        49.25        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 
       67.96        72.30        13.61        40.96        29.92        39.09 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       37.02        38.37        87.98         2.04        42.90        28.41 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
        1.02        18.84        14.04        12.66         5.72         4.64 
TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
       13.87        22.68        13.61         5.42         7.56         6.05 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-73-4658 TCGA-73-4662 
       14.01        13.45         4.24        26.73        52.60        29.98 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-78-7148 TCGA-78-7149 
        4.31         1.32         1.25        39.09        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       21.90        39.52        24.99        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
       31.20         8.02        53.33        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 
       39.75        77.59        10.55        13.87        20.55        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 
       16.70        24.49         4.57        24.33        16.08        15.85 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
       23.05        14.60         1.15        13.91        27.58         0.62 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       13.32        13.32         3.81        17.62        13.64        26.47 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-A4BC 
       10.19        13.71        27.68         1.15        16.60         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 
       19.82         9.76         4.18         1.08        19.00        12.39 
TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       15.65        27.29        21.40        18.18        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92         5.39        18.12        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       21.60        20.58        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
        1.45         5.59        21.63        24.30        23.80        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       16.44        19.00        14.30        14.53         1.91        17.46 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       12.59        27.19         2.76        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        2.43        10.09        29.46        14.66        14.10        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG 
       19.82         9.70 

  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                         0.00                          0.07 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                       211.82                        223.96 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                        18.87                         18.05 
[1] "0.0 - 211.8 (18.9)" "0.1 - 224.0 (18.1)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(3Q26.2) MUTATED         2       43       44        0        21
  AMP PEAK  3(3Q26.2) WILD-TYPE       3       92       96        1        30
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  3(3Q26.2) MUTATED          26         20          3       11
  AMP PEAK  3(3Q26.2) WILD-TYPE        47         52          8       15
D3V3, multiclass
            clus
vv           AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            43                            92
  STAGE IB                            44                            96
  STAGE II                             0                             1
  STAGE IIA                           21                            30
  STAGE IIB                           26                            47
  STAGE IIIA                          20                            52
  STAGE IIIB                           3                             8
  STAGE IV                            11                            15
[1] 9 2
[1] 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(3Q26.2) MUTATED    55  95  15   5
  AMP PEAK  3(3Q26.2) WILD-TYPE 115 183  31  14
D3V4, multiclass
    clus
vv   AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  T1                          55                           115
  T2                          95                           183
  T3                          15                            31
  T4                           5                            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  3(3Q26.2) MUTATED   110  38    20
  AMP PEAK  3(3Q26.2) WILD-TYPE 222  58    56
D3V5, multiclass
       clus
vv      AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  N0                            110                           222
  N1                             38                            58
  N2+N3                          20                            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"
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(3Q26.2) MUTATED   110  11
  AMP PEAK  3(3Q26.2) WILD-TYPE 238  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q26.2) MUTATED    110   11
  AMP PEAK  3(3Q26.2) WILD-TYPE  238   14
   clus
vv  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  0                         110                           238
  1                          11                            14
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(3Q26.2) MUTATED    92  78
  AMP PEAK  3(3Q26.2) WILD-TYPE 183 162
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q26.2) MUTATED     92   78
  AMP PEAK  3(3Q26.2) WILD-TYPE  183  162
        clus
vv       AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  FEMALE                          92                           183
  MALE                            78                           162
[1] 2 2
[1] FALSE
D3V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  3(3Q26.2) MUTATED                            8
  AMP PEAK  3(3Q26.2) WILD-TYPE                         11
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  3(3Q26.2) MUTATED                                  34
  AMP PEAK  3(3Q26.2) WILD-TYPE                                73
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  3(3Q26.2) MUTATED                                                  112
  AMP PEAK  3(3Q26.2) WILD-TYPE                                                207
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  3(3Q26.2) MUTATED                                            2
  AMP PEAK  3(3Q26.2) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  3(3Q26.2) MUTATED                                               5
  AMP PEAK  3(3Q26.2) WILD-TYPE                                            14
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  3(3Q26.2) MUTATED                                1
  AMP PEAK  3(3Q26.2) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  3(3Q26.2) MUTATED                                    1
  AMP PEAK  3(3Q26.2) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  3(3Q26.2) MUTATED                              0
  AMP PEAK  3(3Q26.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  3(3Q26.2) MUTATED                               4
  AMP PEAK  3(3Q26.2) WILD-TYPE                            19
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  3(3Q26.2) MUTATED                                 1
  AMP PEAK  3(3Q26.2) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  3(3Q26.2) MUTATED                                               1
  AMP PEAK  3(3Q26.2) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  3(3Q26.2) MUTATED                              1
  AMP PEAK  3(3Q26.2) WILD-TYPE                            9
D3V9, multiclass
                                                    clus
vv                                                   AMP PEAK  3(3Q26.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         112
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                5
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           1
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                4
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   AMP PEAK  3(3Q26.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           207
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 14
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 19
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  MUCINOUS (COLLOID) CARCINOMA                                                   9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                               cls
clus                              0   1
  AMP PEAK  3(3Q26.2) MUTATED     6 164
  AMP PEAK  3(3Q26.2) WILD-TYPE  15 330
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q26.2) MUTATED      6  164
  AMP PEAK  3(3Q26.2) WILD-TYPE   15  330
     clus
vv    AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  NO                            6                            15
  YES                         164                           330
[1] 2 2
[1] FALSE
D3V11, continuous
D3V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(3Q26.2) MUTATED   114   3   3  10
  AMP PEAK  3(3Q26.2) WILD-TYPE 229   9   1  16
D3V13, multiclass
    clus
vv   AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  R0                         114                           229
  R1                           3                             9
  R2                           3                             1
  RX                          10                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(3Q26.2) MUTATED                                  1     3
  AMP PEAK  3(3Q26.2) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(3Q26.2) MUTATED                          15   125
  AMP PEAK  3(3Q26.2) WILD-TYPE                        36   264
D3V14, multiclass
                                  clus
vv                                 AMP PEAK  3(3Q26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    125
                                  clus
vv                                 AMP PEAK  3(3Q26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      264
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V15, binary
                               cls
clus                              0   1
  AMP PEAK  3(3Q26.2) MUTATED     5 121
  AMP PEAK  3(3Q26.2) WILD-TYPE   2 261
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q26.2) MUTATED      5  121
  AMP PEAK  3(3Q26.2) WILD-TYPE    2  261
                        clus
vv                       AMP PEAK  3(3Q26.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         121
                        clus
vv                       AMP PEAK  3(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           261
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(5P15.33) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  4(5P15.33) MUTATED   216  96
  AMP PEAK  4(5P15.33) WILD-TYPE 121  58
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           312                            179 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                            96                             58 
$`AMP PEAK  4(5P15.33) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 
       19.96        45.01         0.00         9.96        47.05         8.02 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 
       20.05         2.99        29.98        12.00        30.02        26.01 
TCGA-05-4430 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 
       25.02         4.96        29.00        22.03         2.04         0.46 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        5.98         8.68       120.79        37.71        49.05        28.41 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2657 
       11.64        44.61        14.73        26.30        43.53        13.15 
TCGA-44-2659 TCGA-44-3398 TCGA-44-3919 TCGA-44-5644 TCGA-44-6144 TCGA-44-6147 
       44.94        38.24         6.25        28.37        23.77        27.78 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 
       21.63        23.18        32.45        61.28        14.60        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
        7.17        36.07        18.87        29.00        23.64        12.66 
TCGA-44-8119 TCGA-44-A47A TCGA-44-A47F TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 
        3.25        15.32        11.08        13.64        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 
       28.57        12.66        46.72        14.07        32.84        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-6767 
       29.75        55.89        12.13        29.26        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN 
       22.26       153.04        63.95        28.90         8.55        37.32 
TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      123.58       211.82         9.86        71.47        70.55        15.72 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       31.04        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 
       21.47        18.64        25.12        22.55         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-53-7624 
       11.05        12.16        41.69        10.13        25.61        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
       30.54        13.94        23.05        38.73        48.62        45.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
        2.86         0.07         0.79        40.73        15.25        48.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 
        7.79         2.20        45.34        32.71        60.03        40.54 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 
       70.26         0.59         0.20         0.13         3.12        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        1.28         1.28         1.12        18.64         6.48        17.65 
TCGA-55-7994 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8207 
       19.82        19.73         0.13        23.64         1.51         2.17 
TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       22.16         1.45         0.76         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       17.72         0.30         6.64        17.62         0.49         1.58 
TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
        2.17        22.65        20.71         1.58        20.58         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8399 
       15.81        20.19        19.99         4.57        39.98        88.64 
TCGA-62-8402 TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       49.25        54.35        67.96        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       29.92        20.65        55.43        37.02        38.37        87.98 
TCGA-64-5778 TCGA-64-5781 TCGA-67-3770 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       42.90        51.25         1.02         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.64        22.68        13.61         5.42         7.56         6.05 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
        2.93        12.56        14.01         4.24         7.04         2.01 
TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
       52.60        29.98        15.35         1.32         5.39        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7153 
      163.10        27.16         5.69        19.27        35.93        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 
       19.50        38.50        64.90        22.29       223.96         8.48 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 
       26.53        31.20         8.02        10.75        32.68       214.62 
TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 
       77.59       110.50        27.09        12.36         5.88        34.39 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       13.87        19.43        19.89        16.70        24.49         4.08 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       24.33         0.79        15.75        15.85        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-A4D0 
       14.60         1.15        27.58         0.62        14.96         3.81 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 
       10.62        41.36         1.97        13.71        12.23         7.36 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
        1.18         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       18.67        15.68        15.65        27.29         2.76        21.40 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       31.69        64.60        43.79        25.48         5.95         0.59 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 
       18.67        17.92         5.39        15.39        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.58        21.44        19.76        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         5.59        24.30        18.08        35.47 
TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
       19.00         0.20         1.91        17.46        12.59        11.87 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19        38.63         2.76        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-NJ-A4YF 
        2.43        10.09        11.05        14.66        19.13        71.05 
TCGA-NJ-A4YG TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       62.60         0.43        19.82         9.70        59.11        16.87 

$`AMP PEAK  4(5P15.33) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4390 TCGA-05-4397 TCGA-05-4403 
       50.07         3.98        14.01        37.02        24.03        19.00 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4425 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 
       14.96         9.01        21.99        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5429 TCGA-35-4122 TCGA-38-4625 TCGA-38-4630 
       15.02        15.02         9.04         7.40        97.74        35.28 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
        4.37        46.98        24.36        42.08        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 
       25.02        37.15        38.89        34.06        26.56        33.30 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-6779 
       12.59        10.78         9.93        23.15        63.72        16.44 
TCGA-44-7661 TCGA-44-7671 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G 
       12.03        17.59         8.55        15.98         9.44        11.54 
TCGA-44-A4SU TCGA-49-4494 TCGA-49-4507 TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR3 
       13.45        35.54         8.81        14.63        17.16        62.24 
TCGA-49-AARE TCGA-49-AARR TCGA-50-5044 TCGA-50-5055 TCGA-50-5932 TCGA-50-5936 
       40.41       164.12        20.52        60.16        40.60         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 TCGA-50-6595 TCGA-50-6673 TCGA-50-8459 
       15.12        29.03        42.35         6.21         0.72         7.59 
TCGA-50-8460 TCGA-53-A4EZ TCGA-55-6642 TCGA-55-6968 TCGA-55-6971 TCGA-55-6975 
       27.25         9.21        32.65        42.51         0.82         3.88 
TCGA-55-6978 TCGA-55-6984 TCGA-55-6986 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 
        5.49        24.99       107.21         1.15         7.99         1.32 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 
        0.79         1.78         0.53         6.15         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8097 TCGA-55-8203 
       15.19         3.29        19.66         5.06        15.65        17.98 
TCGA-55-8205 TCGA-55-8299 TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 
        1.08        15.42         0.95         0.10         4.80         1.61 
TCGA-55-8621 TCGA-55-A48Z TCGA-55-A492 TCGA-55-A57B TCGA-62-8397 TCGA-62-8398 
       16.93        21.40        19.59        17.95        42.38        14.60 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46V TCGA-64-1676 TCGA-64-1678 
       47.80        19.53        56.71        72.30        56.81        39.09 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
        2.04        28.41        28.47        20.05        18.84        14.04 
TCGA-67-3774 TCGA-69-7761 TCGA-69-7978 TCGA-69-8254 TCGA-69-8453 TCGA-73-4659 
       12.66         6.12         2.30        13.45        26.73        23.38 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7148 
       26.30         4.31         1.25        39.09        11.18        20.58 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 
       21.90        39.52        32.09         5.88         7.07       104.19 
TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8660 
       88.14        53.33        39.35        10.55        39.75        10.55 
TCGA-86-7701 TCGA-86-7714 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8668 
       31.13        20.55         4.57        16.08        15.65        13.91 
TCGA-86-8669 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       30.84        13.32        13.32        17.62        13.64        26.47 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       10.19         2.60        27.68         1.15        16.18        16.60 
TCGA-91-8497 TCGA-93-A4JN TCGA-95-7944 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 
       14.27        23.61        12.39        18.18        19.89        63.52 
TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
        0.72        18.12        16.41        20.19        20.52        17.75 
TCGA-97-A4M5 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E6 
       20.84         1.45        21.63        23.80        16.44        14.30 
TCGA-L9-A443 TCGA-L9-A50W TCGA-MP-A4SV TCGA-MP-A4TE TCGA-MP-A4TI TCGA-MP-A4TJ 
        3.81        14.53        86.14        29.46        14.10        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91         0.13         1.64        29.13         0.26 

  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                           0.0                            0.1 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                        223.96                         164.12 
  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE 
                         19.20                          16.93 
[1] "0.0 - 224.0 (19.2)" "0.1 - 164.1 (16.9)"
[1] "hr=" "1.2"
D4V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(5P15.33) MUTATED         4       89       83        1        39
  AMP PEAK  4(5P15.33) WILD-TYPE       1       46       57        0        12
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  4(5P15.33) MUTATED          40         48          8       16
  AMP PEAK  4(5P15.33) WILD-TYPE        33         24          3       10
D4V3, multiclass
            clus
vv           AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                             89                             46
  STAGE IB                             83                             57
  STAGE II                              1                              0
  STAGE IIA                            39                             12
  STAGE IIB                            40                             33
  STAGE IIIA                           48                             24
  STAGE IIIB                            8                              3
  STAGE IV                             16                             10
[1] 9 2
[1] 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(5P15.33) MUTATED   113 176  24  13
  AMP PEAK  4(5P15.33) WILD-TYPE  57 102  22   6
D4V4, multiclass
    clus
vv   AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  T1                          113                             57
  T2                          176                            102
  T3                           24                             22
  T4                           13                              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  4(5P15.33) MUTATED   203  64    54
  AMP PEAK  4(5P15.33) WILD-TYPE 129  32    22
D4V5, multiclass
       clus
vv      AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  N0                             203                            129
  N1                              64                             32
  N2+N3                           54                             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED   218  15
  AMP PEAK  4(5P15.33) WILD-TYPE 130  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED    218   15
  AMP PEAK  4(5P15.33) WILD-TYPE  130   10
   clus
vv  AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  0                          218                            130
  1                           15                             10
[1] 2 2
[1] FALSE
D4V7, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED   182 146
  AMP PEAK  4(5P15.33) WILD-TYPE  93  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED    182  146
  AMP PEAK  4(5P15.33) WILD-TYPE   93   94
        clus
vv       AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  FEMALE                          182                             93
  MALE                            146                             94
[1] 2 2
[1] FALSE
D4V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  4(5P15.33) MUTATED                           13
  AMP PEAK  4(5P15.33) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  4(5P15.33) MUTATED                                  65
  AMP PEAK  4(5P15.33) WILD-TYPE                                42
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(5P15.33) MUTATED                                                  211
  AMP PEAK  4(5P15.33) WILD-TYPE                                                108
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  4(5P15.33) MUTATED                                            2
  AMP PEAK  4(5P15.33) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  4(5P15.33) MUTATED                                              13
  AMP PEAK  4(5P15.33) WILD-TYPE                                             6
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  4(5P15.33) MUTATED                                2
  AMP PEAK  4(5P15.33) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  4(5P15.33) MUTATED                                    2
  AMP PEAK  4(5P15.33) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  4(5P15.33) MUTATED                              0
  AMP PEAK  4(5P15.33) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  4(5P15.33) MUTATED                              14
  AMP PEAK  4(5P15.33) WILD-TYPE                             9
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  4(5P15.33) MUTATED                                 0
  AMP PEAK  4(5P15.33) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  4(5P15.33) MUTATED                                               3
  AMP PEAK  4(5P15.33) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  4(5P15.33) MUTATED                              3
  AMP PEAK  4(5P15.33) WILD-TYPE                            7
D4V9, multiclass
                                                    clus
vv                                                   AMP PEAK  4(5P15.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          211
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                13
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                14
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   AMP PEAK  4(5P15.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            108
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   6
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                   9
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  MUCINOUS (COLLOID) CARCINOMA                                                    7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED    16 312
  AMP PEAK  4(5P15.33) WILD-TYPE   5 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED     16  312
  AMP PEAK  4(5P15.33) WILD-TYPE    5  182
     clus
vv    AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  NO                            16                              5
  YES                          312                            182
[1] 2 2
[1] FALSE
D4V11, continuous
D4V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  4(5P15.33) MUTATED   217   8   2  19
  AMP PEAK  4(5P15.33) WILD-TYPE 126   4   2   7
D4V13, multiclass
    clus
vv   AMP PEAK  4(5P15.33) MUTATED AMP PEAK  4(5P15.33) WILD-TYPE
  R0                          217                            126
  R1                            8                              4
  R2                            2                              2
  RX                           19                              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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(5P15.33) MUTATED                                  1     6
  AMP PEAK  4(5P15.33) WILD-TYPE                                0     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(5P15.33) MUTATED                          35   247
  AMP PEAK  4(5P15.33) WILD-TYPE                        16   142
D4V14, multiclass
                                  clus
vv                                 AMP PEAK  4(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  35
  WHITE                                                     247
                                  clus
vv                                 AMP PEAK  4(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                       142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, binary
                                cls
clus                               0   1
  AMP PEAK  4(5P15.33) MUTATED     5 244
  AMP PEAK  4(5P15.33) WILD-TYPE   2 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(5P15.33) MUTATED      5  244
  AMP PEAK  4(5P15.33) WILD-TYPE    2  138
                        clus
vv                       AMP PEAK  4(5P15.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          244
                        clus
vv                       AMP PEAK  4(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            138
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(6P21.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(6P21.1) MUTATED   131  52
  AMP PEAK  5(6P21.1) WILD-TYPE 206 102
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          183                           308 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                           52                           102 
$`AMP PEAK  5(6P21.1) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4420 TCGA-05-4427 TCGA-05-4430 TCGA-05-5425 
       50.07        45.01        29.98        26.01        25.02        29.00 
TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-6178 TCGA-44-2659 
        0.46         8.68        97.74        49.05        14.73        44.94 
TCGA-44-2666 TCGA-44-3918 TCGA-44-6147 TCGA-44-6774 TCGA-44-7660 TCGA-44-7662 
        3.19        34.06        27.78        21.63        19.46         7.17 
TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-44-A4SU 
       36.07        29.00        17.59         3.25        11.08        13.45 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 
       28.11        28.57        12.66        29.46        29.75        14.63 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR0 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       11.64        22.26       153.04        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       21.47        18.64        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 
       25.55        41.69         0.72        10.13        34.29        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 
        9.21        23.05        48.62        45.21         2.86        32.65 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6985 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 
       15.25        48.49        40.54         1.15         0.13         1.32 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        1.78        18.64         6.15        19.82         0.16        29.72 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8507 TCGA-55-8511 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.26         0.30         0.10         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A494 
        1.58         2.17        22.65        20.71         1.58        15.81 
TCGA-62-8394 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46S 
        4.57        14.60        88.64        49.25        19.53        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 TCGA-64-1680 
       67.96        72.30        39.25        40.96        20.65        37.02 
TCGA-64-5774 TCGA-64-5779 TCGA-67-3773 TCGA-67-6215 TCGA-69-7763 TCGA-69-7764 
       87.98        28.41        14.04         5.72        22.68        13.61 
TCGA-69-7765 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 TCGA-73-4662 
        5.42         2.93        12.56         4.24         2.01        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       26.30        15.35         4.31         1.25        39.09        23.51 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 
       27.16        19.27        35.93        38.50         5.88        64.90 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 
        7.07       104.19        88.14        26.53        10.75        10.55 
TCGA-78-7633 TCGA-78-8655 TCGA-78-8662 TCGA-86-6851 TCGA-86-7713 TCGA-86-7954 
       32.68        77.59       110.50         5.88        13.87        19.89 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
        0.79        15.75        15.85        23.05        21.47        14.60 
TCGA-86-8672 TCGA-86-8674 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
        0.62        13.32        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7562 TCGA-95-7567 
        7.36         1.18        23.61        19.00         2.86        18.67 
TCGA-95-7944 TCGA-95-7948 TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       12.39        15.65        31.69        43.79        25.48         0.59 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M1 
       18.67         5.39        15.39        16.41        14.30        19.76 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
       20.52        20.68         5.59        23.80        18.08        35.47 
TCGA-L9-A444 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T6 
        0.20        12.59        38.63         2.76        86.14        58.85 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YP 
       10.09        29.46        11.05        73.91        71.05         1.64 
TCGA-NJ-A55A TCGA-NJ-A7XG TCGA-O1-A52J 
        0.26         9.70        59.11 

$`AMP PEAK  5(6P21.1) WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 
        3.98        19.96        14.01        37.02         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
       24.03        47.05         8.02        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96         9.01        12.00        30.02        21.99        26.01 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 
       25.02        24.00        15.02        15.02         4.96        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 
        9.04         2.04         7.40         5.98       120.79        37.71 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        11.64        44.61        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
       43.53        46.98        13.15        24.36        42.08        42.77 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 
       25.02        37.15        38.24        38.89         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       33.30        28.37        12.59        23.77        10.78         9.93 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        23.18        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       14.60        12.03        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
       15.98        15.32         9.44        11.54        13.64        76.21 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 
       35.54        46.72        14.07        32.84         8.81        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       12.13        29.26        17.16        22.26        63.95        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ 
       28.90         8.55        40.41        37.32       123.58       211.82 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      164.12         9.86        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5936 
       60.16        31.04        49.28         8.22         9.27         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-8457 
       15.12        29.03        11.05        12.16         6.21        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1594 TCGA-55-6543 TCGA-55-6712 
        7.59        27.25        30.54        38.73         0.07         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
       42.51        40.73         0.82         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 
        2.20        45.34        32.71        60.03        24.99       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7724 
       70.26         0.59         7.99         0.20         3.12        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 
        1.28         1.28         1.12         0.79         0.53         6.48 
TCGA-55-7911 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       17.65        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        0.13        23.64        15.42         1.45         0.76         0.95 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 
        0.36         0.49        17.72         4.80         1.61        16.93 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG 
       21.40        20.58        19.59         0.92        20.19        19.99 
TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46Y 
       17.95        39.98        42.38        47.80        56.71        13.61 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 
       29.92        56.81        39.09        55.43        38.37         2.04 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       42.90        51.25        28.47         1.02        20.05        18.84 
TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 
       12.66         4.64        13.87         6.64         6.12         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K 
        6.05         2.30        14.01        13.45        26.73         7.04 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS TCGA-78-7143 
       52.60        23.38         1.32         5.39        11.18       163.10 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        5.69        20.58        21.90        39.52        24.99        19.50 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 
       32.09        22.29       223.96         8.48        31.20         8.02 
TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-83-5908 
       53.33        39.35       214.62        39.75        10.55        27.09 
TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
       12.36        31.13        34.39        20.55        19.43        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 
       24.49         4.08         4.57        24.33        16.08        15.65 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 
        1.15        13.91        30.84        27.58        14.96        13.32 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
        3.81        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6836 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
        1.97        13.71         1.15        16.18        16.60        14.27 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO 
        1.45        19.82         9.76         4.18         6.12         1.08 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 
       17.29         1.12         1.22        15.68        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 
       21.40        18.18        19.89        64.60        63.52         5.95 
TCGA-97-7941 TCGA-97-8172 TCGA-97-8175 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
        0.72        17.92        18.12        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        17.75        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-A4AG TCGA-L4-A4E5 
       36.76         1.45        21.63        24.30        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 
       14.30         3.81        14.53         1.91        17.46        11.87 
TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
       27.19        58.45        49.35        37.35        86.04         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI 
        5.29        41.59        31.23         2.43        14.66        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55O 
       11.15        19.13        62.60         0.13        29.13         0.43 
TCGA-NJ-A55R TCGA-S2-AA1A 
       19.82        16.87 

  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          0.1                           0.0 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                       153.04                        223.96 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                       18.670                        18.035 
[1] "0.1 - 153.0 (18.7)" "0.0 - 224.0 (18.0)"
[1] "hr=" "1.2"
D5V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(6P21.1) MUTATED         2       52       53        0        18
  AMP PEAK  5(6P21.1) WILD-TYPE       3       83       87        1        33
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  5(6P21.1) MUTATED          22         24          5       14
  AMP PEAK  5(6P21.1) WILD-TYPE        51         48          6       12
D5V3, multiclass
            clus
vv           AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            52                            83
  STAGE IB                            53                            87
  STAGE II                             0                             1
  STAGE IIA                           18                            33
  STAGE IIB                           22                            51
  STAGE IIIA                          24                            48
  STAGE IIIB                           5                             6
  STAGE IV                            14                            12
[1] 9 2
[1] 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(6P21.1) MUTATED    64 103  13   8
  AMP PEAK  5(6P21.1) WILD-TYPE 106 175  33  11
D5V4, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  T1                          64                           106
  T2                         103                           175
  T3                          13                            33
  T4                           8                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1 N2+N3
  AMP PEAK  5(6P21.1) MUTATED   128  30    27
  AMP PEAK  5(6P21.1) WILD-TYPE 204  66    49
D5V5, multiclass
       clus
vv      AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  N0                            128                           204
  N1                             30                            66
  N2+N3                          27                            49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED   130  13
  AMP PEAK  5(6P21.1) WILD-TYPE 218  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED    130   13
  AMP PEAK  5(6P21.1) WILD-TYPE  218   12
   clus
vv  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  0                         130                           218
  1                          13                            12
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED   100  90
  AMP PEAK  5(6P21.1) WILD-TYPE 175 150
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED    100   90
  AMP PEAK  5(6P21.1) WILD-TYPE  175  150
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  FEMALE                         100                           175
  MALE                            90                           150
[1] 2 2
[1] FALSE
D5V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                           10
  AMP PEAK  5(6P21.1) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  5(6P21.1) MUTATED                                  37
  AMP PEAK  5(6P21.1) WILD-TYPE                                70
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(6P21.1) MUTATED                                                  118
  AMP PEAK  5(6P21.1) WILD-TYPE                                                201
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  5(6P21.1) MUTATED                                            0
  AMP PEAK  5(6P21.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  5(6P21.1) MUTATED                                               8
  AMP PEAK  5(6P21.1) WILD-TYPE                                            11
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                                1
  AMP PEAK  5(6P21.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                                    1
  AMP PEAK  5(6P21.1) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                              0
  AMP PEAK  5(6P21.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                              13
  AMP PEAK  5(6P21.1) WILD-TYPE                            10
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                                 0
  AMP PEAK  5(6P21.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                                               1
  AMP PEAK  5(6P21.1) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                              1
  AMP PEAK  5(6P21.1) WILD-TYPE                            9
D5V9, multiclass
                                                    clus
vv                                                   AMP PEAK  5(6P21.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         118
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                8
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           1
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                               13
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   AMP PEAK  5(6P21.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           201
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 11
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 10
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  MUCINOUS (COLLOID) CARCINOMA                                                   9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED     7 183
  AMP PEAK  5(6P21.1) WILD-TYPE  14 311
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED      7  183
  AMP PEAK  5(6P21.1) WILD-TYPE   14  311
     clus
vv    AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  NO                            7                            14
  YES                         183                           311
[1] 2 2
[1] FALSE
D5V11, continuous
D5V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(6P21.1) MUTATED   127   6   0   9
  AMP PEAK  5(6P21.1) WILD-TYPE 216   6   4  17
D5V13, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  R0                         127                           216
  R1                           6                             6
  R2                           0                             4
  RX                           9                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(6P21.1) MUTATED                                  1     5
  AMP PEAK  5(6P21.1) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(6P21.1) MUTATED                          10   159
  AMP PEAK  5(6P21.1) WILD-TYPE                        41   230
D5V14, multiclass
                                  clus
vv                                 AMP PEAK  5(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                    159
                                  clus
vv                                 AMP PEAK  5(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   41
  WHITE                                                      230
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED     5 148
  AMP PEAK  5(6P21.1) WILD-TYPE   2 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED      5  148
  AMP PEAK  5(6P21.1) WILD-TYPE    2  234
                        clus
vv                       AMP PEAK  5(6P21.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         148
                        clus
vv                       AMP PEAK  5(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           234
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(7P11.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(7P11.2) MUTATED   170  90
  AMP PEAK  6(7P11.2) WILD-TYPE 167  64
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          260                           231 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                           90                            64 
$`AMP PEAK  6(7P11.2) MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4402 
        3.98        19.96        37.02         0.00        47.05         8.02 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-5423 
       20.05         2.99        14.96         9.01        29.98         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-35-4123 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
       29.00        22.03         5.98        37.71        49.05        28.41 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       11.64        44.61        14.73        46.98        13.15        44.94 
TCGA-44-2661 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       24.36        37.15        38.89        34.06         6.25        26.56 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 
       28.37        12.59        23.77        23.18        32.45        16.44 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 
       19.46        12.03         7.17        36.07        18.87        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
        8.55        15.98        11.08        11.54        13.64        13.45 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       29.46        29.75        14.63        17.16        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ 
       22.26       153.04        28.90        40.41       123.58       211.82 
TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
        9.86        71.47        70.55        60.16        31.04         8.22 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 
        9.27        78.67         8.45        15.12        18.64        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       22.55        42.35         3.91        11.05        12.16         6.21 
TCGA-50-6673 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
        0.72        34.29         9.21        38.73        45.21         2.86 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
        0.07         0.79         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6987 
        7.79         2.20        45.34        32.71        40.54        70.26 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 
        1.15         7.99         1.32        23.18         1.28         1.12 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 TCGA-55-8091 
        0.53         6.48        19.82        29.72         3.29        19.73 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 
        5.06        23.64         1.08         1.51         1.45         0.76 
TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 
        0.95        17.72         0.30         6.64         0.49         1.58 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       21.40         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99        17.95         4.57        42.38        14.60        88.64 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 
       47.80        19.53        56.71        13.61        29.92        56.81 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 
       55.43        37.02        38.37        28.41        51.25         1.02 
TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7764 TCGA-69-7765 
       20.05        18.84        13.87         6.64        13.61         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K 
        6.05         2.30         2.93        12.56         4.24         7.04 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
        2.01        52.60        23.38        29.98        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
        1.32         5.39        23.51        11.18       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 
        5.69        19.27        21.90        19.50        38.50        22.29 
TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 TCGA-78-7540 TCGA-78-8655 TCGA-78-8662 
        7.07       223.96        31.20        39.35        77.59       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 
       27.09        12.36        31.13        13.87        19.43        16.70 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 
        4.08        24.33         0.79        15.75        15.65        15.85 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8668 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 
       23.05        14.60        13.91        14.96        13.32        13.64 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-A4BC 
       10.19         2.60        27.68         7.36        16.60         1.45 
TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7562 TCGA-95-7944 
        4.18         1.08        19.00         1.12         2.86        12.39 
TCGA-95-7947 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       15.68         2.76        18.18        43.79        25.48         5.95 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       18.67        18.12        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 
       20.58        19.76        20.68        34.85         5.59        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 
       23.80        18.08        35.47        19.00         3.81         0.20 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.53         1.91        12.59        27.19        38.63         2.76 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 
       58.45        49.35        37.35        58.85         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TK TCGA-NJ-A4YF 
       31.23         2.43        10.09        11.05        19.13        71.05 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

$`AMP PEAK  6(7P11.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 
       50.07        14.01        45.01         9.96        24.03        19.00 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
       12.00        30.02        21.99        26.01        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5429 TCGA-05-5715 
       25.02        24.00        15.02        15.02         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4630 
        0.46         7.40         8.68        97.74       120.79        35.28 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
       26.30         4.37        43.53        42.08        42.77         3.19 
TCGA-44-2668 TCGA-44-3398 TCGA-44-5643 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       25.02        38.24        33.30        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 TCGA-44-7670 
       23.15        21.63        63.72        61.28        14.60        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B TCGA-49-4486 
       17.59        23.64         3.25        15.32         9.44        76.21 
TCGA-49-4487 TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR2 
       28.11         8.81        55.89        12.13        29.26        63.95 
TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARR TCGA-50-5044 TCGA-50-5051 
       62.24         8.55        37.32       164.12        20.52        15.72 
TCGA-50-5068 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 TCGA-50-6592 
       49.28        14.27        40.60        21.47        29.03        25.55 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
       41.69        10.13        25.61         7.59        27.25        30.54 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 
       13.94        23.05        48.62        32.65        42.51        40.73 
TCGA-55-6970 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-7281 TCGA-55-7570 
       15.25        60.03        24.99       107.21         0.59         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        0.13         3.12         1.28         0.79         1.78        18.64 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8087 TCGA-55-8090 TCGA-55-8094 
       17.65         6.15         0.16        15.19        19.66         0.13 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8506 
       15.65        17.98         2.17        22.16        15.42         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 
        0.26         0.49         0.10         4.80        17.62         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A4DF TCGA-62-8395 
        2.17        16.93        22.65        20.71        20.19        39.98 
TCGA-62-8402 TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 
       49.25        54.35        67.96        72.30        39.25        40.96 
TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 
       20.65        39.09        87.98         2.04        42.90        28.47 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
       14.04        12.66         5.72         4.64         6.12        22.68 
TCGA-69-7973 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4666 TCGA-73-4677 
        7.56        14.01        13.45        26.73        26.30         1.25 
TCGA-73-7498 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
       39.09        20.58        35.93        39.52        24.99        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        5.88        64.90       104.19         8.48        88.14        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        8.02        53.33        10.75        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8660 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 
       39.75        10.55         5.88        34.39        20.55        19.89 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 
       24.49         4.57        16.08        21.47         1.15        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 
       27.58         0.62        13.32         3.81        17.62        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-6849 
       10.62        41.36         1.97        13.71        12.23         1.15 
TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 
       16.18        14.27         1.18        19.82         9.76         6.12 
TCGA-93-A4JN TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 TCGA-95-8039 
       23.61        17.29         1.22        18.67        15.65        27.29 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 
       21.40        19.89        31.69        64.60        63.52         0.59 
TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 
        0.72        17.92         5.39        20.19        21.44        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       17.75        20.84        18.67        24.56        36.76         1.45 
TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MP-A4SV 
       21.63        16.44        14.30        17.46        11.87        86.14 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       86.04         5.49        29.46        14.66        14.10        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.43        19.82         9.70 

  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                          0.0                           0.1 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                       223.96                        214.62 
  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE 
                       17.015                        19.820 
[1] "0.0 - 224.0 (17.0)" "0.1 - 214.6 (19.8)"
[1] "hr=" "1.4"
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(7P11.2) MUTATED         5       62       70        1        27
  AMP PEAK  6(7P11.2) WILD-TYPE       0       73       70        0        24
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  6(7P11.2) MUTATED          38         48          6       14
  AMP PEAK  6(7P11.2) WILD-TYPE        35         24          5       12
D6V3, multiclass
            clus
vv           AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  STAGE I                              5                             0
  STAGE IA                            62                            73
  STAGE IB                            70                            70
  STAGE II                             1                             0
  STAGE IIA                           27                            24
  STAGE IIB                           38                            35
  STAGE IIIA                          48                            24
  STAGE IIIB                           6                             5
  STAGE IV                            14                            12
[1] 9 2
[1] 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(7P11.2) MUTATED    81 152  28   8
  AMP PEAK  6(7P11.2) WILD-TYPE  89 126  18  11
D6V4, multiclass
    clus
vv   AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  T1                          81                            89
  T2                         152                           126
  T3                          28                            18
  T4                           8                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1 N2+N3
  AMP PEAK  6(7P11.2) MUTATED   158  51    55
  AMP PEAK  6(7P11.2) WILD-TYPE 174  45    21
D6V5, multiclass
       clus
vv      AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  N0                            158                           174
  N1                             51                            45
  N2+N3                          55                            21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P11.2) MUTATED   179  13
  AMP PEAK  6(7P11.2) WILD-TYPE 169  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED    179   13
  AMP PEAK  6(7P11.2) WILD-TYPE  169   12
   clus
vv  AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  0                         179                           169
  1                          13                            12
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P11.2) MUTATED   151 120
  AMP PEAK  6(7P11.2) WILD-TYPE 124 120
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED    151  120
  AMP PEAK  6(7P11.2) WILD-TYPE  124  120
        clus
vv       AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  FEMALE                         151                           124
  MALE                           120                           120
[1] 2 2
[1] FALSE
D6V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  6(7P11.2) MUTATED                            7
  AMP PEAK  6(7P11.2) WILD-TYPE                         12
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  6(7P11.2) MUTATED                                  53
  AMP PEAK  6(7P11.2) WILD-TYPE                                54
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(7P11.2) MUTATED                                                  179
  AMP PEAK  6(7P11.2) WILD-TYPE                                                140
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  6(7P11.2) MUTATED                                            4
  AMP PEAK  6(7P11.2) WILD-TYPE                                          1
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  6(7P11.2) MUTATED                                              10
  AMP PEAK  6(7P11.2) WILD-TYPE                                             9
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  6(7P11.2) MUTATED                                0
  AMP PEAK  6(7P11.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  6(7P11.2) MUTATED                                    2
  AMP PEAK  6(7P11.2) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  6(7P11.2) MUTATED                              0
  AMP PEAK  6(7P11.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  6(7P11.2) MUTATED                              10
  AMP PEAK  6(7P11.2) WILD-TYPE                            13
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  6(7P11.2) MUTATED                                 0
  AMP PEAK  6(7P11.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  6(7P11.2) MUTATED                                               4
  AMP PEAK  6(7P11.2) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  6(7P11.2) MUTATED                              2
  AMP PEAK  6(7P11.2) WILD-TYPE                            8
D6V9, multiclass
                                                    clus
vv                                                   AMP PEAK  6(7P11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         179
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               10
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                               10
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                4
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   AMP PEAK  6(7P11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           140
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  9
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 13
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  1
  MUCINOUS (COLLOID) CARCINOMA                                                   8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
                               cls
clus                              0   1
  AMP PEAK  6(7P11.2) MUTATED    10 261
  AMP PEAK  6(7P11.2) WILD-TYPE  11 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED     10  261
  AMP PEAK  6(7P11.2) WILD-TYPE   11  233
     clus
vv    AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  NO                           10                            11
  YES                         261                           233
[1] 2 2
[1] FALSE
D6V11, continuous
D6V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(7P11.2) MUTATED   180   6   3  14
  AMP PEAK  6(7P11.2) WILD-TYPE 163   6   1  12
D6V13, multiclass
    clus
vv   AMP PEAK  6(7P11.2) MUTATED AMP PEAK  6(7P11.2) WILD-TYPE
  R0                         180                           163
  R1                           6                             6
  R2                           3                             1
  RX                          14                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(7P11.2) MUTATED                                  1     5
  AMP PEAK  6(7P11.2) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(7P11.2) MUTATED                          32   203
  AMP PEAK  6(7P11.2) WILD-TYPE                        19   186
D6V14, multiclass
                                  clus
vv                                 AMP PEAK  6(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 32
  WHITE                                                    203
                                  clus
vv                                 AMP PEAK  6(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      186
[1] 4 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(7P11.2) MUTATED     4 207
  AMP PEAK  6(7P11.2) WILD-TYPE   3 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P11.2) MUTATED      4  207
  AMP PEAK  6(7P11.2) WILD-TYPE    3  175
                        clus
vv                       AMP PEAK  6(7P11.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         207
                        clus
vv                       AMP PEAK  6(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           175
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(7Q31.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(7Q31.2) MUTATED   140  68
  AMP PEAK  7(7Q31.2) WILD-TYPE 197  86
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                          208                           283 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                           68                            86 
$`AMP PEAK  7(7Q31.2) MUTATED`
TCGA-05-4250 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4420 
        3.98        47.05         8.02        20.05         9.01        29.98 
TCGA-05-4427 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 
       26.01         4.96        29.00        22.03         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 
        8.68        97.74        37.71        49.05        28.41        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-3396 
       44.61        14.73        13.15        44.94        42.08        37.15 
TCGA-44-3917 TCGA-44-3919 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6777 
       38.89         6.25        12.59        23.77        10.78        32.45 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-8117 
       61.28        19.46        12.03         7.17        18.87        12.66 
TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       11.08        13.64        13.45        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4512 TCGA-49-6745 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 
       14.07        29.75        17.16        22.26        22.26        62.24 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5045 
       28.90        40.41       123.58       211.82         9.86        71.47 
TCGA-50-5049 TCGA-50-5066 TCGA-50-5930 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 
       70.55        31.04         9.27        21.47        18.64        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6593 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1596 
       22.55        42.35        11.05         9.21        23.05        45.21 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.07         0.79        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 
        3.88         5.49         7.79         2.20        60.03        40.54 
TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 
       70.26         1.15         7.99         1.32        23.18         1.28 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8091 TCGA-55-8092 
        0.53         6.48        19.82         0.16        19.73         5.06 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
        1.08         1.51         1.45         0.76         0.95         0.26 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A490 
       17.72         0.30         6.64         1.58         2.17         1.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 
       19.59         0.92        15.81         4.57        42.38        14.60 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 
       88.64        47.80        56.71        13.61        29.92        56.81 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5781 TCGA-67-3772 TCGA-69-7764 
       55.43        37.02        38.37        51.25        18.84        13.61 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 
        5.42         6.05         2.30         2.93         7.04         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
       52.60        23.38        29.98        26.30         4.31         1.32 
TCGA-73-4676 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7154 
        5.39        23.51       163.10        27.16        19.27        19.50 
TCGA-78-7160 TCGA-78-7163 TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 
       22.29       223.96        26.53         8.02        39.35        10.55 
TCGA-78-8640 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 
      214.62        77.59        27.09        12.36        31.13        13.87 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 
       19.43        19.89        16.70         4.08        24.33        15.75 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8672 TCGA-86-8673 TCGA-86-A4P7 
       23.05        21.47        14.60         0.62        14.96        13.64 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-A4BC 
        2.60        13.71        27.68         7.36        16.60         1.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        4.18        23.61         1.08         1.12         1.22         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       12.39        15.68         2.76        43.79        25.48         5.95 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8552 TCGA-99-8025 
       18.67        18.12        15.39        14.30        20.58        34.85 
TCGA-99-8033 TCGA-J2-8192 TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV 
        5.59        24.30        19.00         0.20        14.53        12.59 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       27.19        38.63        86.14        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       58.85         5.29        41.59        31.23         2.43        10.09 
TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-O1-A52J TCGA-S2-AA1A 
       19.13        71.05        59.11        16.87 

$`AMP PEAK  7(7Q31.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
        9.96        24.03        19.00         2.99        14.96        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 
       15.02        15.02         9.04         2.04         0.46       120.79 
TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2661 
       35.28        26.30         4.37        43.53        46.98        24.36 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 
       42.77         3.19        25.02        38.24        34.06        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       33.30        28.37         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7659 TCGA-44-7667 TCGA-44-7670 
       23.18        63.72        16.44        14.60        36.07        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       17.59        23.64         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 TCGA-49-4487 TCGA-49-4501 TCGA-49-4506 
        9.44        11.54        76.21        28.11        46.72        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        55.89        14.63        12.13        29.26 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARR 
       11.64       153.04        63.95         8.55        37.32       164.12 
TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
       20.52        15.72        60.16        49.28         8.22        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6591 
       40.60        78.67         8.45        15.12        29.03         3.91 
TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       25.55        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 TCGA-55-6981 
       38.73        48.62         2.86        32.65        42.51        45.34 
TCGA-55-6982 TCGA-55-6984 TCGA-55-6986 TCGA-55-7281 TCGA-55-7570 TCGA-55-7573 
       32.71        24.99       107.21         0.59         0.20         0.13 
TCGA-55-7574 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        3.12         1.28         1.12         0.79         1.78        18.64 
TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       17.65         6.15        29.72        15.19         3.29        19.66 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8207 TCGA-55-8208 
        0.13        23.64        15.65        17.98         2.17        22.16 
TCGA-55-8299 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
       15.42         0.36         0.49         0.10         4.80        17.62 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        0.49         1.61        16.93        22.65        20.71        21.40 
TCGA-55-A491 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8402 
       20.58        20.19        19.99        17.95        39.98        49.25 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 
       19.53        54.35        67.96        72.30        39.25        40.96 
TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       20.65        39.09        87.98         2.04        42.90        28.41 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
       28.47         1.02        20.05        14.04        12.66         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 
        4.64        13.87         6.64         6.12        22.68         7.56 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-73-4668 
       12.56        14.01        13.45         4.24        26.73        15.35 
TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
        1.25        39.09        11.18         5.69        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.52        24.99        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 
       64.90         7.07       104.19         8.48        88.14        31.20 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 
       53.33        10.75        32.68        39.75        10.55       110.50 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-8054 TCGA-86-8056 TCGA-86-8074 
        5.88        34.39        20.55        24.49         4.57         0.79 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       16.08        15.65        15.85         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 
       27.58        13.32        13.32         3.81        17.62        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6849 
       10.62        41.36         1.97        10.19        12.23         1.15 
TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 
       16.18        14.27         1.18        19.82         9.76         6.12 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7567 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
       19.00        17.29        18.67        15.65        27.29        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 
       18.18        19.89        31.69        64.60        63.52         0.59 
TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4LX 
        0.72        17.92         5.39        16.41        21.60        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       21.44        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8194 
       20.68        24.56        36.76         1.45        21.63        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A5IP 
       18.08        35.47        16.44        14.30         3.81         1.91 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TE 
       17.46        11.87         2.76        58.45         5.49        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG 
       11.05        14.66        14.10        11.15        73.91        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-NJ-A7XG 
        9.70 

  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                         0.07                          0.00 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                       223.96                        164.12 
  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE 
                        17.92                         18.67 
[1] "0.1 - 224.0 (17.9)" "0.0 - 164.1 (18.7)"
[1] "hr=" "1"  
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(7Q31.2) MUTATED         3       49       56        1        22
  AMP PEAK  7(7Q31.2) WILD-TYPE       2       86       84        0        29
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  7(7Q31.2) MUTATED          29         39          2       13
  AMP PEAK  7(7Q31.2) WILD-TYPE        44         33          9       13
D7V3, multiclass
            clus
vv           AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            49                            86
  STAGE IB                            56                            84
  STAGE II                             1                             0
  STAGE IIA                           22                            29
  STAGE IIB                           29                            44
  STAGE IIIA                          39                            33
  STAGE IIIB                           2                             9
  STAGE IV                            13                            13
[1] 9 2
[1] 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(7Q31.2) MUTATED    62 125  21   5
  AMP PEAK  7(7Q31.2) WILD-TYPE 108 153  25  14
D7V4, multiclass
    clus
vv   AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  T1                          62                           108
  T2                         125                           153
  T3                          21                            25
  T4                           5                            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  7(7Q31.2) MUTATED   125  42    41
  AMP PEAK  7(7Q31.2) WILD-TYPE 207  54    35
D7V5, multiclass
       clus
vv      AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  N0                            125                           207
  N1                             42                            54
  N2+N3                          41                            35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                               cls
clus                              0   1
  AMP PEAK  7(7Q31.2) MUTATED   136  12
  AMP PEAK  7(7Q31.2) WILD-TYPE 212  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED    136   12
  AMP PEAK  7(7Q31.2) WILD-TYPE  212   13
   clus
vv  AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  0                         136                           212
  1                          12                            13
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(7Q31.2) MUTATED   112 102
  AMP PEAK  7(7Q31.2) WILD-TYPE 163 138
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED    112  102
  AMP PEAK  7(7Q31.2) WILD-TYPE  163  138
        clus
vv       AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  FEMALE                         112                           163
  MALE                           102                           138
[1] 2 2
[1] FALSE
D7V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  7(7Q31.2) MUTATED                            6
  AMP PEAK  7(7Q31.2) WILD-TYPE                         13
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  7(7Q31.2) MUTATED                                  39
  AMP PEAK  7(7Q31.2) WILD-TYPE                                68
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(7Q31.2) MUTATED                                                  144
  AMP PEAK  7(7Q31.2) WILD-TYPE                                                175
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  7(7Q31.2) MUTATED                                            3
  AMP PEAK  7(7Q31.2) WILD-TYPE                                          2
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  7(7Q31.2) MUTATED                                              11
  AMP PEAK  7(7Q31.2) WILD-TYPE                                             8
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  7(7Q31.2) MUTATED                                0
  AMP PEAK  7(7Q31.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  7(7Q31.2) MUTATED                                    1
  AMP PEAK  7(7Q31.2) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  7(7Q31.2) MUTATED                              0
  AMP PEAK  7(7Q31.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  7(7Q31.2) MUTATED                               8
  AMP PEAK  7(7Q31.2) WILD-TYPE                            15
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  7(7Q31.2) MUTATED                                 0
  AMP PEAK  7(7Q31.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  7(7Q31.2) MUTATED                                               1
  AMP PEAK  7(7Q31.2) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  7(7Q31.2) MUTATED                              1
  AMP PEAK  7(7Q31.2) WILD-TYPE                            9
D7V9, multiclass
                                                    clus
vv                                                   AMP PEAK  7(7Q31.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           39
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         144
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               11
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           1
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                8
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   AMP PEAK  7(7Q31.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             68
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           175
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  8
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 15
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  MUCINOUS (COLLOID) CARCINOMA                                                   9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                               cls
clus                              0   1
  AMP PEAK  7(7Q31.2) MUTATED    11 203
  AMP PEAK  7(7Q31.2) WILD-TYPE  10 291
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED     11  203
  AMP PEAK  7(7Q31.2) WILD-TYPE   10  291
     clus
vv    AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  NO                           11                            10
  YES                         203                           291
[1] 2 2
[1] FALSE
D7V11, continuous
D7V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(7Q31.2) MUTATED   143   4   3  12
  AMP PEAK  7(7Q31.2) WILD-TYPE 200   8   1  14
D7V13, multiclass
    clus
vv   AMP PEAK  7(7Q31.2) MUTATED AMP PEAK  7(7Q31.2) WILD-TYPE
  R0                         143                           200
  R1                           4                             8
  R2                           3                             1
  RX                          12                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(7Q31.2) MUTATED                                  0     3
  AMP PEAK  7(7Q31.2) WILD-TYPE                                1     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(7Q31.2) MUTATED                          25   165
  AMP PEAK  7(7Q31.2) WILD-TYPE                        26   224
D7V14, multiclass
                                  clus
vv                                 AMP PEAK  7(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 25
  WHITE                                                    165
                                  clus
vv                                 AMP PEAK  7(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      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"
D7V15, binary
                               cls
clus                              0   1
  AMP PEAK  7(7Q31.2) MUTATED     1 164
  AMP PEAK  7(7Q31.2) WILD-TYPE   6 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q31.2) MUTATED      1  164
  AMP PEAK  7(7Q31.2) WILD-TYPE    6  218
                        clus
vv                       AMP PEAK  7(7Q31.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         164
                        clus
vv                       AMP PEAK  7(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           218
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(8P11.21) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  8(8P11.21) MUTATED   109  54
  AMP PEAK  8(8P11.21) WILD-TYPE 228 100
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                           163                            328 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                            54                            100 
$`AMP PEAK  8(8P11.21) MUTATED`
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4405 
        3.98        45.01        37.02         0.00        47.05        20.05 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-5428 
       14.96         9.01        29.98        30.02        25.02        22.03 
TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 TCGA-44-3917 
        7.40         8.68        97.74        49.05        28.41        38.89 
TCGA-44-6774 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 
       21.63        61.28        19.46         7.17        18.87        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47B TCGA-44-A47F TCGA-49-4488 TCGA-49-4510 
       17.59         3.25         9.44        11.08        28.57        29.46 
TCGA-49-4512 TCGA-49-6767 TCGA-49-AARE TCGA-49-AARO TCGA-4B-A93V TCGA-50-5051 
       29.75        22.26        40.41       123.58         9.86        15.72 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 
       31.04         8.22        14.27        78.67        18.64        25.12 
TCGA-50-5946 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 
       22.55        25.55        11.05         6.21        10.13        25.61 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 
        9.21        23.05         2.86        32.65        40.73        15.25 
TCGA-55-6971 TCGA-55-6978 TCGA-55-7570 TCGA-55-7724 TCGA-55-7903 TCGA-55-7907 
        0.82         5.49         0.20        23.18        18.64         0.53 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        5.06         0.13        23.64        17.98         1.08         1.51 
TCGA-55-8301 TCGA-55-8507 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 
        1.45         0.26         6.64        17.62         1.58         2.17 
TCGA-55-A48Y TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 
       20.71        20.58         0.92        15.81        17.95        39.98 
TCGA-62-8398 TCGA-62-A46P TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 
       14.60        19.53        54.35        39.25        40.96        56.81 
TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 TCGA-69-7760 TCGA-69-7763 
       37.02         2.04        28.41        20.05         6.64        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 TCGA-73-4658 
       13.61         7.56         6.05         2.93         4.24        52.60 
TCGA-73-4659 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-78-7143 TCGA-78-7145 
       23.38         1.32         5.39         1.25       163.10        27.16 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 
       20.58        35.93        24.99        38.50         5.88        64.90 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 TCGA-78-8660 TCGA-78-8662 
       26.53        31.20         8.02        10.55        10.55       110.50 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7954 TCGA-86-7955 TCGA-86-8279 TCGA-86-8585 
        5.88        31.13        19.89        16.70        15.85         1.15 
TCGA-86-8669 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 
       30.84        14.96        13.32         3.81        13.64        10.62 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BC 
       10.19        13.71        12.23         7.36         1.18         1.45 
TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JO TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VN 
        9.76         6.12         1.08         1.22        15.65        18.18 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 
       19.89        64.60        43.79        25.48        18.67        17.92 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8032 TCGA-99-8033 
       15.39        14.30        20.58        20.52         1.45         5.59 
TCGA-L9-A444 TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4TA TCGA-MP-A4TE 
        0.20         2.76        49.35        37.35        31.23        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG 
       11.05        14.66        11.15        19.13        71.05        62.60 
TCGA-NJ-A4YI 
        0.13 

$`AMP PEAK  8(8P11.21) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 
       50.07        19.96        14.01         9.96        24.03         8.02 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       19.00         2.99        12.00        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       25.02        24.00        15.02        15.02         4.96        29.00 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 
        9.04         2.04         0.46         5.98       120.79        37.71 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       35.28        11.64        44.61        14.73        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
       43.53        46.98        13.15        44.94        24.36        42.08 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       42.77         3.19        25.02        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        6.25        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 
       10.78         9.93        27.78        23.15        23.18        63.72 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7667 TCGA-44-7672 
       32.45        16.44        14.60        12.03        36.07        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS 
       12.66         8.55        15.98        15.32        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        76.21        28.11        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       14.07        32.84         8.81        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       29.26        17.16        11.64        22.26       153.04        63.95 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR 
       62.24        28.90         8.55        37.32       211.82       164.12 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 
       20.52        71.47        70.55        60.16        49.28         9.27 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 
       40.60        21.47         8.45        15.12        29.03        42.35 
TCGA-50-6591 TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 TCGA-50-8459 TCGA-50-8460 
        3.91        12.16        41.69         0.72         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
       34.29        30.54        13.94        38.73        48.62        45.21 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6972 TCGA-55-6975 TCGA-55-6979 
        0.07         0.79        42.51        48.49         3.88         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
      107.21        70.26         0.59         1.15         7.99         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        3.12         1.32         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        1.78         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 
       29.72        15.19         3.29        19.66        19.73        15.65 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
        2.17        22.16        15.42         0.76         0.95         0.36 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 
        0.49        17.72         0.30         0.10         4.80         0.49 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 
        1.61        16.93        22.65        21.40         1.58        19.59 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 
       20.19        19.99         4.57        42.38        88.64        49.25 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 
       47.80        56.71        67.96        72.30        13.61        29.92 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
       20.65        39.09        55.43        38.37        87.98        42.90 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       51.25        28.47         1.02        18.84        14.04        12.66 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7765 TCGA-69-7978 
        5.72         4.64        13.87         6.12         5.42         2.30 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 
       12.56        14.01        13.45        26.73         7.04         2.01 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-7498 TCGA-73-7499 
       29.98        26.30        15.35         4.31        39.09        23.51 
TCGA-73-A9RS TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
       11.18         5.69        19.27        21.90        39.52        19.50 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       32.09        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 
       88.14        53.33        10.75        39.35        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-7711 TCGA-86-7713 
       39.75        77.59        27.09        12.36        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       20.55        19.43        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 
        0.79        15.75        16.08        15.65        23.05        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-A456 TCGA-86-A4JF 
       14.60        13.91        27.58         0.62        13.32        17.62 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 
       26.47        41.36         1.97         2.60        27.68         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JN 
       16.18        16.60        14.27        19.82         4.18        23.61 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.12         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 
       15.68        27.29         2.76        21.40        31.69        63.52 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
        5.95         0.59         0.72         5.39        18.12        16.41 
TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M3 TCGA-97-A4M5 
       21.60        20.19        21.44        19.76        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R 
       18.67        20.68        24.56        34.85        36.76        21.63 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV 
       14.30         3.81        14.53         1.91        17.46        12.59 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
       11.87        27.19        38.63        86.14        58.45        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD 
       58.85         5.49         5.29        41.59         2.43        10.09 
TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       14.10        73.91         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82         9.70        59.11        16.87 

  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                          0.00                           0.07 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                        163.10                         223.96 
  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE 
                         17.62                          19.00 
[1] "0.0 - 163.1 (17.6)" "0.1 - 224.0 (19.0)"
[1] "hr=" "1.3"
D8V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(8P11.21) MUTATED         1       44       56        0        16
  AMP PEAK  8(8P11.21) WILD-TYPE       4       91       84        1        35
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  8(8P11.21) MUTATED          18         25          5        8
  AMP PEAK  8(8P11.21) WILD-TYPE        55         47          6       18
D8V3, multiclass
            clus
vv           AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             44                             91
  STAGE IB                             56                             84
  STAGE II                              0                              1
  STAGE IIA                            16                             35
  STAGE IIB                            18                             55
  STAGE IIIA                           25                             47
  STAGE IIIB                            5                              6
  STAGE IV                              8                             18
[1] 9 2
[1] 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(8P11.21) MUTATED    51 103  11   7
  AMP PEAK  8(8P11.21) WILD-TYPE 119 175  35  12
D8V4, multiclass
    clus
vv   AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  T1                           51                            119
  T2                          103                            175
  T3                           11                             35
  T4                            7                             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  8(8P11.21) MUTATED   117  26    28
  AMP PEAK  8(8P11.21) WILD-TYPE 215  70    48
D8V5, multiclass
       clus
vv      AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  N0                             117                            215
  N1                              26                             70
  N2+N3                           28                             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED   119   8
  AMP PEAK  8(8P11.21) WILD-TYPE 229  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED    119    8
  AMP PEAK  8(8P11.21) WILD-TYPE  229   17
   clus
vv  AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  0                          119                            229
  1                            8                             17
[1] 2 2
[1] FALSE
D8V7, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED    80  93
  AMP PEAK  8(8P11.21) WILD-TYPE 195 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED     80   93
  AMP PEAK  8(8P11.21) WILD-TYPE  195  147
        clus
vv       AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  FEMALE                           80                            195
  MALE                             93                            147
[1] 2 2
[1] FALSE
D8V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                           10
  AMP PEAK  8(8P11.21) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  8(8P11.21) MUTATED                                  39
  AMP PEAK  8(8P11.21) WILD-TYPE                                68
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(8P11.21) MUTATED                                                  106
  AMP PEAK  8(8P11.21) WILD-TYPE                                                213
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  8(8P11.21) MUTATED                                            0
  AMP PEAK  8(8P11.21) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  8(8P11.21) MUTATED                                               5
  AMP PEAK  8(8P11.21) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                                0
  AMP PEAK  8(8P11.21) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                                    0
  AMP PEAK  8(8P11.21) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                              0
  AMP PEAK  8(8P11.21) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                               8
  AMP PEAK  8(8P11.21) WILD-TYPE                            15
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                                 1
  AMP PEAK  8(8P11.21) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                                               4
  AMP PEAK  8(8P11.21) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  8(8P11.21) MUTATED                              0
  AMP PEAK  8(8P11.21) WILD-TYPE                           10
D8V9, multiclass
                                                    clus
vv                                                   AMP PEAK  8(8P11.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            39
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          106
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 5
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            0
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 8
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 4
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK  8(8P11.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              68
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            213
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  14
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              3
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  15
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   1
  MUCINOUS (COLLOID) CARCINOMA                                                   10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED    10 163
  AMP PEAK  8(8P11.21) WILD-TYPE  11 331
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED     10  163
  AMP PEAK  8(8P11.21) WILD-TYPE   11  331
     clus
vv    AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  NO                            10                             11
  YES                          163                            331
[1] 2 2
[1] FALSE
D8V11, continuous
D8V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  8(8P11.21) MUTATED   116   5   1   7
  AMP PEAK  8(8P11.21) WILD-TYPE 227   7   3  19
D8V13, multiclass
    clus
vv   AMP PEAK  8(8P11.21) MUTATED AMP PEAK  8(8P11.21) WILD-TYPE
  R0                          116                            227
  R1                            5                              7
  R2                            1                              3
  RX                            7                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(8P11.21) MUTATED                                  0     2
  AMP PEAK  8(8P11.21) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(8P11.21) MUTATED                          14   132
  AMP PEAK  8(8P11.21) WILD-TYPE                        37   257
D8V14, multiclass
                                  clus
vv                                 AMP PEAK  8(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     132
                                  clus
vv                                 AMP PEAK  8(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       257
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V15, binary
                                cls
clus                               0   1
  AMP PEAK  8(8P11.21) MUTATED     3 121
  AMP PEAK  8(8P11.21) WILD-TYPE   4 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8P11.21) MUTATED      3  121
  AMP PEAK  8(8P11.21) WILD-TYPE    4  261
                        clus
vv                       AMP PEAK  8(8P11.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          121
                        clus
vv                       AMP PEAK  8(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            261
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(8Q24.21) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(8Q24.21) MUTATED   199 105
  AMP PEAK  9(8Q24.21) WILD-TYPE 138  49
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           304                            187 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           105                             49 
$`AMP PEAK  9(8Q24.21) MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 
       50.07         3.98        45.01        37.02         0.00        47.05 
TCGA-05-4402 TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
        8.02        20.05        14.96         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4432 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       30.02        21.99        25.02        15.02        15.02         4.96 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 
       22.03         7.40         5.98         8.68        97.74        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 
       28.41        35.28        11.64        44.61        14.73        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 
       13.15        42.77        25.02        37.15        38.89        34.06 
TCGA-44-3919 TCGA-44-5644 TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6777 
        6.25        28.37        23.77        27.78        21.63        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       61.28        16.44        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47B 
       29.00        17.59        23.64         3.25         8.55         9.44 
TCGA-44-A47F TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 
       11.08        13.45        76.21        28.57        12.66        46.72 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6761 TCGA-49-6767 
       14.07         8.81        29.46        29.75        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARE TCGA-49-AARO 
       22.26       153.04        63.95        62.24        40.41       123.58 
TCGA-4B-A93V TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        9.86        70.55        15.72        31.04        49.28         8.22 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
       14.27        40.60        78.67        18.64        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 
       42.35         3.91        25.55        11.05         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
        0.72        10.13        25.61        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       48.62        45.21         2.86         0.07        32.65         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 
       40.73        15.25         0.82        48.49         5.49         7.79 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7574 
       45.34        32.71        40.54        70.26         1.15         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7903 TCGA-55-7907 
        1.32        23.18         1.28         1.28        18.64         0.53 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 
       17.65         6.15        19.82        29.72         3.29         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8507 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 
        1.45         0.76         0.26         0.30         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
        0.49         1.58         2.17        16.93        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B 
        1.58        20.58         0.92        15.81        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
        4.57        39.98        14.60        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       56.71        54.35        39.25        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
       20.65        39.09        37.02        87.98         2.04        28.41 
TCGA-67-3770 TCGA-67-3771 TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 
        1.02        20.05        13.87         6.64        22.68        13.61 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
        7.56         6.05         2.93         4.24         7.04         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
       52.60        23.38        29.98        15.35         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        20.58        35.93        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 
       19.50        38.50         5.88        64.90         7.07       104.19 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
        8.48        88.14        26.53        31.20         8.02        10.75 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 TCGA-86-7701 
       10.55       214.62        10.55       110.50         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8073 
       34.39        13.87        19.89        16.70        24.49        24.33 
TCGA-86-8074 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
        0.79        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       30.84         0.62        14.96        13.32        13.32         3.81 
TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       13.64        10.62        10.19        13.71        12.23        27.68 
TCGA-91-7771 TCGA-91-8499 TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP 
       16.18         1.18         9.76         6.12         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7567 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VN 
       17.29         2.86        18.67        15.65         2.76        18.18 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       19.89        64.60        43.79        25.48         5.95         0.59 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.67        17.92        15.39        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.19        21.44        20.52        34.85        36.76         1.45 
TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L9-A443 TCGA-L9-A444 
        5.59        23.80        18.08        35.47         3.81         0.20 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
       14.53         1.91        17.46        12.59        11.87        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       38.63         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       86.04         5.49         5.29        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
       29.46        11.05        14.66        14.10        11.15        19.13 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A7XG 
       71.05        62.60         1.64         9.70 

$`AMP PEAK  9(8Q24.21) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 TCGA-05-4415 
       19.96        14.01         9.96        24.03        19.00         2.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5425 TCGA-05-5429 
       26.01        26.01        25.02        24.00        29.00         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 TCGA-38-7271 TCGA-38-A44F 
        2.04         0.46       120.79        37.71        26.30         4.37 
TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2666 TCGA-44-3398 
       43.53        44.94        24.36        42.08         3.19        38.24 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
       26.56        33.30        12.59        10.78         9.93        23.15 
TCGA-44-6775 TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 TCGA-44-8117 TCGA-44-A479 
       23.18        63.72        14.60        19.46        12.66        15.98 
TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4487 TCGA-49-4494 TCGA-49-4506 
       15.32        11.54        13.64        28.11        35.54        32.84 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-AAR4 
       55.89        14.63        12.13        29.26        17.16        28.90 
TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 
        8.55        37.32       211.82       164.12        20.52        71.47 
TCGA-50-5055 TCGA-50-5930 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
       60.16         9.27        21.47         8.45        15.12        29.03 
TCGA-50-6594 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 
       12.16         7.59        27.25        34.29        30.54        38.73 
TCGA-55-6968 TCGA-55-6975 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 
       42.51         3.88         2.20        60.03        24.99       107.21 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7727 TCGA-55-7728 
        0.59         7.99         0.20         0.13         1.12         0.79 
TCGA-55-7815 TCGA-55-7910 TCGA-55-7995 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
        1.78         6.48         0.16        15.19        19.66        19.73 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
        2.17        22.16        15.42         0.95         0.36         0.49 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-A48X TCGA-55-A492 
       17.72         0.10         4.80         1.61        22.65        19.59 
TCGA-55-A4DF TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       20.19        42.38        88.64        67.96        72.30        13.61 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
       55.43        38.37        42.90        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7765 
       14.04        12.66         5.72         4.64         6.12         5.42 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4666 
        2.30        12.56        14.01        13.45        26.73        26.30 
TCGA-73-A9RS TCGA-78-7150 TCGA-78-7156 TCGA-78-7160 TCGA-78-7163 TCGA-78-7537 
       11.18        21.90        32.09        22.29       223.96        53.33 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 
       39.35        32.68        39.75        77.59        27.09        12.36 
TCGA-86-7714 TCGA-86-7953 TCGA-86-8055 TCGA-86-8056 TCGA-86-8075 TCGA-86-8076 
       20.55        19.43         4.08         4.57        15.75        16.08 
TCGA-86-8278 TCGA-86-8668 TCGA-86-8671 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6829 
       15.65        13.91        27.58        17.62        26.47        41.36 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
        1.97         2.60         7.36         1.15        16.60        14.27 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JN TCGA-95-7039 TCGA-95-7043 
        1.45        19.82         4.18        23.61         1.12         1.22 
TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 
       12.39        15.68        27.29        21.40        31.69        63.52 
TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-A4M1 TCGA-97-A4M3 
        0.72         5.39        18.12        16.41        19.76        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-AA5R TCGA-J2-8192 
       20.84        18.67        20.68        24.56        21.63        24.30 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A5C7 
       16.44        19.00        14.30        58.85        41.59        73.91 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13        29.13         0.26         0.43        19.82        59.11 
TCGA-S2-AA1A 
       16.87 

  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           0.0                            0.1 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                        214.62                         223.96 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                        17.965                         19.000 
[1] "0.0 - 214.6 (18.0)" "0.1 - 224.0 (19.0)"
[1] "hr=" "1.3"
D9V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(8Q24.21) MUTATED         2       76       94        1        33
  AMP PEAK  9(8Q24.21) WILD-TYPE       3       59       46        0        18
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  9(8Q24.21) MUTATED          44         45          8       18
  AMP PEAK  9(8Q24.21) WILD-TYPE        29         27          3        8
D9V3, multiclass
            clus
vv           AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             76                             59
  STAGE IB                             94                             46
  STAGE II                              1                              0
  STAGE IIA                            33                             18
  STAGE IIB                            44                             29
  STAGE IIIA                           45                             27
  STAGE IIIB                            8                              3
  STAGE IV                             18                              8
[1] 9 2
[1] 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(8Q24.21) MUTATED    92 188  28  11
  AMP PEAK  9(8Q24.21) WILD-TYPE  78  90  18   8
D9V4, multiclass
    clus
vv   AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  T1                           92                             78
  T2                          188                             90
  T3                           28                             18
  T4                           11                              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
  AMP PEAK  9(8Q24.21) MUTATED   203  62    49
  AMP PEAK  9(8Q24.21) WILD-TYPE 129  34    27
D9V5, multiclass
       clus
vv      AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  N0                             203                            129
  N1                              62                             34
  N2+N3                           49                             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED   221  18
  AMP PEAK  9(8Q24.21) WILD-TYPE 127   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED    221   18
  AMP PEAK  9(8Q24.21) WILD-TYPE  127    7
   clus
vv  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  0                          221                            127
  1                           18                              7
[1] 2 2
[1] FALSE
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED   165 156
  AMP PEAK  9(8Q24.21) WILD-TYPE 110  84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED    165  156
  AMP PEAK  9(8Q24.21) WILD-TYPE  110   84
        clus
vv       AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  FEMALE                          165                            110
  MALE                            156                             84
[1] 2 2
[1] FALSE
D9V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  9(8Q24.21) MUTATED                           13
  AMP PEAK  9(8Q24.21) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  9(8Q24.21) MUTATED                                  62
  AMP PEAK  9(8Q24.21) WILD-TYPE                                45
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(8Q24.21) MUTATED                                                  210
  AMP PEAK  9(8Q24.21) WILD-TYPE                                                109
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  9(8Q24.21) MUTATED                                            1
  AMP PEAK  9(8Q24.21) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  9(8Q24.21) MUTATED                                              11
  AMP PEAK  9(8Q24.21) WILD-TYPE                                             8
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  9(8Q24.21) MUTATED                                1
  AMP PEAK  9(8Q24.21) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  9(8Q24.21) MUTATED                                    2
  AMP PEAK  9(8Q24.21) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  9(8Q24.21) MUTATED                              0
  AMP PEAK  9(8Q24.21) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  9(8Q24.21) MUTATED                              16
  AMP PEAK  9(8Q24.21) WILD-TYPE                             7
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  9(8Q24.21) MUTATED                                 1
  AMP PEAK  9(8Q24.21) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  9(8Q24.21) MUTATED                                               4
  AMP PEAK  9(8Q24.21) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  9(8Q24.21) MUTATED                              0
  AMP PEAK  9(8Q24.21) WILD-TYPE                           10
D9V9, multiclass
                                                    clus
vv                                                   AMP PEAK  9(8Q24.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          210
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                11
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                16
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 4
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK  9(8Q24.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            109
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   8
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                   7
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   1
  MUCINOUS (COLLOID) CARCINOMA                                                   10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED    15 306
  AMP PEAK  9(8Q24.21) WILD-TYPE   6 188
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED     15  306
  AMP PEAK  9(8Q24.21) WILD-TYPE    6  188
     clus
vv    AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  NO                            15                              6
  YES                          306                            188
[1] 2 2
[1] FALSE
D9V11, continuous
D9V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  9(8Q24.21) MUTATED   217  11   4  15
  AMP PEAK  9(8Q24.21) WILD-TYPE 126   1   0  11
D9V13, multiclass
    clus
vv   AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  R0                          217                            126
  R1                           11                              1
  R2                            4                              0
  RX                           15                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(8Q24.21) MUTATED                                  1     7
  AMP PEAK  9(8Q24.21) WILD-TYPE                                0     0
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(8Q24.21) MUTATED                          31   238
  AMP PEAK  9(8Q24.21) WILD-TYPE                        20   151
D9V14, multiclass
                                  clus
vv                                 AMP PEAK  9(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  31
  WHITE                                                     238
                                  clus
vv                                 AMP PEAK  9(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         0
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       151
[1] 4 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(8Q24.21) MUTATED     4 229
  AMP PEAK  9(8Q24.21) WILD-TYPE   3 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED      4  229
  AMP PEAK  9(8Q24.21) WILD-TYPE    3  153
                        clus
vv                       AMP PEAK  9(8Q24.21) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          229
                        clus
vv                       AMP PEAK  9(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            153
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(11Q13.3) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(11Q13.3) MUTATED   109  56
  AMP PEAK 10(11Q13.3) WILD-TYPE 228  98
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                           165                            326 
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                            56                             98 
$`AMP PEAK 10(11Q13.3) MUTATED`
TCGA-05-4389 TCGA-05-4402 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 
       45.01         8.02         2.99        14.96        29.98        21.99 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-38-4628 
       25.02        24.00        15.02         4.96         9.04        49.05 
TCGA-38-4629 TCGA-38-4632 TCGA-44-2659 TCGA-44-5644 TCGA-44-5645 TCGA-44-6774 
       28.41        44.61        44.94        28.37        12.59        21.63 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 
       61.28        16.44        19.46        12.03         7.17        18.87 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-4494 
       12.66         3.25        15.98        15.32         9.44        35.54 
TCGA-49-4512 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AARE TCGA-4B-A93V TCGA-50-5932 
       29.75        22.26        62.24        40.41         9.86        40.60 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6593 TCGA-50-6597 TCGA-53-7624 
       78.67        18.64        22.55        11.05        41.69        34.29 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
       13.94        23.05        38.73        48.62        45.21         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6975 TCGA-55-6979 
        0.07        32.65         0.79         0.82         3.88         7.79 
TCGA-55-6981 TCGA-55-7576 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8092 
       45.34         1.32         6.48        19.82         0.16         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 TCGA-55-8506 TCGA-55-8507 
        0.13        23.64        17.98         1.08         0.36         0.26 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A490 
       17.72         0.30         6.64         0.49         1.58         1.58 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8399 TCGA-62-8402 
       15.81        19.99        17.95         4.57        88.64        49.25 
TCGA-62-A46O TCGA-62-A470 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1681 
       47.80        39.25        56.81        20.65        39.09        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       87.98         2.04        28.41        28.47         1.02        20.05 
TCGA-67-6215 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K 
        5.72         7.56         6.05         2.93         4.24         7.04 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 
        2.01        52.60        29.98        26.30        15.35         5.39 
TCGA-73-A9RS TCGA-78-7147 TCGA-78-7148 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 
       11.18        19.27        20.58        19.50        38.50        64.90 
TCGA-78-7161 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
        7.07       223.96        88.14        26.53        31.20         8.02 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 TCGA-86-6851 TCGA-86-7701 
       10.75        10.55        77.59       110.50         5.88        31.13 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
       19.43        16.70        24.49        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6831 TCGA-91-6836 
       21.47        14.60         3.81        41.36        10.19        13.71 
TCGA-91-6840 TCGA-91-6848 TCGA-91-A4BC TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO 
       12.23         7.36         1.45         4.18         6.12         1.08 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-8494 TCGA-97-7553 TCGA-97-7937 
        1.12         1.22         2.86         2.76        43.79         5.95 
TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M3 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD 
        5.39        16.41        17.75         1.45         5.59        18.08 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
        3.81         0.20         1.91        12.59        11.87        27.19 
TCGA-MN-A4N4 TCGA-MP-A4T6 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TJ 
       38.63        58.85        31.23         2.43        14.10        11.15 
TCGA-NJ-A4YF TCGA-O1-A52J TCGA-S2-AA1A 
       71.05        59.11        16.87 

$`AMP PEAK 10(11Q13.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        19.96        14.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4418 
        9.96        24.03        47.05        19.00        20.05         9.01 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4434 
       12.00        30.02        26.01        26.01        25.02        15.02 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         2.04         0.46         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-4631 
        8.68        97.74       120.79        37.71        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        13.15 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       24.36        42.08        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       38.24        38.89        34.06         6.25        26.56        33.30 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 
       23.77        10.78         9.93        27.78        23.15        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 
       63.72        32.45        14.60        36.07        29.00        17.59 
TCGA-44-7672 TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       23.64         8.55        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 
       76.21        28.11        28.57        12.66        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       32.84         8.81        29.46        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       29.26        17.16        11.64        22.26       153.04        63.95 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       28.90         8.55        37.32       123.58       211.82       164.12 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47        70.55        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 TCGA-50-5936 
       49.28         8.22         9.27        14.27        21.47         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       15.12        29.03        25.12        42.35         3.91        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       27.25        30.54         9.21        42.51        40.73        15.25 
TCGA-55-6972 TCGA-55-6978 TCGA-55-6980 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
       48.49         5.49         2.20        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.20         0.13         3.12        23.18         1.28         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
        1.12         0.79         1.78        18.64         0.53        17.65 
TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
        6.15        29.72        15.19         3.29        19.66        19.73 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       15.65         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
        0.76         0.95         0.49         0.10         4.80        17.62 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        1.61         2.17        16.93        22.65        20.71        21.40 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 
       20.58        19.59         0.92        20.19        39.98        42.38 
TCGA-62-8398 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       14.60        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 TCGA-64-5778 
       13.61        40.96        29.92        55.43        37.02        42.90 
TCGA-64-5781 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 
       51.25        18.84        14.04        12.66         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 
        6.64         6.12        22.68        13.61         5.42         2.30 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4659 TCGA-73-4670 
       12.56        14.01        13.45        26.73        23.38         4.31 
TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        1.32         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
        5.69        35.93        21.90        39.52        24.99        32.09 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 TCGA-78-7537 TCGA-78-7540 
        5.88        22.29       104.19         8.48        53.33        39.35 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 
       32.68       214.62        39.75        10.55        27.09        12.36 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 
       34.39        13.87        20.55        19.89         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8585 TCGA-86-8668 
       24.33         0.79        15.75        16.08         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 
       17.62        13.64        26.47        10.62         1.97         2.60 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7567 
       19.82         9.76        23.61        19.00        17.29        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
       12.39        15.68        15.65        27.29        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7938 
       19.89        31.69        64.60        63.52        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
        0.72        18.67        17.92        18.12        15.39        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.63        24.30        23.80        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       14.30        14.53        17.46         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        86.04         5.49         5.29        41.59 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 
       10.09        29.46        11.05        14.66        19.13        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG 
       19.82         9.70 

  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                        223.96                         214.62 
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                         15.98                          19.56 
[1] "0.1 - 224.0 (16.0)" "0.0 - 214.6 (19.6)"
[1] "hr=" "1.2"
D10V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(11Q13.3) MUTATED         0       40       45        0        18
  AMP PEAK 10(11Q13.3) WILD-TYPE       5       95       95        1        33
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 10(11Q13.3) MUTATED          28         24          4       11
  AMP PEAK 10(11Q13.3) WILD-TYPE        45         48          7       15
D10V3, multiclass
            clus
vv           AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                             40                             95
  STAGE IB                             45                             95
  STAGE II                              0                              1
  STAGE IIA                            18                             33
  STAGE IIB                            28                             45
  STAGE IIIA                           24                             48
  STAGE IIIB                            4                              7
  STAGE IV                             11                             15
[1] 9 2
[1] 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(11Q13.3) MUTATED    49  99  16   5
  AMP PEAK 10(11Q13.3) WILD-TYPE 121 179  30  14
D10V4, multiclass
    clus
vv   AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  T1                           49                            121
  T2                           99                            179
  T3                           16                             30
  T4                            5                             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(11Q13.3) MUTATED   109  29    28
  AMP PEAK 10(11Q13.3) WILD-TYPE 223  67    48
D10V5, multiclass
       clus
vv      AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  N0                             109                            223
  N1                              29                             67
  N2+N3                           28                             48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                                cls
clus                               0   1
  AMP PEAK 10(11Q13.3) MUTATED   108  11
  AMP PEAK 10(11Q13.3) WILD-TYPE 240  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11Q13.3) MUTATED    108   11
  AMP PEAK 10(11Q13.3) WILD-TYPE  240   14
   clus
vv  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  0                          108                            240
  1                           11                             14
[1] 2 2
[1] FALSE
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(11Q13.3) MUTATED    90  80
  AMP PEAK 10(11Q13.3) WILD-TYPE 185 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11Q13.3) MUTATED     90   80
  AMP PEAK 10(11Q13.3) WILD-TYPE  185  160
        clus
vv       AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  FEMALE                           90                            185
  MALE                             80                            160
[1] 2 2
[1] FALSE
D10V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 10(11Q13.3) MUTATED                            4
  AMP PEAK 10(11Q13.3) WILD-TYPE                         15
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 10(11Q13.3) MUTATED                                  34
  AMP PEAK 10(11Q13.3) WILD-TYPE                                73
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(11Q13.3) MUTATED                                                  117
  AMP PEAK 10(11Q13.3) WILD-TYPE                                                202
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 10(11Q13.3) MUTATED                                            2
  AMP PEAK 10(11Q13.3) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 10(11Q13.3) MUTATED                                               4
  AMP PEAK 10(11Q13.3) WILD-TYPE                                            15
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 10(11Q13.3) MUTATED                                1
  AMP PEAK 10(11Q13.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 10(11Q13.3) MUTATED                                    2
  AMP PEAK 10(11Q13.3) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 10(11Q13.3) MUTATED                              0
  AMP PEAK 10(11Q13.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 10(11Q13.3) MUTATED                               4
  AMP PEAK 10(11Q13.3) WILD-TYPE                            19
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 10(11Q13.3) MUTATED                                 1
  AMP PEAK 10(11Q13.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 10(11Q13.3) MUTATED                                               1
  AMP PEAK 10(11Q13.3) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 10(11Q13.3) MUTATED                              0
  AMP PEAK 10(11Q13.3) WILD-TYPE                           10
D10V9, multiclass
                                                    clus
vv                                                   AMP PEAK 10(11Q13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          117
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 4
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 4
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK 10(11Q13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            202
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  15
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  19
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   4
  MUCINOUS (COLLOID) CARCINOMA                                                   10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
                                cls
clus                               0   1
  AMP PEAK 10(11Q13.3) MUTATED     8 162
  AMP PEAK 10(11Q13.3) WILD-TYPE  13 332
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11Q13.3) MUTATED      8  162
  AMP PEAK 10(11Q13.3) WILD-TYPE   13  332
     clus
vv    AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  NO                             8                             13
  YES                          162                            332
[1] 2 2
[1] FALSE
D10V11, continuous
D10V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 10(11Q13.3) MUTATED   114   4   1   9
  AMP PEAK 10(11Q13.3) WILD-TYPE 229   8   3  17
D10V13, multiclass
    clus
vv   AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  R0                          114                            229
  R1                            4                              8
  R2                            1                              3
  RX                            9                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(11Q13.3) MUTATED                                  1     4
  AMP PEAK 10(11Q13.3) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(11Q13.3) MUTATED                          22   124
  AMP PEAK 10(11Q13.3) WILD-TYPE                        29   265
D10V14, multiclass
                                  clus
vv                                 AMP PEAK 10(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     124
                                  clus
vv                                 AMP PEAK 10(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    29
  WHITE                                                       265
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
                                cls
clus                               0   1
  AMP PEAK 10(11Q13.3) MUTATED     2 126
  AMP PEAK 10(11Q13.3) WILD-TYPE   5 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11Q13.3) MUTATED      2  126
  AMP PEAK 10(11Q13.3) WILD-TYPE    5  256
                        clus
vv                       AMP PEAK 10(11Q13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          126
                        clus
vv                       AMP PEAK 10(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            256
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(12P12.1) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(12P12.1) MUTATED   114  59
  AMP PEAK 11(12P12.1) WILD-TYPE 223  95
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                           173                            318 
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                            59                             95 
$`AMP PEAK 11(12P12.1) MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4402 
        3.98        19.96        45.01        37.02         0.00         8.02 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4432 TCGA-05-4433 
        2.99        14.96         9.01        29.98        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5428 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 
       15.02        15.02        22.03         7.40         8.68        97.74 
TCGA-38-4628 TCGA-38-4632 TCGA-44-2657 TCGA-44-2668 TCGA-44-5643 TCGA-44-5644 
       49.05        44.61        13.15        25.02        33.30        28.37 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-4488 
       29.00        23.64        15.98        15.32         9.44        28.57 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6745 TCGA-49-6767 
        8.81        29.46        29.75        14.63        17.16        22.26 
TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-50-5045 TCGA-50-5072 TCGA-50-5931 
        8.55       123.58       211.82        71.47         8.22        14.27 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-6592 TCGA-50-6597 TCGA-50-6673 
       21.47        18.64        25.12        25.55        41.69         0.72 
TCGA-50-8459 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 
        7.59        23.05        38.73        48.62        45.21        32.65 
TCGA-55-6712 TCGA-55-6971 TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6984 
        0.79         0.82         5.49         2.20        45.34        24.99 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7726 
       40.54        70.26         1.15         7.99         1.32         1.28 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 
        0.79         1.78         0.53         6.48        17.65         0.16 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8208 TCGA-55-8302 
        3.29         5.06         0.13        23.64        22.16         0.76 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 TCGA-55-A490 TCGA-55-A493 
        0.95         0.26         0.49         0.49         1.58         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46Y 
       15.81        20.19        14.60        49.25        47.80        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 TCGA-64-1681 TCGA-64-5775 TCGA-67-3774 
       39.25        40.96        39.09        38.37         2.04        12.66 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K 
        7.56         6.05         2.93        12.56         4.24         7.04 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-78-7145 
       29.98        26.30        15.35         4.31         1.32        27.16 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 
        5.69        20.58        19.50        38.50        64.90         7.07 
TCGA-78-7167 TCGA-78-7220 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       88.14        26.53        77.59        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8278 TCGA-86-8280 
       31.13        13.87        19.43        19.89        15.65        23.05 
TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 
       30.84        14.96         3.81        10.62        41.36         2.60 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-93-8067 
       13.71        27.68         7.36        16.18         1.18         6.12 
TCGA-93-A4JO TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
        1.08        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7554 TCGA-97-8176 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 
       25.48        15.39        20.58        20.68        36.76         1.45 
TCGA-99-8033 TCGA-L9-A443 TCGA-L9-A5IP TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
        5.59         3.81         1.91        27.19        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T7 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       86.14        49.35         5.49        10.09        29.46        11.05 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A55R TCGA-S2-AA1A 
       14.10        19.13        71.05        19.82        16.87 

$`AMP PEAK 11(12P12.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       50.07        14.01         9.96        24.03        47.05        19.00 
TCGA-05-4405 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       20.05        12.00        30.02        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       25.02         4.96        29.00         9.04         2.04         0.46 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
        5.98       120.79        37.71        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 
       14.73        26.30         4.37        43.53        46.98        44.94 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
       24.36        42.08        42.77         3.19        37.15        38.24 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 
       38.89        34.06         6.25        26.56        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7671 TCGA-44-8117 
       63.72        32.45        61.28        14.60        17.59        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
        3.25         8.55        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       76.21        28.11        12.66        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-AAQV 
       32.84        55.89        12.13        29.26        11.64        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARN 
      153.04        63.95        62.24        28.90        40.41        37.32 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
      164.12         9.86        20.52        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 
       31.04        49.28         9.27        40.60        78.67         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 
       15.12        29.03        22.55        42.35         3.91        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8460 TCGA-53-7624 
       12.16         6.21        10.13        25.61        27.25        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6968 
       30.54        13.94         9.21         2.86         0.07        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6979 TCGA-55-6982 
       40.73        15.25        48.49         3.88         7.79        32.71 
TCGA-55-6983 TCGA-55-6986 TCGA-55-7281 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
       60.03       107.21         0.59         0.20         0.13         3.12 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 
       23.18         1.28         1.12        18.64         6.15        19.82 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8097 TCGA-55-8203 
       29.72        15.19        19.66        19.73        15.65        17.98 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 
        1.08         1.51         2.17        15.42         1.45         0.36 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       21.40        20.58        19.59        19.99        17.95         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       39.98        42.38        88.64        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       67.96        72.30        29.92        56.81        20.65        55.43 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       37.02        87.98        42.90        28.41        51.25        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 
        1.02        20.05        18.84        14.04         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 
        2.30        14.01        13.45        26.73         2.01        52.60 
TCGA-73-4659 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
       23.38         5.39         1.25        39.09        23.51        11.18 
TCGA-78-7143 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
      163.10        19.27        35.93        21.90        39.52        24.99 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       32.09         5.88        22.29       104.19       223.96         8.48 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-86-7711 
       32.68       214.62        39.75        10.55       110.50        34.39 
TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       20.55        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 
        0.79        15.75        16.08        15.85        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
        1.15        13.91        27.58         0.62        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 
       17.62        13.64        26.47         1.97        10.19        12.23 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
        4.18        23.61        19.00        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 
        2.86        15.68        15.65        21.40        18.18        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        43.79         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92         5.39        18.12        16.41        14.30 
TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       21.60        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-AA5R TCGA-J2-8192 
       20.84        18.67        24.56        34.85        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SW 
        0.20        14.53        17.46        12.59        11.87        58.45 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       37.35        86.04        58.85         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
        2.43        14.66        11.15        73.91        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
        1.64        29.13         0.26         0.43         9.70        59.11 

  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                          0.00                           0.07 
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                        211.82                         223.96 
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                         15.98                          19.00 
[1] "0.0 - 211.8 (16.0)" "0.1 - 224.0 (19.0)"
[1] "hr=" "1.4"
D11V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(12P12.1) MUTATED         4       42       43        0        20
  AMP PEAK 11(12P12.1) WILD-TYPE       1       93       97        1        31
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 11(12P12.1) MUTATED          24         31          2       12
  AMP PEAK 11(12P12.1) WILD-TYPE        49         41          9       14
D11V3, multiclass
            clus
vv           AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                             42                             93
  STAGE IB                             43                             97
  STAGE II                              0                              1
  STAGE IIA                            20                             31
  STAGE IIB                            24                             49
  STAGE IIIA                           31                             41
  STAGE IIIB                            2                              9
  STAGE IV                             12                             14
[1] 9 2
[1] 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(12P12.1) MUTATED    50 103  19   5
  AMP PEAK 11(12P12.1) WILD-TYPE 120 175  27  14
D11V4, multiclass
    clus
vv   AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  T1                           50                            120
  T2                          103                            175
  T3                           19                             27
  T4                            5                             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 11(12P12.1) MUTATED   111  34    29
  AMP PEAK 11(12P12.1) WILD-TYPE 221  62    47
D11V5, multiclass
       clus
vv      AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  N0                             111                            221
  N1                              34                             62
  N2+N3                           29                             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                                cls
clus                               0   1
  AMP PEAK 11(12P12.1) MUTATED   114  12
  AMP PEAK 11(12P12.1) WILD-TYPE 234  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(12P12.1) MUTATED    114   12
  AMP PEAK 11(12P12.1) WILD-TYPE  234   13
   clus
vv  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  0                          114                            234
  1                           12                             13
[1] 2 2
[1] FALSE
D11V7, binary
                                cls
clus                               0   1
  AMP PEAK 11(12P12.1) MUTATED    92  86
  AMP PEAK 11(12P12.1) WILD-TYPE 183 154
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(12P12.1) MUTATED     92   86
  AMP PEAK 11(12P12.1) WILD-TYPE  183  154
        clus
vv       AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  FEMALE                           92                            183
  MALE                             86                            154
[1] 2 2
[1] FALSE
D11V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 11(12P12.1) MUTATED                            6
  AMP PEAK 11(12P12.1) WILD-TYPE                         13
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 11(12P12.1) MUTATED                                  30
  AMP PEAK 11(12P12.1) WILD-TYPE                                77
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(12P12.1) MUTATED                                                  122
  AMP PEAK 11(12P12.1) WILD-TYPE                                                197
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 11(12P12.1) MUTATED                                            1
  AMP PEAK 11(12P12.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 11(12P12.1) MUTATED                                               8
  AMP PEAK 11(12P12.1) WILD-TYPE                                            11
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 11(12P12.1) MUTATED                                1
  AMP PEAK 11(12P12.1) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 11(12P12.1) MUTATED                                    1
  AMP PEAK 11(12P12.1) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(12P12.1) MUTATED                              0
  AMP PEAK 11(12P12.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 11(12P12.1) MUTATED                               4
  AMP PEAK 11(12P12.1) WILD-TYPE                            19
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 11(12P12.1) MUTATED                                 0
  AMP PEAK 11(12P12.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 11(12P12.1) MUTATED                                               1
  AMP PEAK 11(12P12.1) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 11(12P12.1) MUTATED                              4
  AMP PEAK 11(12P12.1) WILD-TYPE                            6
D11V9, multiclass
                                                    clus
vv                                                   AMP PEAK 11(12P12.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          122
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 8
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 4
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  4
                                                    clus
vv                                                   AMP PEAK 11(12P12.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            197
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  11
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  19
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   4
  MUCINOUS (COLLOID) CARCINOMA                                                    6
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                                cls
clus                               0   1
  AMP PEAK 11(12P12.1) MUTATED     8 170
  AMP PEAK 11(12P12.1) WILD-TYPE  13 324
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(12P12.1) MUTATED      8  170
  AMP PEAK 11(12P12.1) WILD-TYPE   13  324
     clus
vv    AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  NO                             8                             13
  YES                          170                            324
[1] 2 2
[1] FALSE
D11V11, continuous
D11V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 11(12P12.1) MUTATED   120   4   4   8
  AMP PEAK 11(12P12.1) WILD-TYPE 223   8   0  18
D11V13, multiclass
    clus
vv   AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  R0                          120                            223
  R1                            4                              8
  R2                            4                              0
  RX                            8                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(12P12.1) MUTATED                                  1     3
  AMP PEAK 11(12P12.1) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(12P12.1) MUTATED                          18   130
  AMP PEAK 11(12P12.1) WILD-TYPE                        33   259
D11V14, multiclass
                                  clus
vv                                 AMP PEAK 11(12P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     130
                                  clus
vv                                 AMP PEAK 11(12P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    33
  WHITE                                                       259
[1] 4 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(12P12.1) MUTATED     2 127
  AMP PEAK 11(12P12.1) WILD-TYPE   5 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(12P12.1) MUTATED      2  127
  AMP PEAK 11(12P12.1) WILD-TYPE    5  255
                        clus
vv                       AMP PEAK 11(12P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          127
                        clus
vv                       AMP PEAK 11(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            255
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(12Q14.1) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(12Q14.1) MUTATED   105  57
  AMP PEAK 12(12Q14.1) WILD-TYPE 232  97
  AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE 
                           162                            329 
  AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE 
                            57                             97 
$`AMP PEAK 12(12Q14.1) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4402 TCGA-05-4415 TCGA-05-4417 
       45.01        37.02         0.00         8.02         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4430 TCGA-05-4432 TCGA-05-4434 TCGA-05-5420 
        9.01        29.98        25.02        25.02        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-35-4122 TCGA-35-5375 TCGA-38-4628 TCGA-38-4631 
        4.96        29.00         7.40         8.68        49.05        11.64 
TCGA-44-2657 TCGA-44-2668 TCGA-44-5644 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       13.15        25.02        28.37        61.28        16.44        19.46 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 
       36.07        18.87        29.00        23.64         3.25        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 
       15.32         9.44         8.81        29.46        55.89        14.63 
TCGA-49-6745 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR9 TCGA-49-AARE 
       17.16        22.26        22.26       153.04         8.55        40.41 
TCGA-49-AARO TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5931 
      123.58        71.47        15.72        60.16         8.22        14.27 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 TCGA-50-6597 TCGA-50-6673 TCGA-53-7624 
       25.12        22.55        25.55        41.69         0.72        34.29 
TCGA-53-7813 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 
       13.94        38.73        48.62        45.21        32.65         0.79 
TCGA-55-6971 TCGA-55-6978 TCGA-55-6980 TCGA-55-6982 TCGA-55-6987 TCGA-55-7284 
        0.82         5.49         2.20        32.71        70.26         7.99 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 
        1.28         0.79         1.78         0.53         6.48         0.16 
TCGA-55-8089 TCGA-55-8096 TCGA-55-8208 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 
        3.29        23.64        22.16         0.76         0.95         0.26 
TCGA-55-8508 TCGA-55-8615 TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
        0.49         0.49         1.58         0.92        15.81        20.19 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 
       14.60        49.25        47.80        72.30        39.25        40.96 
TCGA-64-1678 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-67-3774 TCGA-69-7760 
       39.09        38.37         2.04        28.41        12.66         6.64 
TCGA-69-7973 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 
        7.56        12.56         4.24         7.04        26.30         4.31 
TCGA-73-4675 TCGA-73-A9RS TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7161 
        1.32        11.18        27.16         5.69        20.58         7.07 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-8655 TCGA-86-6562 TCGA-86-7701 
       88.14        26.53         8.02        77.59        12.36        31.13 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8278 TCGA-86-8279 
       13.87        19.43        19.89        16.70        15.65        15.85 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 
       21.47        14.60         1.15        30.84         3.81        10.62 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-93-8067 
       13.71        12.23         7.36         1.15        16.18         6.12 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 TCGA-95-A4VP TCGA-97-8176 TCGA-97-8177 
       18.67        12.39         2.76        19.89        15.39        16.41 
TCGA-97-8552 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A443 
       20.58        18.67        20.68         1.45         5.59         3.81 
TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
        1.91        11.87        27.19        38.63         2.76        86.14 
TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TI 
       49.35        58.85         5.49        10.09        29.46        14.10 
TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       19.13        71.05         0.13        19.82        59.11        16.87 

$`AMP PEAK 12(12Q14.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 
       50.07         3.98        19.96        14.01         9.96        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       47.05        19.00        20.05        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       26.01        26.01        24.00        22.03         9.04         2.04 
TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
        0.46         5.98        97.74       120.79        37.71        28.41 
TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       35.28        44.61        14.73        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
       46.98        44.94        24.36        42.08        42.77         3.19 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       37.15        38.24        38.89        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 
       23.15        21.63        23.18        63.72        32.45        14.60 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F 
       12.03         7.17        17.59        12.66         8.55        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       11.54        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 
       12.66        35.54        46.72        14.07        32.84        29.75 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       12.13        29.26        11.64        63.95        62.24        28.90 
TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5049 
       37.32       211.82       164.12         9.86        20.52        70.55 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       31.04        49.28         9.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-6590 TCGA-50-6591 
        8.45        15.12        18.64        29.03        42.35         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       11.05        12.16         6.21        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 
       27.25        30.54         9.21        23.05         2.86         0.07 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6979 
       42.51        40.73        15.25        48.49         3.88         7.79 
TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 
       45.34        60.03        24.99        40.54       107.21         0.59 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        1.15         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.28         1.12        18.64        17.65         6.15        19.82 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 
       29.72        15.19        19.66        19.73         5.06         0.13 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 
       15.65        17.98         1.08         1.51         2.17        15.42 
TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        1.45         0.36        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        6.64        17.62         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DG 
       22.65        20.71        21.40        20.58        19.59        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46P 
       17.95         4.57        39.98        42.38        88.64        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 
       56.71        54.35        67.96        13.61        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 
       20.65        55.43        37.02        87.98        42.90        51.25 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 
       28.47         1.02        20.05        18.84        14.04         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64        13.87         6.12        22.68        13.61         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        6.05         2.30         2.93        14.01        13.45        26.73 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 TCGA-73-4676 
        2.01        52.60        23.38        29.98        15.35         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7147 TCGA-78-7149 
        1.25        39.09        23.51       163.10        19.27        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        5.88        64.90        22.29       104.19       223.96         8.48 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
       31.20        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 
      214.62        39.75        10.55       110.50        27.09         5.88 
TCGA-86-7711 TCGA-86-7714 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       34.39        20.55        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8280 TCGA-86-8668 TCGA-86-8671 
        0.79        15.75        16.08        23.05        13.91        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 
       26.47        41.36         1.97        10.19         2.60        27.68 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        4.18        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
        1.22         2.86        15.68        15.65        27.29        21.40 
TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       18.18        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
        5.95         0.59         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       18.12        14.30        21.60        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.52        17.75        20.84        24.56        34.85        36.76 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       21.63        24.30        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
       19.00        14.30         0.20        14.53        17.46        12.59 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       58.45        37.35        86.04         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG 
        2.43        11.05        14.66        11.15        73.91        62.60 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A7XG 
        1.64        29.13         0.26         0.43         9.70 

  AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE 
                          0.00                           0.07 
  AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE 
                        153.04                         223.96 
  AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE 
                        15.765                         19.530 
[1] "0.0 - 153.0 (15.8)" "0.1 - 224.0 (19.5)"
[1] "hr=" "1.4"
D12V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(12Q14.1) MUTATED         3       38       40        1        18
  AMP PEAK 12(12Q14.1) WILD-TYPE       2       97      100        0        33
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 12(12Q14.1) MUTATED          26         28          3       11
  AMP PEAK 12(12Q14.1) WILD-TYPE        47         44          8       15
D12V3, multiclass
            clus
vv           AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             38                             97
  STAGE IB                             40                            100
  STAGE II                              1                              0
  STAGE IIA                            18                             33
  STAGE IIB                            26                             47
  STAGE IIIA                           28                             44
  STAGE IIIB                            3                              8
  STAGE IV                             11                             15
[1] 9 2
[1] 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(12Q14.1) MUTATED    47  96  18   6
  AMP PEAK 12(12Q14.1) WILD-TYPE 123 182  28  13
D12V4, multiclass
    clus
vv   AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE
  T1                           47                            123
  T2                           96                            182
  T3                           18                             28
  T4                            6                             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 12(12Q14.1) MUTATED   104  34    27
  AMP PEAK 12(12Q14.1) WILD-TYPE 228  62    49
D12V5, multiclass
       clus
vv      AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE
  N0                             104                            228
  N1                              34                             62
  N2+N3                           27                             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                                cls
clus                               0   1
  AMP PEAK 12(12Q14.1) MUTATED   111  11
  AMP PEAK 12(12Q14.1) WILD-TYPE 237  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(12Q14.1) MUTATED    111   11
  AMP PEAK 12(12Q14.1) WILD-TYPE  237   14
   clus
vv  AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE
  0                          111                            237
  1                           11                             14
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(12Q14.1) MUTATED    84  84
  AMP PEAK 12(12Q14.1) WILD-TYPE 191 156
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(12Q14.1) MUTATED     84   84
  AMP PEAK 12(12Q14.1) WILD-TYPE  191  156
        clus
vv       AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE
  FEMALE                           84                            191
  MALE                             84                            156
[1] 2 2
[1] FALSE
D12V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 12(12Q14.1) MUTATED                            6
  AMP PEAK 12(12Q14.1) WILD-TYPE                         13
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 12(12Q14.1) MUTATED                                  31
  AMP PEAK 12(12Q14.1) WILD-TYPE                                76
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(12Q14.1) MUTATED                                                  114
  AMP PEAK 12(12Q14.1) WILD-TYPE                                                205
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 12(12Q14.1) MUTATED                                            1
  AMP PEAK 12(12Q14.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 12(12Q14.1) MUTATED                                               5
  AMP PEAK 12(12Q14.1) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 12(12Q14.1) MUTATED                                1
  AMP PEAK 12(12Q14.1) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 12(12Q14.1) MUTATED                                    0
  AMP PEAK 12(12Q14.1) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(12Q14.1) MUTATED                              0
  AMP PEAK 12(12Q14.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 12(12Q14.1) MUTATED                               5
  AMP PEAK 12(12Q14.1) WILD-TYPE                            18
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 12(12Q14.1) MUTATED                                 0
  AMP PEAK 12(12Q14.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 12(12Q14.1) MUTATED                                               2
  AMP PEAK 12(12Q14.1) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 12(12Q14.1) MUTATED                              3
  AMP PEAK 12(12Q14.1) WILD-TYPE                            7
D12V9, multiclass
                                                    clus
vv                                                   AMP PEAK 12(12Q14.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            31
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          114
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 5
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            0
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 5
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   AMP PEAK 12(12Q14.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            205
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  14
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              3
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  18
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   3
  MUCINOUS (COLLOID) CARCINOMA                                                    7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
                                cls
clus                               0   1
  AMP PEAK 12(12Q14.1) MUTATED     8 160
  AMP PEAK 12(12Q14.1) WILD-TYPE  13 334
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(12Q14.1) MUTATED      8  160
  AMP PEAK 12(12Q14.1) WILD-TYPE   13  334
     clus
vv    AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE
  NO                             8                             13
  YES                          160                            334
[1] 2 2
[1] FALSE
D12V11, continuous
D12V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 12(12Q14.1) MUTATED   115   3   3   7
  AMP PEAK 12(12Q14.1) WILD-TYPE 228   9   1  19
D12V13, multiclass
    clus
vv   AMP PEAK 12(12Q14.1) MUTATED AMP PEAK 12(12Q14.1) WILD-TYPE
  R0                          115                            228
  R1                            3                              9
  R2                            3                              1
  RX                            7                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(12Q14.1) MUTATED                                  0     3
  AMP PEAK 12(12Q14.1) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(12Q14.1) MUTATED                          20   119
  AMP PEAK 12(12Q14.1) WILD-TYPE                        31   270
D12V14, multiclass
                                  clus
vv                                 AMP PEAK 12(12Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     119
                                  clus
vv                                 AMP PEAK 12(12Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    31
  WHITE                                                       270
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V15, binary
                                cls
clus                               0   1
  AMP PEAK 12(12Q14.1) MUTATED     3 115
  AMP PEAK 12(12Q14.1) WILD-TYPE   4 267
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(12Q14.1) MUTATED      3  115
  AMP PEAK 12(12Q14.1) WILD-TYPE    4  267
                        clus
vv                       AMP PEAK 12(12Q14.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          115
                        clus
vv                       AMP PEAK 12(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            267
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(12Q15) MUTATION ANALYSIS
D13V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 13(12Q15) MUTATED   103  61
  AMP PEAK 13(12Q15) WILD-TYPE 234  93
  AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE 
                         164                          327 
  AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE 
                          61                           93 
$`AMP PEAK 13(12Q15) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4402 TCGA-05-4415 
       19.96        45.01        37.02         0.00         8.02         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       14.96         9.01        29.98        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 TCGA-35-4122 TCGA-35-5375 TCGA-38-4628 
       15.02        15.02        29.00         7.40         8.68        49.05 
TCGA-38-4631 TCGA-44-2666 TCGA-44-5644 TCGA-44-5645 TCGA-44-6778 TCGA-44-6779 
       11.64         3.19        28.37        12.59        61.28        16.44 
TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8119 TCGA-44-A479 
       19.46        36.07        18.87        29.00         3.25        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-49-4488 TCGA-49-4501 TCGA-49-4507 TCGA-49-4510 
       15.32         9.44        28.57        46.72         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-AAQV 
       29.75        55.89        14.63        29.26        17.16        22.26 
TCGA-49-AAR0 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-50-5045 TCGA-50-5049 
      153.04         8.55        40.41        37.32        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5931 TCGA-50-5944 TCGA-50-5946 
       15.72        60.16         8.22        14.27        25.12        22.55 
TCGA-50-6592 TCGA-50-6597 TCGA-50-6673 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 
       25.55        41.69         0.72        34.29        13.94        38.73 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6978 
       48.62        45.21        32.65         0.79         0.82         5.49 
TCGA-55-6982 TCGA-55-6984 TCGA-55-6987 TCGA-55-7284 TCGA-55-7726 TCGA-55-7728 
       32.71        24.99        70.26         7.99         1.28         0.79 
TCGA-55-7815 TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 
        1.78         6.48         0.16        29.72         3.29        19.66 
TCGA-55-8208 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 
       22.16         0.76         0.95         0.26         0.49         0.49 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
       20.71         1.58        20.58         0.92        15.81        20.19 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 
       14.60        49.25        47.80        72.30        39.25        40.96 
TCGA-64-1678 TCGA-64-1681 TCGA-64-5779 TCGA-67-3774 TCGA-69-7760 TCGA-69-7973 
       39.09        38.37        28.41        12.66         6.64         7.56 
TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4675 TCGA-73-A9RS 
       12.56         4.24         7.04        26.30         1.32        11.18 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7161 TCGA-78-7167 
      163.10        27.16         5.69        20.58         7.07        88.14 
TCGA-78-7220 TCGA-78-7536 TCGA-78-8655 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       26.53         8.02        77.59        12.36         5.88        31.13 
TCGA-86-7713 TCGA-86-7953 TCGA-86-8074 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 
       13.87        19.43         0.79        15.65        15.85        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6831 
       14.60         1.15        30.84         3.81        10.62        10.19 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-93-8067 
       13.71        12.23         7.36        16.18         1.18         6.12 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 TCGA-95-A4VP TCGA-97-8176 
       18.67        12.39        15.68         2.76        19.89        15.39 
TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 
       16.41        20.58        18.67        20.68         1.45         5.59 
TCGA-L9-A443 TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
        3.81         1.91        11.87        86.14        58.45        49.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TI TCGA-NJ-A4YI 
       58.85         5.49        10.09        29.46        14.10         0.13 
TCGA-NJ-A55R TCGA-S2-AA1A 
       19.82        16.87 

$`AMP PEAK 13(12Q15) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 
       50.07         3.98        14.01         9.96        24.03        47.05 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       19.00        20.05        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       26.01         4.96        22.03         9.04         2.04         0.46 
TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 
        5.98        97.74       120.79        37.71        28.41        35.28 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       44.61        14.73        26.30         4.37        43.53        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 
       13.15        44.94        24.36        42.08        42.77        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       37.15        38.24        38.89        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       33.30        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 
       21.63        23.18        63.72        32.45        14.60        12.03 
TCGA-44-7662 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F 
        7.17        17.59        23.64        12.66         8.55        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 
       11.54        13.64        13.45        76.21        28.11        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-6743 TCGA-49-6761 TCGA-49-6767 
       35.54        14.07        32.84        12.13        11.64        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       63.95        62.24        28.90       123.58       211.82       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 
        9.86        20.52        31.04        49.28         9.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 
       42.35         3.91        11.05        12.16         6.21        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 
       25.61         7.59        27.25        30.54         9.21        23.05 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
        2.86         0.07        42.51        40.73        15.25        48.49 
TCGA-55-6975 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6985 
        3.88         7.79         2.20        45.34        60.03        40.54 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
      107.21         0.59         1.15         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 
        1.32        23.18         1.28         1.12        18.64         0.53 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8087 TCGA-55-8091 TCGA-55-8092 
       17.65         6.15        19.82        15.19        19.73         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 
        0.13        23.64        15.65        17.98         1.08         1.51 
TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 
        2.17        15.42         1.45         0.36        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
        0.10         4.80         6.64        17.62         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A492 TCGA-55-A4DG 
        2.17        16.93        22.65        21.40        19.59        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46P 
       17.95         4.57        39.98        42.38        88.64        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 
       56.71        54.35        67.96        13.61        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        37.02        87.98         2.04        42.90 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       51.25        28.47         1.02        20.05        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        5.72         4.64        13.87         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        5.42         6.05         2.30         2.93        14.01        13.45 
TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4668 
       26.73         2.01        52.60        23.38        29.98        15.35 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7147 
        4.31         5.39         1.25        39.09        23.51        19.27 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 
       32.09         5.88        64.90        22.29       104.19       223.96 
TCGA-78-7166 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
        8.48        31.20        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
       32.68       214.62        39.75        10.55       110.50        27.09 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       34.39        20.55        19.89        16.70        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8280 TCGA-86-8668 
        4.57        24.33        15.75        16.08        23.05        13.91 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       27.58         0.62        14.96        13.32        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 
       13.64        26.47        41.36         1.97         2.60        27.68 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        4.18        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN 
        1.22         2.86        15.65        27.29        21.40        18.18 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       14.30        21.60        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R 
       17.75        20.84        24.56        34.85        36.76        21.63 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 
       14.30         0.20        14.53        17.46        12.59        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 
       38.63         2.76        37.35        86.04         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK 
       31.23         2.43        11.05        14.66        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        71.05        62.60         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
        0.43         9.70        59.11 

  AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE 
                        0.00                         0.07 
  AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE 
                      163.10                       223.96 
  AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE 
                      15.915                       19.000 
[1] "0.0 - 163.1 (15.9)" "0.1 - 224.0 (19.0)"
[1] "hr=" "1.4"
D13V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(12Q15) MUTATED         3       40       41        1        20
  AMP PEAK 13(12Q15) WILD-TYPE       2       95       99        0        31
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 13(12Q15) MUTATED          25         28          3       10
  AMP PEAK 13(12Q15) WILD-TYPE        48         44          8       16
D13V3, multiclass
            clus
vv           AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE
  STAGE I                             3                            2
  STAGE IA                           40                           95
  STAGE IB                           41                           99
  STAGE II                            1                            0
  STAGE IIA                          20                           31
  STAGE IIB                          25                           48
  STAGE IIIA                         28                           44
  STAGE IIIB                          3                            8
  STAGE IV                           10                           16
[1] 9 2
[1] 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(12Q15) MUTATED    50  98  17   5
  AMP PEAK 13(12Q15) WILD-TYPE 120 180  29  14
D13V4, multiclass
    clus
vv   AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE
  T1                         50                          120
  T2                         98                          180
  T3                         17                           29
  T4                          5                           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 13(12Q15) MUTATED   105  35    28
  AMP PEAK 13(12Q15) WILD-TYPE 227  61    48
D13V5, multiclass
       clus
vv      AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE
  N0                           105                          227
  N1                            35                           61
  N2+N3                         28                           48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                              cls
clus                             0   1
  AMP PEAK 13(12Q15) MUTATED   114  10
  AMP PEAK 13(12Q15) WILD-TYPE 234  15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(12Q15) MUTATED    114   10
  AMP PEAK 13(12Q15) WILD-TYPE  234   15
   clus
vv  AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE
  0                        114                          234
  1                         10                           15
[1] 2 2
[1] FALSE
D13V7, binary
                              cls
clus                             0   1
  AMP PEAK 13(12Q15) MUTATED    85  86
  AMP PEAK 13(12Q15) WILD-TYPE 190 154
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(12Q15) MUTATED     85   86
  AMP PEAK 13(12Q15) WILD-TYPE  190  154
        clus
vv       AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE
  FEMALE                         85                          190
  MALE                           86                          154
[1] 2 2
[1] FALSE
D13V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 13(12Q15) MUTATED                            6
  AMP PEAK 13(12Q15) WILD-TYPE                         13
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 13(12Q15) MUTATED                                  34
  AMP PEAK 13(12Q15) WILD-TYPE                                73
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(12Q15) MUTATED                                                  115
  AMP PEAK 13(12Q15) WILD-TYPE                                                204
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 13(12Q15) MUTATED                                            1
  AMP PEAK 13(12Q15) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 13(12Q15) MUTATED                                               4
  AMP PEAK 13(12Q15) WILD-TYPE                                            15
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 13(12Q15) MUTATED                                1
  AMP PEAK 13(12Q15) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 13(12Q15) MUTATED                                    0
  AMP PEAK 13(12Q15) WILD-TYPE                                  3
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(12Q15) MUTATED                              0
  AMP PEAK 13(12Q15) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 13(12Q15) MUTATED                               5
  AMP PEAK 13(12Q15) WILD-TYPE                            18
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 13(12Q15) MUTATED                                 0
  AMP PEAK 13(12Q15) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 13(12Q15) MUTATED                                               2
  AMP PEAK 13(12Q15) WILD-TYPE                                             3
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 13(12Q15) MUTATED                              3
  AMP PEAK 13(12Q15) WILD-TYPE                            7
D13V9, multiclass
                                                    clus
vv                                                   AMP PEAK 13(12Q15) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        115
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               4
  LUNG CLEAR CELL ADENOCARCINOMA                                              1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          0
  LUNG MUCINOUS ADENOCARCINOMA                                                0
  LUNG PAPILLARY ADENOCARCINOMA                                               5
  LUNG SIGNET RING ADENOCARCINOMA                                             0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               2
  MUCINOUS (COLLOID) CARCINOMA                                                3
                                                    clus
vv                                                   AMP PEAK 13(12Q15) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          204
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                15
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  2
  LUNG PAPILLARY ADENOCARCINOMA                                                18
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                              cls
clus                             0   1
  AMP PEAK 13(12Q15) MUTATED     9 162
  AMP PEAK 13(12Q15) WILD-TYPE  12 332
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(12Q15) MUTATED      9  162
  AMP PEAK 13(12Q15) WILD-TYPE   12  332
     clus
vv    AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE
  NO                           9                           12
  YES                        162                          332
[1] 2 2
[1] FALSE
D13V11, continuous
D13V12, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 13(12Q15) MUTATED   117   4   3   6
  AMP PEAK 13(12Q15) WILD-TYPE 226   8   1  20
D13V13, multiclass
    clus
vv   AMP PEAK 13(12Q15) MUTATED AMP PEAK 13(12Q15) WILD-TYPE
  R0                        117                          226
  R1                          4                            8
  R2                          3                            1
  RX                          6                           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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(12Q15) MUTATED                                  0     3
  AMP PEAK 13(12Q15) WILD-TYPE                                1     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(12Q15) MUTATED                          18   123
  AMP PEAK 13(12Q15) WILD-TYPE                        33   266
D13V14, multiclass
                                  clus
vv                                 AMP PEAK 13(12Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                18
  WHITE                                                   123
                                  clus
vv                                 AMP PEAK 13(12Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  33
  WHITE                                                     266
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, binary
                              cls
clus                             0   1
  AMP PEAK 13(12Q15) MUTATED     4 115
  AMP PEAK 13(12Q15) WILD-TYPE   3 267
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 13(12Q15) MUTATED      4  115
  AMP PEAK 13(12Q15) WILD-TYPE    3  267
                        clus
vv                       AMP PEAK 13(12Q15) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        115
                        clus
vv                       AMP PEAK 13(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          267
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(14Q13.3) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(14Q13.3) MUTATED   153  66
  AMP PEAK 14(14Q13.3) WILD-TYPE 184  88
  AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE 
                           219                            272 
  AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE 
                            66                             88 
$`AMP PEAK 14(14Q13.3) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 
       45.01        37.02        47.05         8.02        20.05         2.99 
TCGA-05-4417 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 TCGA-05-5423 TCGA-05-5715 
       14.96        30.02        26.01        25.02         4.96         2.04 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        5.98         8.68        37.71        49.05        28.41        35.28 
TCGA-38-4632 TCGA-44-2659 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-6147 
       44.61        44.94        38.24        38.89        34.06        27.78 
TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       21.63        61.28        16.44        14.60        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 
       36.07        18.87        29.00        23.64         3.25        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       15.32         9.44        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4512 TCGA-49-6761 TCGA-49-6767 
       12.66        35.54        46.72        29.75        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V 
       22.26       153.04        28.90       123.58       211.82         9.86 
TCGA-50-5045 TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       71.47        21.47        18.64        22.55        42.35         3.91 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-53-7813 
       12.16         6.21         0.72        10.13        25.61        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        9.21        38.73        48.62         2.86         0.07        32.65 
TCGA-55-6712 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6981 TCGA-55-6983 
        0.79        15.25         0.82         3.88        45.34        60.03 
TCGA-55-7281 TCGA-55-7724 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
        0.59        23.18         1.12         1.78        18.64         0.53 
TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8091 TCGA-55-8096 
        6.48         6.15         0.16        29.72        19.73        23.64 
TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
       17.98         1.51         2.17         1.45         0.76         0.36 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.26        17.72         0.30         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF 
        1.58        20.71        21.40         1.58         0.92        20.19 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8402 TCGA-62-A46U TCGA-64-1676 
       19.99        17.95         4.57        49.25        67.96        56.81 
TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 
       20.65        39.09        87.98         2.04        28.41        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6217 TCGA-69-7760 
        1.02        20.05        18.84        14.04        13.87         6.64 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 
       22.68         7.56         6.05         2.93         7.04         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4677 TCGA-73-7499 
       52.60        23.38        29.98        26.30         1.25        23.51 
TCGA-73-A9RS TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7155 
       11.18        27.16         5.69        20.58        35.93        38.50 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 
       64.90         7.07        88.14         8.02        10.75       214.62 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 
       10.55       110.50        27.09        12.36        31.13        13.87 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8278 
       19.43        16.70        24.49         4.08         0.79        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 
       15.85        23.05        21.47         1.15        30.84        14.96 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
        3.81        10.62        41.36        10.19         2.60        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP TCGA-93-A4JQ 
        1.18         1.45         6.12        23.61        19.00        17.29 
TCGA-95-7562 TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 
        2.86        18.67         2.76        19.89        31.69        25.48 
TCGA-97-7937 TCGA-97-8171 TCGA-97-8179 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
        5.95        18.67        14.30        20.19        21.44        19.76 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-A4AG TCGA-L9-A443 
       18.67        24.56         1.45        24.30        16.44         3.81 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 
        0.20        27.19        38.63        86.14        49.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK 
       58.85         5.29        41.59        29.46        11.05        19.13 
TCGA-NJ-A4YF TCGA-NJ-A55R TCGA-O1-A52J 
       71.05        19.82        59.11 

$`AMP PEAK 14(14Q13.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        19.96        14.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4403 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
       24.03        19.00         9.01        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 
       26.01        25.02        24.00        15.02        15.02        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 TCGA-38-4625 TCGA-38-4626 
       22.03         9.04         0.46         7.40        97.74       120.79 
TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       11.64        14.73        26.30         4.37        43.53        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       13.15        24.36        42.08        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       37.15         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 
       23.77        10.78         9.93        23.15        23.18        63.72 
TCGA-44-6777 TCGA-44-7661 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F 
       32.45        12.03        17.59        12.66         8.55        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       11.54        13.64        14.07        32.84         8.81        29.46 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-AAR2 
       55.89        14.63        12.13        29.26        17.16        63.95 
TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARR TCGA-50-5044 
       62.24         8.55        40.41        37.32       164.12        20.52 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       70.55        15.72        60.16        31.04        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        9.27        14.27        40.60        78.67         8.45        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6592 TCGA-50-6593 TCGA-50-6597 TCGA-50-8459 
       29.03        25.12        25.55        11.05        41.69         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1592 TCGA-55-1596 TCGA-55-6968 
       27.25        34.29        30.54        23.05        45.21        42.51 
TCGA-55-6969 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6982 
       40.73        48.49         5.49         7.79         2.20        32.71 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 
       24.99        40.54       107.21        70.26         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 
        0.20         0.13         3.12         1.32         1.28         1.28 
TCGA-55-7728 TCGA-55-7911 TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        0.79        17.65        19.82        15.19         3.29        19.66 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 
        5.06         0.13        15.65         1.08        22.16        15.42 
TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8620 
        0.95         0.49         0.10         4.80         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-62-8395 
       16.93        22.65        20.58        19.59        15.81        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       42.38        14.60        88.64        47.80        19.53        56.71 
TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       54.35        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-64-5781 TCGA-67-3774 
       55.43        37.02        38.37        42.90        51.25        12.66 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 
        5.72         4.64         6.12        13.61         5.42         2.30 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-73-4668 
       12.56        14.01        13.45         4.24        26.73        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-78-7143 TCGA-78-7147 
        4.31         1.32         5.39        39.09       163.10        19.27 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       21.90        39.52        24.99        19.50        32.09         5.88 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 
       22.29       104.19       223.96         8.48        26.53        31.20 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       53.33        39.35        10.55        32.68        39.75        77.59 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8056 TCGA-86-8073 
        5.88        34.39        20.55        19.89         4.57        24.33 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
       15.75        16.08        14.60        13.91        27.58         0.62 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 
       13.32        13.32        17.62        13.64        26.47         1.97 
TCGA-91-6849 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-95-7039 
        1.15        19.82         9.76         4.18         1.08         1.12 
TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
        1.22        12.39        15.68        15.65        27.29        21.40 
TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 
       18.18        64.60        63.52        43.79         0.59         0.72 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       17.92         5.39        18.12        15.39        16.41        21.60 
TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-8025 
       20.58        20.52        17.75        20.84        20.68        34.85 
TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         5.59        21.63        23.80        18.08        35.47 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV 
       19.00        14.30        14.53         1.91        17.46        12.59 
TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TA 
       11.87         2.76        58.45        37.35         5.49        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 
        2.43        10.09        14.66        14.10        11.15        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A7XG TCGA-S2-AA1A 
        9.70        16.87 

  AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE 
                          0.07                           0.00 
  AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE 
                        214.62                         223.96 
  AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE 
                        18.670                         17.835 
[1] "0.1 - 214.6 (18.7)" "0.0 - 224.0 (17.8)"
[1] "hr=" "1"  
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(14Q13.3) MUTATED         2       61       58        1        29
  AMP PEAK 14(14Q13.3) WILD-TYPE       3       74       82        0        22
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 14(14Q13.3) MUTATED          29         31          6       11
  AMP PEAK 14(14Q13.3) WILD-TYPE        44         41          5       15
D14V3, multiclass
            clus
vv           AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             61                             74
  STAGE IB                             58                             82
  STAGE II                              1                              0
  STAGE IIA                            29                             22
  STAGE IIB                            29                             44
  STAGE IIIA                           31                             41
  STAGE IIIB                            6                              5
  STAGE IV                             11                             15
[1] 9 2
[1] 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(14Q13.3) MUTATED    76 128  15   8
  AMP PEAK 14(14Q13.3) WILD-TYPE  94 150  31  11
D14V4, multiclass
    clus
vv   AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE
  T1                           76                             94
  T2                          128                            150
  T3                           15                             31
  T4                            8                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1 N2+N3
  AMP PEAK 14(14Q13.3) MUTATED   147  41    35
  AMP PEAK 14(14Q13.3) WILD-TYPE 185  55    41
D14V5, multiclass
       clus
vv      AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE
  N0                             147                            185
  N1                              41                             55
  N2+N3                           35                             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                                cls
clus                               0   1
  AMP PEAK 14(14Q13.3) MUTATED   141  11
  AMP PEAK 14(14Q13.3) WILD-TYPE 207  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(14Q13.3) MUTATED    141   11
  AMP PEAK 14(14Q13.3) WILD-TYPE  207   14
   clus
vv  AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE
  0                          141                            207
  1                           11                             14
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(14Q13.3) MUTATED   125 103
  AMP PEAK 14(14Q13.3) WILD-TYPE 150 137
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(14Q13.3) MUTATED    125  103
  AMP PEAK 14(14Q13.3) WILD-TYPE  150  137
        clus
vv       AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE
  FEMALE                          125                            150
  MALE                            103                            137
[1] 2 2
[1] FALSE
D14V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 14(14Q13.3) MUTATED                           11
  AMP PEAK 14(14Q13.3) WILD-TYPE                          8
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 14(14Q13.3) MUTATED                                  40
  AMP PEAK 14(14Q13.3) WILD-TYPE                                67
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(14Q13.3) MUTATED                                                  155
  AMP PEAK 14(14Q13.3) WILD-TYPE                                                164
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 14(14Q13.3) MUTATED                                            1
  AMP PEAK 14(14Q13.3) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 14(14Q13.3) MUTATED                                               6
  AMP PEAK 14(14Q13.3) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 14(14Q13.3) MUTATED                                1
  AMP PEAK 14(14Q13.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 14(14Q13.3) MUTATED                                    2
  AMP PEAK 14(14Q13.3) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(14Q13.3) MUTATED                              0
  AMP PEAK 14(14Q13.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 14(14Q13.3) MUTATED                               9
  AMP PEAK 14(14Q13.3) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 14(14Q13.3) MUTATED                                 0
  AMP PEAK 14(14Q13.3) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 14(14Q13.3) MUTATED                                               2
  AMP PEAK 14(14Q13.3) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 14(14Q13.3) MUTATED                              1
  AMP PEAK 14(14Q13.3) WILD-TYPE                            9
D14V9, multiclass
                                                    clus
vv                                                   AMP PEAK 14(14Q13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          155
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 6
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 9
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   AMP PEAK 14(14Q13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              67
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            164
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  14
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   3
  MUCINOUS (COLLOID) CARCINOMA                                                    9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, binary
                                cls
clus                               0   1
  AMP PEAK 14(14Q13.3) MUTATED     7 221
  AMP PEAK 14(14Q13.3) WILD-TYPE  14 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(14Q13.3) MUTATED      7  221
  AMP PEAK 14(14Q13.3) WILD-TYPE   14  273
     clus
vv    AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE
  NO                             7                             14
  YES                          221                            273
[1] 2 2
[1] FALSE
D14V11, continuous
D14V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(14Q13.3) MUTATED   150   6   1  12
  AMP PEAK 14(14Q13.3) WILD-TYPE 193   6   3  14
D14V13, multiclass
    clus
vv   AMP PEAK 14(14Q13.3) MUTATED AMP PEAK 14(14Q13.3) WILD-TYPE
  R0                          150                            193
  R1                            6                              6
  R2                            1                              3
  RX                           12                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(14Q13.3) MUTATED                                  0     5
  AMP PEAK 14(14Q13.3) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(14Q13.3) MUTATED                          22   174
  AMP PEAK 14(14Q13.3) WILD-TYPE                        29   215
D14V14, multiclass
                                  clus
vv                                 AMP PEAK 14(14Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     174
                                  clus
vv                                 AMP PEAK 14(14Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    29
  WHITE                                                       215
[1] 4 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(14Q13.3) MUTATED     2 174
  AMP PEAK 14(14Q13.3) WILD-TYPE   5 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(14Q13.3) MUTATED      2  174
  AMP PEAK 14(14Q13.3) WILD-TYPE    5  208
                        clus
vv                       AMP PEAK 14(14Q13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          174
                        clus
vv                       AMP PEAK 14(14Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            208
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(17Q12) MUTATION ANALYSIS
D15V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 15(17Q12) MUTATED   153  66
  AMP PEAK 15(17Q12) WILD-TYPE 184  88
  AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE 
                         219                          272 
  AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE 
                          66                           88 
$`AMP PEAK 15(17Q12) MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4395 TCGA-05-4398 
       50.07         3.98        19.96        45.01         0.00        47.05 
TCGA-05-4402 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4424 TCGA-05-4425 
        8.02         2.99        14.96         9.01        30.02        21.99 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-5715 TCGA-35-4122 TCGA-38-4628 
       26.01        25.02        25.02         2.04         7.40        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-44-3396 TCGA-44-3918 
       28.41        35.28        11.64        44.61        37.15        34.06 
TCGA-44-3919 TCGA-44-6144 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
        6.25        23.77        23.15        23.18        32.45        61.28 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-8119 
       19.46        12.03         7.17        36.07        29.00         3.25 
TCGA-44-8120 TCGA-44-A47B TCGA-44-A4SS TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 
        8.55         9.44        13.64        12.66        46.72        14.07 
TCGA-49-4507 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-AAR4 
        8.81        14.63        12.13        29.26        17.16        28.90 
TCGA-49-AARO TCGA-49-AARQ TCGA-50-5049 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
      123.58       211.82        70.55         9.27        14.27        78.67 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 
       21.47        18.64        25.12        22.55         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
       11.05        12.16        41.69        13.94        23.05        38.73 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6978 
       48.62        45.21         2.86        32.65         0.79         5.49 
TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 TCGA-55-7281 TCGA-55-7576 TCGA-55-7727 
        7.79        45.34        32.71         0.59         1.32         1.12 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
        1.78        18.64         0.53        17.65        19.82         0.16 
TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8205 TCGA-55-8207 
       29.72         3.29         5.06         0.13         1.08         2.17 
TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 
       22.16         0.76         0.26        17.72         0.30         6.64 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A494 
        1.58         2.17        21.40         1.58        20.58        15.81 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46R 
       19.99        17.95         4.57        14.60        49.25        56.71 
TCGA-62-A46S TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 
       54.35        13.61        39.25        40.96        56.81        20.65 
TCGA-64-1680 TCGA-64-5774 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 
       37.02        87.98         1.02        20.05        18.84         5.72 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
        6.64         6.12         7.56         6.05         2.30        12.56 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        7.04         2.01        52.60        29.98        26.30        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.32         5.39        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7154 TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 
       19.27        35.93        19.50        32.09        64.90         7.07 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-78-8640 
       88.14        26.53         8.02        10.75        32.68       214.62 
TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
       10.55       110.50        12.36         5.88        34.39        13.87 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 
       19.43        19.89        16.70         4.08         0.79        15.75 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-A4D0 
       15.85        21.47         1.15        13.91        30.84         3.81 
TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       13.64        10.62         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        7.36         4.18         6.12        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 
        1.22        18.67        12.39        15.68        27.29         2.76 
TCGA-95-A4VN TCGA-97-7553 TCGA-97-7554 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
       18.18        43.79        25.48        18.12        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8032 TCGA-J2-A4AD 
       21.60        20.58        18.67        34.85         1.45        18.08 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
        3.81         0.20        17.46        12.59        11.87        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 
       38.63         2.76        86.14        49.35        86.04        58.85 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TK TCGA-NJ-A4YF 
        5.29        41.59        10.09        29.46        19.13        71.05 
TCGA-NJ-A4YG TCGA-NJ-A7XG TCGA-O1-A52J 
       62.60         9.70        59.11 

$`AMP PEAK 15(17Q12) WILD-TYPE`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 TCGA-05-4405 
       14.01        37.02         9.96        24.03        19.00        20.05 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4426 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       29.98        12.00        26.01        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 
        4.96        29.00        22.03         9.04         0.46         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-6178 TCGA-38-7271 
        8.68        97.74       120.79        37.71        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
        4.37        43.53        46.98        13.15        44.94        24.36 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 TCGA-44-3917 
       42.08        42.77         3.19        25.02        38.24        38.89 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        28.37        12.59        10.78         9.93 
TCGA-44-6147 TCGA-44-6774 TCGA-44-6776 TCGA-44-6779 TCGA-44-7659 TCGA-44-7669 
       27.78        21.63        63.72        16.44        14.60        18.87 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F 
       17.59        23.64        12.66        15.98        15.32        11.08 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 
       11.54        13.45        76.21        28.11        28.57        35.54 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6761 TCGA-49-6767 
       32.84        29.46        29.75        55.89        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARE 
       22.26       153.04        63.95        62.24         8.55        40.41 
TCGA-49-AARN TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 
       37.32       164.12         9.86        20.52        71.47        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5932 TCGA-50-5936 
       60.16        31.04        49.28         8.22        40.60         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       15.12        29.03        42.35         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
       25.61         7.59        27.25        34.29        30.54         9.21 
TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        0.07        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
        3.88         2.20        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
       70.26         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7910 TCGA-55-7914 
       23.18         1.28         1.28         0.79         6.48         6.15 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 
       15.19        19.66        19.73        23.64        15.65        17.98 
TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
        1.51        15.42         1.45         0.95         0.36         0.49 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 
        0.10         4.80        17.62         0.49         1.61        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-62-8395 
       22.65        20.71        19.59         0.92        20.19        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U TCGA-62-A46V 
       42.38        88.64        47.80        19.53        67.96        72.30 
TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
       29.92        39.09        55.43        38.37         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 
       28.41        51.25        28.47        14.04        12.66         4.64 
TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-69-8253 
       13.87        22.68        13.61         5.42         2.93        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-73-4659 TCGA-73-4670 TCGA-73-4677 
       13.45         4.24        26.73        23.38         4.31         1.25 
TCGA-73-7498 TCGA-73-A9RS TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       39.09        11.18        20.58        21.90        39.52        24.99 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       38.50         5.88        22.29       104.19       223.96         8.48 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 
       31.20        53.33        39.35        10.55        39.75        77.59 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       27.09        31.13        20.55        24.49         4.57        24.33 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8671 TCGA-86-8672 
       16.08        15.65        23.05        14.60        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6829 
       14.96        13.32        13.32        17.62        26.47        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
        1.97        10.19         1.15        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO 
        1.18         1.45        19.82         9.76        23.61         1.08 
TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        2.86        15.65        21.40        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       63.52         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8176 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
        5.39        15.39        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8033 
       17.75        20.84        20.68        24.56        36.76         5.59 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.63        24.30        23.80        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 
       14.30        14.53         1.91        58.45        37.35         5.49 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       31.23         2.43        11.05        14.66        14.10        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       73.91         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-S2-AA1A 
       19.82        16.87 

  AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE 
                        0.00                         0.07 
  AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE 
                      214.62                       223.96 
  AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE 
                      17.650                       19.625 
[1] "0.0 - 214.6 (17.6)" "0.1 - 224.0 (19.6)"
[1] "hr=" "1"  
D15V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(17Q12) MUTATED         3       56       59        0        23
  AMP PEAK 15(17Q12) WILD-TYPE       2       79       81        1        28
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 15(17Q12) MUTATED          29         35          8       13
  AMP PEAK 15(17Q12) WILD-TYPE        44         37          3       13
D15V3, multiclass
            clus
vv           AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE
  STAGE I                             3                            2
  STAGE IA                           56                           79
  STAGE IB                           59                           81
  STAGE II                            0                            1
  STAGE IIA                          23                           28
  STAGE IIB                          29                           44
  STAGE IIIA                         35                           37
  STAGE IIIB                          8                            3
  STAGE IV                           13                           13
[1] 9 2
[1] 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(17Q12) MUTATED    67 130  18  10
  AMP PEAK 15(17Q12) WILD-TYPE 103 148  28   9
D15V4, multiclass
    clus
vv   AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE
  T1                         67                          103
  T2                        130                          148
  T3                         18                           28
  T4                         10                            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 15(17Q12) MUTATED   139  44    39
  AMP PEAK 15(17Q12) WILD-TYPE 193  52    37
D15V5, multiclass
       clus
vv      AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE
  N0                           139                          193
  N1                            44                           52
  N2+N3                         39                           37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                              cls
clus                             0   1
  AMP PEAK 15(17Q12) MUTATED   156  13
  AMP PEAK 15(17Q12) WILD-TYPE 192  12
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(17Q12) MUTATED    156   13
  AMP PEAK 15(17Q12) WILD-TYPE  192   12
   clus
vv  AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE
  0                        156                          192
  1                         13                           12
[1] 2 2
[1] FALSE
D15V7, binary
                              cls
clus                             0   1
  AMP PEAK 15(17Q12) MUTATED   117 109
  AMP PEAK 15(17Q12) WILD-TYPE 158 131
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(17Q12) MUTATED    117  109
  AMP PEAK 15(17Q12) WILD-TYPE  158  131
        clus
vv       AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE
  FEMALE                        117                          158
  MALE                          109                          131
[1] 2 2
[1] FALSE
D15V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 15(17Q12) MUTATED                            8
  AMP PEAK 15(17Q12) WILD-TYPE                         11
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 15(17Q12) MUTATED                                  49
  AMP PEAK 15(17Q12) WILD-TYPE                                58
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(17Q12) MUTATED                                                  146
  AMP PEAK 15(17Q12) WILD-TYPE                                                173
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 15(17Q12) MUTATED                                            1
  AMP PEAK 15(17Q12) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 15(17Q12) MUTATED                                               5
  AMP PEAK 15(17Q12) WILD-TYPE                                            14
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 15(17Q12) MUTATED                                2
  AMP PEAK 15(17Q12) WILD-TYPE                              0
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 15(17Q12) MUTATED                                    1
  AMP PEAK 15(17Q12) WILD-TYPE                                  2
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(17Q12) MUTATED                              1
  AMP PEAK 15(17Q12) WILD-TYPE                            1
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 15(17Q12) MUTATED                               8
  AMP PEAK 15(17Q12) WILD-TYPE                            15
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 15(17Q12) MUTATED                                 0
  AMP PEAK 15(17Q12) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 15(17Q12) MUTATED                                               4
  AMP PEAK 15(17Q12) WILD-TYPE                                             1
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 15(17Q12) MUTATED                              1
  AMP PEAK 15(17Q12) WILD-TYPE                            9
D15V9, multiclass
                                                    clus
vv                                                   AMP PEAK 15(17Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        146
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               5
  LUNG CLEAR CELL ADENOCARCINOMA                                              2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          1
  LUNG MUCINOUS ADENOCARCINOMA                                                1
  LUNG PAPILLARY ADENOCARCINOMA                                               8
  LUNG SIGNET RING ADENOCARCINOMA                                             0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               4
  MUCINOUS (COLLOID) CARCINOMA                                                1
                                                    clus
vv                                                   AMP PEAK 15(17Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            58
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          173
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                14
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                15
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, binary
                              cls
clus                             0   1
  AMP PEAK 15(17Q12) MUTATED    12 214
  AMP PEAK 15(17Q12) WILD-TYPE   9 280
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(17Q12) MUTATED     12  214
  AMP PEAK 15(17Q12) WILD-TYPE    9  280
     clus
vv    AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE
  NO                          12                            9
  YES                        214                          280
[1] 2 2
[1] FALSE
D15V11, continuous
D15V12, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 15(17Q12) MUTATED   147   5   2  17
  AMP PEAK 15(17Q12) WILD-TYPE 196   7   2   9
D15V13, multiclass
    clus
vv   AMP PEAK 15(17Q12) MUTATED AMP PEAK 15(17Q12) WILD-TYPE
  R0                        147                          196
  R1                          5                            7
  R2                          2                            2
  RX                         17                            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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(17Q12) MUTATED                                  1     5
  AMP PEAK 15(17Q12) WILD-TYPE                                0     2
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(17Q12) MUTATED                          19   170
  AMP PEAK 15(17Q12) WILD-TYPE                        32   219
D15V14, multiclass
                                  clus
vv                                 AMP PEAK 15(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     5
  BLACK OR AFRICAN AMERICAN                                19
  WHITE                                                   170
                                  clus
vv                                 AMP PEAK 15(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  32
  WHITE                                                     219
[1] 4 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(17Q12) MUTATED     3 161
  AMP PEAK 15(17Q12) WILD-TYPE   4 221
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(17Q12) MUTATED      3  161
  AMP PEAK 15(17Q12) WILD-TYPE    4  221
                        clus
vv                       AMP PEAK 15(17Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        161
                        clus
vv                       AMP PEAK 15(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          221
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(17Q23.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(17Q23.1) MUTATED   166  74
  AMP PEAK 16(17Q23.1) WILD-TYPE 171  80
  AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE 
                           240                            251 
  AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE 
                            74                             80 
$`AMP PEAK 16(17Q23.1) MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        19.96        45.01         0.00        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 
       47.05         8.02         2.99        14.96         9.01        29.98 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-35-4122 
       30.02        21.99        26.01        25.02        25.02         7.40 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 
       49.05        28.41        11.64        44.61        46.98        13.15 
TCGA-44-2662 TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-6144 
       42.08        25.02        37.15        34.06         6.25        23.77 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 
       23.15        23.18        32.45        16.44        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
        7.17        36.07        29.00        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 
       15.98        15.32         9.44        12.66        46.72        14.07 
TCGA-49-4507 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        8.81        14.63        12.13        29.26        17.16        11.64 
TCGA-49-AAR4 TCGA-49-AARN TCGA-49-AARO TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
       28.90        37.32       123.58        49.28         9.27        14.27 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
       78.67        21.47        18.64        25.12        22.55         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-53-7624 TCGA-53-7813 
       25.55        11.05        12.16        41.69        34.29        13.94 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
       23.05        38.73        48.62         2.86        32.65         0.79 
TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 TCGA-55-7281 
        0.82         5.49         7.79        45.34        32.71         0.59 
TCGA-55-7283 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
        1.15         1.32         1.12         1.78        18.64         0.53 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 TCGA-55-8094 TCGA-55-8205 
       17.65        19.82         0.16         3.29         0.13         1.08 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 
        2.17        22.16         0.76         0.36         0.26        17.72 
TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        6.64         1.58         2.17        21.40         1.58        20.58 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 TCGA-62-8402 
       15.81        19.99        17.95         4.57        14.60        49.25 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 
       47.80        56.71        54.35        67.96        13.61        39.25 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 TCGA-64-5815 
       40.96        56.81        20.65        37.02        87.98        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 
        1.02        20.05        18.84         5.72        13.87         6.64 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 
       13.61         7.56         6.05         2.30        12.56         4.24 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 
        2.01        52.60        29.98        26.30        15.35         1.32 
TCGA-73-4676 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        5.39        23.51       163.10        27.16         5.69        19.27 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 
       35.93        19.50        64.90         7.07        88.14        26.53 
TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 
       10.75        10.55        32.68       214.62        77.59        10.55 
TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
      110.50        12.36         5.88        34.39        13.87        19.43 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
       16.70         4.08         4.57         0.79        15.75        15.85 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 
       21.47         1.15        13.91        30.84         0.62        14.96 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 
       13.32         3.81        13.64        10.62         2.60        13.71 
TCGA-91-6847 TCGA-91-6848 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP 
       27.68         7.36         4.18         6.12         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
       17.29         1.12         1.22        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
        2.76        21.40        18.18        43.79        25.48         5.95 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       19.76        18.67        34.85        36.76         1.45         5.59 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV 
       18.08        19.00         3.81         0.20        17.46        12.59 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY 
       11.87        27.19        38.63         2.76        86.14        49.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TD TCGA-MP-A4TE 
       86.04        58.85         5.29        41.59        10.09        29.46 
TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A7XG TCGA-O1-A52J 
       19.13        62.60         0.13        29.13         9.70        59.11 

$`AMP PEAK 16(17Q23.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4390 TCGA-05-4396 TCGA-05-4403 TCGA-05-4405 TCGA-05-4422 
       14.01        37.02         9.96        19.00        20.05        12.00 
TCGA-05-4426 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       26.01        24.00        15.02        15.02         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 
       22.03         9.04         2.04         0.46         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       97.74       120.79        37.71        35.28        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 
        4.37        43.53        44.94        24.36        42.77         3.19 
TCGA-44-3398 TCGA-44-3917 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       38.24        38.89        26.56        33.30        28.37        12.59 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 
       10.78         9.93        27.78        21.63        63.72        61.28 
TCGA-44-7659 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47F TCGA-44-A47G 
       14.60        18.87        17.59        23.64        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 
       13.64        13.45        76.21        28.11        28.57        35.54 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6767 TCGA-49-AAQV 
       32.84        29.46        29.75        55.89        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARQ 
      153.04        63.95        62.24         8.55        40.41       211.82 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      164.12         9.86        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5932 TCGA-50-5936 TCGA-50-5939 
       60.16        31.04         8.22        40.60         8.45        15.12 
TCGA-50-5942 TCGA-50-6590 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       29.03        42.35         6.21         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-6543 
        7.59        27.25        30.54         9.21        45.21         0.07 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       42.51        40.73        15.25        48.49         3.88         2.20 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 
       60.03        24.99        40.54       107.21        70.26         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.20         0.13         3.12        23.18         1.28         1.28 
TCGA-55-7728 TCGA-55-7910 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        0.79         6.48         6.15        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 
       19.73         5.06        23.64        15.65        17.98         1.51 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 
       15.42         1.45         0.95         0.49         0.30         0.10 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
        4.80        17.62         0.49         1.61        16.93        22.65 
TCGA-55-A48Y TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8397 
       20.71        19.59         0.92        20.19        39.98        42.38 
TCGA-62-8399 TCGA-62-A46P TCGA-62-A46V TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 
       88.64        19.53        72.30        29.92        39.09        55.43 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3773 
       38.37         2.04        42.90        28.41        51.25        14.04 
TCGA-67-3774 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7979 
       12.66         4.64         6.12        22.68         5.42         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4670 
       14.01        13.45        26.73         7.04        23.38         4.31 
TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
        1.25        39.09        11.18        20.58        21.90        39.52 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 
       24.99        38.50        32.09         5.88        22.29       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
      223.96         8.48        31.20         8.02        53.33        39.35 
TCGA-78-8648 TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
       39.75        27.09        31.13        20.55        19.89        24.49 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8671 
       24.33        16.08        15.65        23.05        14.60        27.58 
TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.32        17.62        26.47        41.36         1.97        10.19 
TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       12.23         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-95-7562 TCGA-95-7947 
        1.45        19.82         9.76        23.61         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 
       15.65        19.89        31.69        64.60        63.52         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-A4LX TCGA-97-A4M0 
        0.72        18.67        17.92         5.39        20.19        21.44 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-AA5R 
       20.52        17.75        20.84        20.68        24.56        21.63 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W 
       24.30        23.80        35.47        16.44        14.30        14.53 
TCGA-L9-A5IP TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TC 
        1.91        58.45        37.35         5.49        31.23         2.43 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.66        14.10        11.15        73.91        71.05 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        1.64         0.26         0.43        19.82        16.87 

  AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE 
                          0.00                           0.07 
  AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE 
                        214.62                         223.96 
  AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE 
                        17.225                         19.820 
[1] "0.0 - 214.6 (17.2)" "0.1 - 224.0 (19.8)"
[1] "hr=" "1.1"
D16V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(17Q23.1) MUTATED         3       58       68        0        24
  AMP PEAK 16(17Q23.1) WILD-TYPE       2       77       72        1        27
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 16(17Q23.1) MUTATED          33         41          8       14
  AMP PEAK 16(17Q23.1) WILD-TYPE        40         31          3       12
D16V3, multiclass
            clus
vv           AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             58                             77
  STAGE IB                             68                             72
  STAGE II                              0                              1
  STAGE IIA                            24                             27
  STAGE IIB                            33                             40
  STAGE IIIA                           41                             31
  STAGE IIIB                            8                              3
  STAGE IV                             14                             12
[1] 9 2
[1] 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(17Q23.1) MUTATED    72 145  20  10
  AMP PEAK 16(17Q23.1) WILD-TYPE  98 133  26   9
D16V4, multiclass
    clus
vv   AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE
  T1                           72                             98
  T2                          145                            133
  T3                           20                             26
  T4                           10                              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 16(17Q23.1) MUTATED   151  49    43
  AMP PEAK 16(17Q23.1) WILD-TYPE 181  47    33
D16V5, multiclass
       clus
vv      AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE
  N0                             151                            181
  N1                              49                             47
  N2+N3                           43                             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"
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(17Q23.1) MUTATED   172  14
  AMP PEAK 16(17Q23.1) WILD-TYPE 176  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(17Q23.1) MUTATED    172   14
  AMP PEAK 16(17Q23.1) WILD-TYPE  176   11
   clus
vv  AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE
  0                          172                            176
  1                           14                             11
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(17Q23.1) MUTATED   135 114
  AMP PEAK 16(17Q23.1) WILD-TYPE 140 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(17Q23.1) MUTATED    135  114
  AMP PEAK 16(17Q23.1) WILD-TYPE  140  126
        clus
vv       AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE
  FEMALE                          135                            140
  MALE                            114                            126
[1] 2 2
[1] FALSE
D16V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 16(17Q23.1) MUTATED                            8
  AMP PEAK 16(17Q23.1) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 16(17Q23.1) MUTATED                                  54
  AMP PEAK 16(17Q23.1) WILD-TYPE                                53
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(17Q23.1) MUTATED                                                  161
  AMP PEAK 16(17Q23.1) WILD-TYPE                                                158
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 16(17Q23.1) MUTATED                                            1
  AMP PEAK 16(17Q23.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 16(17Q23.1) MUTATED                                               6
  AMP PEAK 16(17Q23.1) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 16(17Q23.1) MUTATED                                2
  AMP PEAK 16(17Q23.1) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 16(17Q23.1) MUTATED                                    2
  AMP PEAK 16(17Q23.1) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 16(17Q23.1) MUTATED                              1
  AMP PEAK 16(17Q23.1) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 16(17Q23.1) MUTATED                               8
  AMP PEAK 16(17Q23.1) WILD-TYPE                            15
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 16(17Q23.1) MUTATED                                 0
  AMP PEAK 16(17Q23.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 16(17Q23.1) MUTATED                                               5
  AMP PEAK 16(17Q23.1) WILD-TYPE                                             0
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 16(17Q23.1) MUTATED                              1
  AMP PEAK 16(17Q23.1) WILD-TYPE                            9
D16V9, multiclass
                                                    clus
vv                                                   AMP PEAK 16(17Q23.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          161
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 6
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                 8
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 5
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   AMP PEAK 16(17Q23.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            158
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                                  15
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   0
  MUCINOUS (COLLOID) CARCINOMA                                                    9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, binary
                                cls
clus                               0   1
  AMP PEAK 16(17Q23.1) MUTATED    10 239
  AMP PEAK 16(17Q23.1) WILD-TYPE  11 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(17Q23.1) MUTATED     10  239
  AMP PEAK 16(17Q23.1) WILD-TYPE   11  255
     clus
vv    AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE
  NO                            10                             11
  YES                          239                            255
[1] 2 2
[1] FALSE
D16V11, continuous
D16V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(17Q23.1) MUTATED   164   4   2  20
  AMP PEAK 16(17Q23.1) WILD-TYPE 179   8   2   6
D16V13, multiclass
    clus
vv   AMP PEAK 16(17Q23.1) MUTATED AMP PEAK 16(17Q23.1) WILD-TYPE
  R0                          164                            179
  R1                            4                              8
  R2                            2                              2
  RX                           20                              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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(17Q23.1) MUTATED                                  1     5
  AMP PEAK 16(17Q23.1) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(17Q23.1) MUTATED                          18   190
  AMP PEAK 16(17Q23.1) WILD-TYPE                        33   199
D16V14, multiclass
                                  clus
vv                                 AMP PEAK 16(17Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     190
                                  clus
vv                                 AMP PEAK 16(17Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    33
  WHITE                                                       199
[1] 4 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(17Q23.1) MUTATED     5 177
  AMP PEAK 16(17Q23.1) WILD-TYPE   2 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(17Q23.1) MUTATED      5  177
  AMP PEAK 16(17Q23.1) WILD-TYPE    2  205
                        clus
vv                       AMP PEAK 16(17Q23.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          177
                        clus
vv                       AMP PEAK 16(17Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            205
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(18Q11.2) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(18Q11.2) MUTATED    70  28
  AMP PEAK 17(18Q11.2) WILD-TYPE 267 126
  AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE 
                            98                            393 
  AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE 
                            28                            126 
$`AMP PEAK 17(18Q11.2) MUTATED`
TCGA-05-4390 TCGA-05-4396 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4433 
       37.02         9.96         2.99        29.98        30.02        24.00 
TCGA-05-5425 TCGA-05-5428 TCGA-38-4631 TCGA-38-4632 TCGA-44-2659 TCGA-44-5644 
       29.00        22.03        11.64        44.61        44.94        28.37 
TCGA-44-6144 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       23.77        61.28        19.46         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-A47A TCGA-49-4514 TCGA-49-6743 
       29.00        23.64         3.25        15.32        55.89        12.13 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR2 TCGA-4B-A93V TCGA-50-5068 TCGA-50-5931 
       17.16        11.64        63.95         9.86        49.28        14.27 
TCGA-50-6673 TCGA-53-7813 TCGA-55-1592 TCGA-55-1595 TCGA-55-6642 TCGA-55-6970 
        0.72        13.94        23.05        48.62        32.65        15.25 
TCGA-55-6980 TCGA-55-7728 TCGA-55-7907 TCGA-55-8089 TCGA-55-8096 TCGA-55-8508 
        2.20         0.79         0.53         3.29        23.64         0.49 
TCGA-55-8511 TCGA-55-8615 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8398 
        0.30         0.49        15.81        20.19        19.99        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-5779 
       88.64        49.25        56.81        20.65        39.09        28.41 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8453 
       13.61         7.56         2.93        12.56        14.01        26.73 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-78-7148 TCGA-78-7150 
       29.98        15.35         1.32         5.39        20.58        21.90 
TCGA-78-7155 TCGA-78-7167 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 TCGA-86-7713 
       38.50        88.14        10.55        77.59       110.50        13.87 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8358 
       16.70         4.08        24.33         0.79        15.75        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 
       14.60         1.15         3.81        41.36        10.19        12.23 
TCGA-91-8499 TCGA-93-A4JN TCGA-95-7562 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 
        1.18        23.61         2.86        31.69        64.60        25.48 
TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-L9-A7SV TCGA-MP-A4TD TCGA-NJ-A55R 
       18.12        14.30        20.58        12.59        10.09        19.82 
TCGA-NJ-A7XG TCGA-S2-AA1A 
        9.70        16.87 

$`AMP PEAK 17(18Q11.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 
       24.03        47.05         8.02        19.00        20.05        14.96 
TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
        9.01        12.00        21.99        26.01        26.01        25.02 
TCGA-05-4432 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 
       25.02        15.02        15.02         4.96         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        0.46         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       37.71        49.05        28.41        35.28        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
        4.37        43.53        46.98        13.15        24.36        42.08 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       42.77         3.19        25.02        37.15        38.24        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 
       34.06         6.25        26.56        33.30        12.59        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 TCGA-44-8117 
       32.45        16.44        14.60        12.03        17.59        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98         9.44        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       46.72        14.07        32.84         8.81        29.46        29.75 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR3 
       14.63        29.26        22.26        22.26       153.04        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ 
       28.90         8.55        40.41        37.32       123.58       211.82 
TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
      164.12        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       31.04         8.22         9.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        18.64        29.03        25.12        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       42.35         3.91        25.55        11.05        12.16         6.21 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
       41.69        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
       30.54         9.21        38.73        45.21         2.86         0.07 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        0.79        42.51        40.73         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        5.49         7.79        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        1.28         1.12         1.78        18.64         6.48        17.65 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
        6.15        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         5.06         0.13        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.95         0.36         0.26        17.72         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        6.64        17.62         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       22.65        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-A46O 
        0.92        17.95         4.57        39.98        42.38        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.53        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       39.25        40.96        29.92        55.43        37.02        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       87.98         2.04        42.90        51.25        28.47         1.02 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        12.66         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 
       13.87         6.64         6.12        22.68         5.42         6.05 
TCGA-69-7978 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
        2.30        13.45         4.24         7.04         2.01        52.60 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       23.38        26.30         4.31         1.25        39.09        23.51 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
       11.18       163.10        27.16         5.69        19.27        35.93 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
       22.29         7.07       104.19       223.96         8.48        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
       31.20         8.02        53.33        10.75        39.35        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
      214.62        39.75        10.55        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 
       31.13        34.39        20.55        19.43        19.89        24.49 
TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8668 
        4.57        16.08        15.65        15.85        23.05        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       30.84        27.58         0.62        14.96        13.32        13.32 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 
       17.62        13.64        26.47        10.62         1.97         2.60 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       13.71        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
       14.27         1.45        19.82         9.76         4.18         6.12 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
        1.08        19.00        17.29         1.12         1.22        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       12.39        15.68        15.65        27.29         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
       18.18        19.89        63.52        43.79         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 
        0.72        18.67        17.92         5.39        15.39        16.41 
TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       21.60        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.84        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
        1.45         5.59        21.63        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       35.47        16.44        19.00        14.30         3.81         0.20 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
       14.53         1.91        17.46        11.87        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        2.76        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
       29.46        11.05        14.66        14.10        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-O1-A52J 
        0.26         0.43        59.11 

  AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE 
                           0.3                            0.0 
  AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE 
                        110.50                         223.96 
  AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE 
                         17.64                          18.64 
[1] "0.3 - 110.5 (17.6)" "0.0 - 224.0 (18.6)"
[1] "hr=" "1.1"
D17V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(18Q11.2) MUTATED         3       21       33        0        14
  AMP PEAK 17(18Q11.2) WILD-TYPE       2      114      107        1        37
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 17(18Q11.2) MUTATED          10         16          3        3
  AMP PEAK 17(18Q11.2) WILD-TYPE        63         56          8       23
D17V3, multiclass
            clus
vv           AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             21                            114
  STAGE IB                             33                            107
  STAGE II                              0                              1
  STAGE IIA                            14                             37
  STAGE IIB                            10                             63
  STAGE IIIA                           16                             56
  STAGE IIIB                            3                              8
  STAGE IV                              3                             23
[1] 9 2
[1] 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(18Q11.2) MUTATED    31  61   7   4
  AMP PEAK 17(18Q11.2) WILD-TYPE 139 217  39  15
D17V4, multiclass
    clus
vv   AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE
  T1                           31                            139
  T2                           61                            217
  T3                            7                             39
  T4                            4                             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 17(18Q11.2) MUTATED    67  21    15
  AMP PEAK 17(18Q11.2) WILD-TYPE 265  75    61
D17V5, multiclass
       clus
vv      AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE
  N0                              67                            265
  N1                              21                             75
  N2+N3                           15                             61
[1] 3 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(18Q11.2) MUTATED    68   3
  AMP PEAK 17(18Q11.2) WILD-TYPE 280  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(18Q11.2) MUTATED     68    3
  AMP PEAK 17(18Q11.2) WILD-TYPE  280   22
   clus
vv  AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE
  0                           68                            280
  1                            3                             22
[1] 2 2
[1] FALSE
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(18Q11.2) MUTATED    48  55
  AMP PEAK 17(18Q11.2) WILD-TYPE 227 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(18Q11.2) MUTATED     48   55
  AMP PEAK 17(18Q11.2) WILD-TYPE  227  185
        clus
vv       AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE
  FEMALE                           48                            227
  MALE                             55                            185
[1] 2 2
[1] FALSE
D17V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 17(18Q11.2) MUTATED                            6
  AMP PEAK 17(18Q11.2) WILD-TYPE                         13
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 17(18Q11.2) MUTATED                                  17
  AMP PEAK 17(18Q11.2) WILD-TYPE                                90
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(18Q11.2) MUTATED                                                   60
  AMP PEAK 17(18Q11.2) WILD-TYPE                                                259
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 17(18Q11.2) MUTATED                                            1
  AMP PEAK 17(18Q11.2) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 17(18Q11.2) MUTATED                                               5
  AMP PEAK 17(18Q11.2) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 17(18Q11.2) MUTATED                                2
  AMP PEAK 17(18Q11.2) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 17(18Q11.2) MUTATED                                    1
  AMP PEAK 17(18Q11.2) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(18Q11.2) MUTATED                              0
  AMP PEAK 17(18Q11.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 17(18Q11.2) MUTATED                               6
  AMP PEAK 17(18Q11.2) WILD-TYPE                            17
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 17(18Q11.2) MUTATED                                 0
  AMP PEAK 17(18Q11.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 17(18Q11.2) MUTATED                                               2
  AMP PEAK 17(18Q11.2) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 17(18Q11.2) MUTATED                              3
  AMP PEAK 17(18Q11.2) WILD-TYPE                            7
D17V9, multiclass
                                                    clus
vv                                                   AMP PEAK 17(18Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           60
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 5
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 6
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   AMP PEAK 17(18Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              90
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            259
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  14
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  17
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   3
  MUCINOUS (COLLOID) CARCINOMA                                                    7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                                cls
clus                               0   1
  AMP PEAK 17(18Q11.2) MUTATED     2 101
  AMP PEAK 17(18Q11.2) WILD-TYPE  19 393
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(18Q11.2) MUTATED      2  101
  AMP PEAK 17(18Q11.2) WILD-TYPE   19  393
     clus
vv    AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE
  NO                             2                             19
  YES                          101                            393
[1] 2 2
[1] FALSE
D17V11, continuous
D17V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 17(18Q11.2) MUTATED    65   2   0   7
  AMP PEAK 17(18Q11.2) WILD-TYPE 278  10   4  19
D17V13, multiclass
    clus
vv   AMP PEAK 17(18Q11.2) MUTATED AMP PEAK 17(18Q11.2) WILD-TYPE
  R0                           65                            278
  R1                            2                             10
  R2                            0                              4
  RX                            7                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(18Q11.2) MUTATED                                  1     1
  AMP PEAK 17(18Q11.2) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(18Q11.2) MUTATED                          11    74
  AMP PEAK 17(18Q11.2) WILD-TYPE                        40   315
D17V14, multiclass
                                  clus
vv                                 AMP PEAK 17(18Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      74
                                  clus
vv                                 AMP PEAK 17(18Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    40
  WHITE                                                       315
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V15, binary
                                cls
clus                               0   1
  AMP PEAK 17(18Q11.2) MUTATED     1  72
  AMP PEAK 17(18Q11.2) WILD-TYPE   6 310
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(18Q11.2) MUTATED      1   72
  AMP PEAK 17(18Q11.2) WILD-TYPE    6  310
                        clus
vv                       AMP PEAK 17(18Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           72
                        clus
vv                       AMP PEAK 17(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            310
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(19Q12) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 18(19Q12) MUTATED    92  38
  AMP PEAK 18(19Q12) WILD-TYPE 245 116
  AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE 
                         130                          361 
  AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE 
                          38                          116 
$`AMP PEAK 18(19Q12) MUTATED`
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4415 TCGA-05-4418 
        3.98        45.01        37.02        47.05         2.99         9.01 
TCGA-05-4424 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 
       30.02        25.02        29.00        22.03         7.40         5.98 
TCGA-35-5375 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-44-2662 
        8.68        49.05        35.28        11.64        44.61        42.08 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6776 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       28.37        23.77        63.72        19.46        36.07        18.87 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS 
       17.59         3.25        15.32         9.44        11.08        13.64 
TCGA-49-4487 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR4 
       28.11        14.63        12.13        29.26        22.26        28.90 
TCGA-49-AARE TCGA-50-5049 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5936 
       40.41        70.55        31.04         8.22         9.27         8.45 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6594 TCGA-50-6597 TCGA-53-7624 TCGA-53-7813 
       22.55         3.91        12.16        41.69        34.29        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 
        9.21        38.73        15.25         0.82        48.49         5.49 
TCGA-55-6979 TCGA-55-7907 TCGA-55-7995 TCGA-55-8085 TCGA-55-8092 TCGA-55-8301 
        7.79         0.53         0.16        29.72         5.06         1.45 
TCGA-55-8302 TCGA-55-8507 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Z 
        0.76         0.26        17.62         0.49         2.17        21.40 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8399 TCGA-62-A46O 
       20.58         0.92        20.19         4.57        88.64        47.80 
TCGA-62-A46S TCGA-64-1678 TCGA-64-1679 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       54.35        39.09        55.43        42.90        28.41        51.25 
TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
        6.64        22.68        13.61         7.56         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8453 TCGA-69-A59K TCGA-73-4675 TCGA-78-7148 
       12.56        14.01        26.73         7.04         1.32        20.58 
TCGA-78-7150 TCGA-78-7154 TCGA-86-7713 TCGA-86-7953 TCGA-86-8055 TCGA-86-8073 
       21.90        19.50        13.87        19.43         4.08        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8673 
        0.79        15.75        21.47        14.60         1.15        14.96 
TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6840 TCGA-93-A4JN TCGA-93-A4JP 
       13.32        41.36         1.97        12.23        23.61        19.00 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VK TCGA-97-7554 TCGA-97-7937 
        1.22        18.67        12.39        21.40        25.48         5.95 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-99-8025 TCGA-99-8033 
       17.92         5.39        18.12        14.30        34.85         5.59 
TCGA-L9-A443 TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T7 
        3.81         1.91        11.87        38.63        86.04         5.49 
TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-NJ-A55O TCGA-S2-AA1A 
       14.66        11.15         0.43        16.87 

$`AMP PEAK 18(19Q12) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
       50.07        19.96        14.01         0.00         9.96        24.03 
TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
        8.02        19.00        20.05        14.96        29.98        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 
       15.02         4.96         9.04         2.04         0.46        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
      120.79        37.71        28.41        14.73        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 
       43.53        46.98        13.15        44.94        24.36        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 
        3.19        25.02        37.15        38.24        38.89        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
        6.25        26.56        33.30        12.59        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       27.78        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7670 TCGA-44-7672 
       16.44        14.60        12.03         7.17        29.00        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 
       12.66         8.55        15.98        11.54        13.45        76.21 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6745 TCGA-49-6761 
        8.81        29.46        29.75        55.89        17.16        11.64 
TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARN 
       22.26       153.04        63.95        62.24         8.55        37.32 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
      123.58       211.82       164.12         9.86        20.52        71.47 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       15.72        60.16        49.28        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
       21.47        15.12        18.64        29.03        25.12        42.35 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       25.55        11.05         6.21         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 
        7.59        27.25        30.54        23.05        48.62        45.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
        1.28         1.12         0.79         1.78        18.64         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       17.65         6.15        19.82        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8506 
        1.51         2.17        22.16        15.42         0.95         0.36 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
        1.58         1.61        16.93        22.65        20.71         1.58 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 
       19.59        15.81        19.99        17.95        39.98        42.38 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V 
       14.60        49.25        19.53        56.71        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 
       37.02        38.37        87.98         2.04        28.47         1.02 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        12.66         5.72         4.64 
TCGA-67-6217 TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 TCGA-69-8254 TCGA-69-8255 
       13.87         6.12         5.42         6.05        13.45         4.24 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        2.01        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
        4.31         5.39         1.25        39.09        23.51        11.18 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7152 
      163.10        27.16         5.69        19.27        35.93        39.52 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       24.99        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        7.07       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       31.20         8.02        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
       27.09        12.36         5.88        31.13        34.39        20.55 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 
       19.89        16.70        24.49         4.57        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       15.85        23.05        13.91        30.84        27.58         0.62 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32         3.81        17.62        13.64        26.47        10.62 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.19         2.60        13.71        27.68         7.36         1.15 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7039 
        9.76         4.18         6.12         1.08        17.29         1.12 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN 
        2.86        15.68        15.65        27.29         2.76        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 
       19.89        31.69        64.60        63.52        43.79         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 
        0.72        18.67        15.39        16.41        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.19        21.44        19.76        20.52        17.75        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R 
       18.67        20.68        24.56        36.76         1.45        21.63 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 
       14.30         0.20        14.53        17.46        12.59        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 
        2.76        86.14        58.45        49.35        37.35        58.85 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       11.05        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.13         1.64        29.13         0.26        19.82         9.70 
TCGA-O1-A52J 
       59.11 

  AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE 
                        0.16                         0.00 
  AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE 
                       88.64                       223.96 
  AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE 
                      15.285                       19.130 
[1] "0.2 - 88.6 (15.3)"  "0.0 - 224.0 (19.1)"
[1] "hr=" "1.2"
D18V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(19Q12) MUTATED         1       29       37        1        14
  AMP PEAK 18(19Q12) WILD-TYPE       4      106      103        0        37
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 18(19Q12) MUTATED          18         22          5        9
  AMP PEAK 18(19Q12) WILD-TYPE        55         50          6       17
D18V3, multiclass
            clus
vv           AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE
  STAGE I                             1                            4
  STAGE IA                           29                          106
  STAGE IB                           37                          103
  STAGE II                            1                            0
  STAGE IIA                          14                           37
  STAGE IIB                          18                           55
  STAGE IIIA                         22                           50
  STAGE IIIB                          5                            6
  STAGE IV                            9                           17
[1] 9 2
[1] 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(19Q12) MUTATED    40  74  16   4
  AMP PEAK 18(19Q12) WILD-TYPE 130 204  30  15
D18V4, multiclass
    clus
vv   AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE
  T1                         40                          130
  T2                         74                          204
  T3                         16                           30
  T4                          4                           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 18(19Q12) MUTATED    83  26    25
  AMP PEAK 18(19Q12) WILD-TYPE 249  70    51
D18V5, multiclass
       clus
vv      AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE
  N0                            83                          249
  N1                            26                           70
  N2+N3                         25                           51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                              cls
clus                             0   1
  AMP PEAK 18(19Q12) MUTATED    91   9
  AMP PEAK 18(19Q12) WILD-TYPE 257  16
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(19Q12) MUTATED     91    9
  AMP PEAK 18(19Q12) WILD-TYPE  257   16
   clus
vv  AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE
  0                         91                          257
  1                          9                           16
[1] 2 2
[1] FALSE
D18V7, binary
                              cls
clus                             0   1
  AMP PEAK 18(19Q12) MUTATED    62  74
  AMP PEAK 18(19Q12) WILD-TYPE 213 166
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(19Q12) MUTATED     62   74
  AMP PEAK 18(19Q12) WILD-TYPE  213  166
        clus
vv       AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE
  FEMALE                         62                          213
  MALE                           74                          166
[1] 2 2
[1] FALSE
D18V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 18(19Q12) MUTATED                            7
  AMP PEAK 18(19Q12) WILD-TYPE                         12
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 18(19Q12) MUTATED                                  29
  AMP PEAK 18(19Q12) WILD-TYPE                                78
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(19Q12) MUTATED                                                   75
  AMP PEAK 18(19Q12) WILD-TYPE                                                244
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 18(19Q12) MUTATED                                            1
  AMP PEAK 18(19Q12) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 18(19Q12) MUTATED                                               5
  AMP PEAK 18(19Q12) WILD-TYPE                                            14
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 18(19Q12) MUTATED                                1
  AMP PEAK 18(19Q12) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 18(19Q12) MUTATED                                    1
  AMP PEAK 18(19Q12) WILD-TYPE                                  2
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 18(19Q12) MUTATED                              0
  AMP PEAK 18(19Q12) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 18(19Q12) MUTATED                              10
  AMP PEAK 18(19Q12) WILD-TYPE                            13
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 18(19Q12) MUTATED                                 1
  AMP PEAK 18(19Q12) WILD-TYPE                               0
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 18(19Q12) MUTATED                                               2
  AMP PEAK 18(19Q12) WILD-TYPE                                             3
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 18(19Q12) MUTATED                              4
  AMP PEAK 18(19Q12) WILD-TYPE                            6
D18V9, multiclass
                                                    clus
vv                                                   AMP PEAK 18(19Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          29
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         75
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               5
  LUNG CLEAR CELL ADENOCARCINOMA                                              1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          1
  LUNG MUCINOUS ADENOCARCINOMA                                                0
  LUNG PAPILLARY ADENOCARCINOMA                                              10
  LUNG SIGNET RING ADENOCARCINOMA                                             1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               2
  MUCINOUS (COLLOID) CARCINOMA                                                4
                                                    clus
vv                                                   AMP PEAK 18(19Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          244
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                14
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  2
  LUNG PAPILLARY ADENOCARCINOMA                                                13
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  6
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, binary
                              cls
clus                             0   1
  AMP PEAK 18(19Q12) MUTATED     4 132
  AMP PEAK 18(19Q12) WILD-TYPE  17 362
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(19Q12) MUTATED      4  132
  AMP PEAK 18(19Q12) WILD-TYPE   17  362
     clus
vv    AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE
  NO                           4                           17
  YES                        132                          362
[1] 2 2
[1] FALSE
D18V11, continuous
D18V12, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 18(19Q12) MUTATED    84   4   1   8
  AMP PEAK 18(19Q12) WILD-TYPE 259   8   3  18
D18V13, multiclass
    clus
vv   AMP PEAK 18(19Q12) MUTATED AMP PEAK 18(19Q12) WILD-TYPE
  R0                         84                          259
  R1                          4                            8
  R2                          1                            3
  RX                          8                           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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(19Q12) MUTATED                                  0     2
  AMP PEAK 18(19Q12) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(19Q12) MUTATED                          14   102
  AMP PEAK 18(19Q12) WILD-TYPE                        37   287
D18V14, multiclass
                                  clus
vv                                 AMP PEAK 18(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                14
  WHITE                                                   102
                                  clus
vv                                 AMP PEAK 18(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  37
  WHITE                                                     287
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V15, binary
                              cls
clus                             0   1
  AMP PEAK 18(19Q12) MUTATED     2 104
  AMP PEAK 18(19Q12) WILD-TYPE   5 278
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(19Q12) MUTATED      2  104
  AMP PEAK 18(19Q12) WILD-TYPE    5  278
                        clus
vv                       AMP PEAK 18(19Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                        104
                        clus
vv                       AMP PEAK 18(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          278
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(20Q13.33) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 19(20Q13.33) MUTATED   160  72
  AMP PEAK 19(20Q13.33) WILD-TYPE 177  82
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                            232                             259 
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                             72                              82 
$`AMP PEAK 19(20Q13.33) MUTATED`
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4405 TCGA-05-4415 
        3.98        45.01        37.02        24.03        20.05         2.99 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4432 TCGA-05-5423 TCGA-05-5428 
       29.98        12.00        30.02        25.02         4.96        22.03 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 
        8.68        97.74        37.71        49.05        28.41        11.64 
TCGA-38-6178 TCGA-44-2657 TCGA-44-3919 TCGA-44-5644 TCGA-44-6144 TCGA-44-6774 
       14.73        13.15         6.25        28.37        23.77        21.63 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       61.28        19.46         7.17        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
       17.59        23.64        12.66         3.25        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SU TCGA-49-4487 TCGA-49-4494 TCGA-49-4501 
        9.44        11.08        13.45        28.11        35.54        46.72 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6767 TCGA-49-AAR0 
       32.84        29.46        29.75        55.89        22.26       153.04 
TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ 
       63.95         8.55        40.41        37.32       123.58       211.82 
TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 
        9.86        71.47        70.55        31.04        49.28        14.27 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       78.67        21.47        18.64        25.12        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-53-7813 
        3.91        25.55         6.21        41.69         0.72        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
        9.21        23.05        38.73        45.21         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6978 
       32.65         0.79        40.73        15.25        48.49         5.49 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 
        7.79         7.99        23.18         1.28         0.53         6.48 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
        0.16        29.72        15.19         5.06        23.64        15.65 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 
        1.08         1.51         2.17        22.16         0.76         0.26 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8514 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Z 
        0.49         0.10         6.64         0.49         2.17        21.40 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 
       20.58         0.92        15.81        20.19        19.99         4.57 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46S TCGA-64-1676 
       42.38        88.64        49.25        19.53        54.35        56.81 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 
       20.65        39.09        38.37        87.98        28.41        51.25 
TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
       20.05        18.84         5.72         4.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
       13.61         7.56         2.30         2.93        12.56        14.01 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        4.24         2.01        52.60        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 
        4.31         1.32         1.25        23.51        11.18       163.10 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 
       39.52        24.99        19.50        38.50        64.90         7.07 
TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7542 
      223.96        26.53        31.20         8.02        53.33        10.55 
TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7954 
      214.62        10.55        27.09        12.36         5.88        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 
       16.70        24.49         4.08        24.33        15.75        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-91-6828 
       15.85        23.05        14.60         1.15        30.84        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-7771 
       41.36        10.19         2.60        13.71        27.68        16.18 
TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        1.18         1.45         6.12        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7947 TCGA-95-8494 
        1.12         1.22         2.86        18.67        15.68         2.76 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
       31.69        43.79         5.95        18.12        16.41        14.30 
TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M3 TCGA-99-8025 TCGA-J2-A4AE TCGA-L4-A4E5 
       20.58        19.76        17.75        34.85        35.47        19.00 
TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
        0.20         1.91        12.59        11.87        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 
        2.76        86.14        49.35        37.35        58.85         5.49 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-NJ-A4YP 
       29.46        11.05        14.66        11.15        71.05         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       29.13        19.82        59.11        16.87 

$`AMP PEAK 19(20Q13.33) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 
       50.07        19.96        14.01         0.00         9.96        47.05 
TCGA-05-4402 TCGA-05-4403 TCGA-05-4417 TCGA-05-4418 TCGA-05-4425 TCGA-05-4426 
        8.02        19.00        14.96         9.01        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 
       26.01        25.02        24.00        15.02        15.02        29.00 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4626 
        9.04         2.04         0.46         7.40         5.98       120.79 
TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       35.28        44.61        26.30         4.37        43.53        46.98 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.94        24.36        42.08        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        38.89        34.06        26.56        33.30 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 
       12.59        10.78         9.93        27.78        23.15        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-8120 
       63.72        32.45        16.44        14.60        12.03         8.55 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 
       11.54        13.64        76.21        28.57        12.66        14.07 
TCGA-49-4507 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        8.81        14.63        12.13        29.26        17.16        11.64 
TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARR TCGA-50-5044 TCGA-50-5051 
       22.26        62.24        28.90       164.12        20.52        15.72 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5936 TCGA-50-5939 
       60.16         8.22         9.27        40.60         8.45        15.12 
TCGA-50-5942 TCGA-50-6593 TCGA-50-6594 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       29.03        11.05        12.16        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1595 TCGA-55-6968 TCGA-55-6971 
       27.25        34.29        30.54        48.62        42.51         0.82 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
       40.54       107.21        70.26         0.59         1.15         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
        0.13         3.12         1.32         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8089 
        1.78        18.64        17.65         6.15        19.82         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8203 TCGA-55-8299 TCGA-55-8301 
       19.66        19.73         0.13        17.98        15.42         1.45 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8614 
        0.95         0.36        17.72         0.30         4.80        17.62 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 
        1.58         1.61        16.93        22.65        20.71         1.58 
TCGA-55-A492 TCGA-55-A57B TCGA-62-8395 TCGA-62-8398 TCGA-62-A46O TCGA-62-A46R 
       19.59        17.95        39.98        14.60        47.80        56.71 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       67.96        72.30        13.61        39.25        40.96        29.92 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 
       55.43        37.02         2.04        42.90        28.47         1.02 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 TCGA-69-7974 
       14.04        12.66        13.87         6.64         5.42         6.05 
TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4676 TCGA-73-7498 
       13.45        26.73         7.04        23.38         5.39        39.09 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 
       32.09         5.88        22.29       104.19         8.48        88.14 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       10.75        39.35        32.68        39.75        77.59       110.50 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8056 
       31.13        34.39        13.87        20.55        19.43         4.57 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
        0.79        16.08        21.47        13.91        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
       14.96        13.32        13.32         3.81        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       26.47         1.97        12.23         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JQ TCGA-95-7944 
       14.27        19.82         9.76         4.18        17.29        12.39 
TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
       15.65        27.29        21.40        18.18        19.89        64.60 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       63.52        25.48         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 
        5.39        15.39        21.60        20.19        21.44        20.52 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        20.68        24.56        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG 
        5.59        21.63        24.30        23.80        18.08        16.44 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A743 TCGA-MP-A4SW TCGA-MP-A4T4 
       14.30         3.81        14.53        17.46        58.45        86.04 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TI 
        5.29        41.59        31.23         2.43        10.09        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A55A TCGA-NJ-A55O 
       19.13        73.91        62.60         0.13         0.26         0.43 
TCGA-NJ-A7XG 
        9.70 

  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                           0.07                            0.00 
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                         223.96                          164.12 
  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE 
                         18.935                          17.950 
[1] "0.1 - 224.0 (18.9)" "0.0 - 164.1 (17.9)"
[1] "hr=" "1.1"
D19V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(20Q13.33) MUTATED         5       67       74        0        25
  AMP PEAK 19(20Q13.33) WILD-TYPE       0       68       66        1        26
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 19(20Q13.33) MUTATED          32         25          5       10
  AMP PEAK 19(20Q13.33) WILD-TYPE        41         47          6       16
D19V3, multiclass
            clus
vv           AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  STAGE I                                5                               0
  STAGE IA                              67                              68
  STAGE IB                              74                              66
  STAGE II                               0                               1
  STAGE IIA                             25                              26
  STAGE IIB                             32                              41
  STAGE IIIA                            25                              47
  STAGE IIIB                             5                               6
  STAGE IV                              10                              16
[1] 9 2
[1] 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(20Q13.33) MUTATED    80 136  22   4
  AMP PEAK 19(20Q13.33) WILD-TYPE  90 142  24  15
D19V4, multiclass
    clus
vv   AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  T1                            80                              90
  T2                           136                             142
  T3                            22                              24
  T4                             4                              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 19(20Q13.33) MUTATED   169  42    29
  AMP PEAK 19(20Q13.33) WILD-TYPE 163  54    47
D19V5, multiclass
       clus
vv      AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  N0                              169                             163
  N1                               42                              54
  N2+N3                            29                              47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20Q13.33) MUTATED   161  10
  AMP PEAK 19(20Q13.33) WILD-TYPE 187  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q13.33) MUTATED    161   10
  AMP PEAK 19(20Q13.33) WILD-TYPE  187   15
   clus
vv  AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  0                           161                             187
  1                            10                              15
[1] 2 2
[1] FALSE
D19V7, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20Q13.33) MUTATED   129 114
  AMP PEAK 19(20Q13.33) WILD-TYPE 146 126
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q13.33) MUTATED    129  114
  AMP PEAK 19(20Q13.33) WILD-TYPE  146  126
        clus
vv       AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  FEMALE                           129                             146
  MALE                             114                             126
[1] 2 2
[1] FALSE
D19V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 19(20Q13.33) MUTATED                           11
  AMP PEAK 19(20Q13.33) WILD-TYPE                          8
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 19(20Q13.33) MUTATED                                  43
  AMP PEAK 19(20Q13.33) WILD-TYPE                                64
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(20Q13.33) MUTATED                                                  158
  AMP PEAK 19(20Q13.33) WILD-TYPE                                                161
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 19(20Q13.33) MUTATED                                            2
  AMP PEAK 19(20Q13.33) WILD-TYPE                                          3
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 19(20Q13.33) MUTATED                                              10
  AMP PEAK 19(20Q13.33) WILD-TYPE                                             9
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 19(20Q13.33) MUTATED                                0
  AMP PEAK 19(20Q13.33) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 19(20Q13.33) MUTATED                                    2
  AMP PEAK 19(20Q13.33) WILD-TYPE                                  1
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 19(20Q13.33) MUTATED                              0
  AMP PEAK 19(20Q13.33) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 19(20Q13.33) MUTATED                              11
  AMP PEAK 19(20Q13.33) WILD-TYPE                            12
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 19(20Q13.33) MUTATED                                 1
  AMP PEAK 19(20Q13.33) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 19(20Q13.33) MUTATED                                               4
  AMP PEAK 19(20Q13.33) WILD-TYPE                                             1
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 19(20Q13.33) MUTATED                              1
  AMP PEAK 19(20Q13.33) WILD-TYPE                            9
D19V9, multiclass
                                                    clus
vv                                                   AMP PEAK 19(20Q13.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             43
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           158
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 10
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                                 11
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  MUCINOUS (COLLOID) CARCINOMA                                                   1
                                                    clus
vv                                                   AMP PEAK 19(20Q13.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               64
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             161
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    9
  LUNG CLEAR CELL ADENOCARCINOMA                                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               1
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   12
  LUNG SIGNET RING ADENOCARCINOMA                                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    1
  MUCINOUS (COLLOID) CARCINOMA                                                     9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20Q13.33) MUTATED     9 234
  AMP PEAK 19(20Q13.33) WILD-TYPE  12 260
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q13.33) MUTATED      9  234
  AMP PEAK 19(20Q13.33) WILD-TYPE   12  260
     clus
vv    AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  NO                              9                              12
  YES                           234                             260
[1] 2 2
[1] FALSE
D19V11, continuous
D19V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 19(20Q13.33) MUTATED   157   7   2  13
  AMP PEAK 19(20Q13.33) WILD-TYPE 186   5   2  13
D19V13, multiclass
    clus
vv   AMP PEAK 19(20Q13.33) MUTATED AMP PEAK 19(20Q13.33) WILD-TYPE
  R0                           157                             186
  R1                             7                               5
  R2                             2                               2
  RX                            13                              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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(20Q13.33) MUTATED                                  1     4
  AMP PEAK 19(20Q13.33) WILD-TYPE                                0     3
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(20Q13.33) MUTATED                          29   180
  AMP PEAK 19(20Q13.33) WILD-TYPE                        22   209
D19V14, multiclass
                                  clus
vv                                 AMP PEAK 19(20Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      180
                                  clus
vv                                 AMP PEAK 19(20Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          3
  BLACK OR AFRICAN AMERICAN                                     22
  WHITE                                                        209
[1] 4 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(20Q13.33) MUTATED     3 185
  AMP PEAK 19(20Q13.33) WILD-TYPE   4 197
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q13.33) MUTATED      3  185
  AMP PEAK 19(20Q13.33) WILD-TYPE    4  197
                        clus
vv                       AMP PEAK 19(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           185
                        clus
vv                       AMP PEAK 19(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             197
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(22Q11.22) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 20(22Q11.22) MUTATED    54  27
  AMP PEAK 20(22Q11.22) WILD-TYPE 283 127
  AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE 
                             81                             410 
  AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE 
                             27                             127 
$`AMP PEAK 20(22Q11.22) MUTATED`
TCGA-05-4398 TCGA-05-4420 TCGA-05-5428 TCGA-38-4625 TCGA-38-A44F TCGA-44-3398 
       47.05        29.98        22.03        97.74         4.37        38.24 
TCGA-44-3919 TCGA-44-5644 TCGA-44-6777 TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 
        6.25        28.37        32.45        16.44         7.17        18.87 
TCGA-44-7670 TCGA-44-8117 TCGA-44-A47A TCGA-44-A47F TCGA-49-4488 TCGA-49-6742 
       29.00        12.66        15.32        11.08        28.57        14.63 
TCGA-49-6743 TCGA-49-6767 TCGA-49-AARE TCGA-50-5931 TCGA-50-5944 TCGA-50-5946 
       12.13        22.26        40.41        14.27        25.12        22.55 
TCGA-50-6594 TCGA-50-6673 TCGA-55-1592 TCGA-55-1596 TCGA-55-6712 TCGA-55-6981 
       12.16         0.72        23.05        45.21         0.79        45.34 
TCGA-55-6982 TCGA-55-7574 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-8091 
       32.71         3.12        23.18         1.28         0.53        19.73 
TCGA-55-8096 TCGA-55-8208 TCGA-55-8506 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 
       23.64        22.16         0.36         0.30         6.64        17.62 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A57B TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
        1.58        20.58        17.95        42.38        14.60        49.25 
TCGA-62-A46O TCGA-64-1679 TCGA-67-3770 TCGA-67-3771 TCGA-69-7979 TCGA-69-8253 
       47.80        55.43         1.02        20.05         2.93        14.01 
TCGA-73-4675 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7536 TCGA-78-8662 
        1.32        21.90        19.50        38.50         8.02       110.50 
TCGA-86-6562 TCGA-86-7713 TCGA-86-7955 TCGA-86-8055 TCGA-86-8280 TCGA-86-8358 
       12.36        13.87        16.70         4.08        23.05        21.47 
TCGA-86-A4D0 TCGA-91-6847 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 TCGA-97-7553 
        3.81        27.68        18.67        12.39         2.76        43.79 
TCGA-97-8174 TCGA-97-8552 TCGA-J2-A4AE TCGA-L9-A8F4 TCGA-MP-A4SW TCGA-MP-A4T7 
        5.39        20.58        35.47        11.87        58.45         5.49 
TCGA-MP-A4TC TCGA-MP-A5C7 TCGA-NJ-A4YF 
        2.43        73.91        71.05 

$`AMP PEAK 20(22Q11.22) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03         8.02        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        2.99        14.96         9.01        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       15.02         4.96        29.00         9.04         2.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
       43.53        46.98        13.15        44.94        24.36        42.08 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 
       42.77         3.19        25.02        37.15        38.89        34.06 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 
       27.78        23.15        21.63        23.18        63.72        61.28 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 
       14.60        19.46        12.03        36.07        17.59        23.64 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        3.25         8.55        15.98         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 
       13.45        76.21        28.11        12.66        35.54        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       14.07        32.84         8.81        29.46        29.75        55.89 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       29.26        17.16        11.64        22.26       153.04        63.95 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ 
       62.24        28.90         8.55        37.32       123.58       211.82 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      164.12         9.86        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 
       60.16        31.04        49.28         8.22         9.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       78.67        21.47         8.45        15.12        18.64        29.03 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 
       42.35         3.91        25.55        11.05         6.21        41.69 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        25.61         7.59        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-5899 TCGA-55-6543 
       13.94         9.21        38.73        48.62         2.86         0.07 
TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       32.65        42.51        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 
        3.88         5.49         7.79         2.20        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
        0.20         0.13         1.32         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.78        18.64         6.48        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 
        0.16        29.72        15.19         3.29        19.66         5.06 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
        0.13        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.76         0.95         0.26         0.49 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
       17.72         0.10         4.80         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A492 
        2.17        16.93        22.65        20.71        21.40        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        20.19        19.99         4.57        39.98 
TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       88.64        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       13.61        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       39.09        37.02        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       28.41        51.25        28.47        18.84        14.04        12.66 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
        5.72         4.64        13.87         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 
       13.61         5.42         7.56         6.05         2.30        12.56 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
       13.45         4.24        26.73         7.04         2.01        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
       23.38        29.98        26.30        15.35         4.31         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
        1.25        39.09        23.51        11.18       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        20.58        35.93        39.52        24.99 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 
      223.96         8.48        88.14        26.53        31.20        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       10.75        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       77.59        10.55        27.09         5.88        31.13        34.39 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       20.55        19.43        19.89        24.49         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8359 
        0.79        15.75        16.08        15.65        15.85        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32        17.62        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        7.36         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.45        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
        1.08        19.00        17.29         1.12         1.22         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       15.68        15.65        27.29        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       31.69        64.60        63.52        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.72        18.67        17.92        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       14.30        21.60        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       17.75        20.84        18.67        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 
       36.76         1.45         5.59        21.63        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       18.08        16.44        19.00        14.30         3.81         0.20 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 
       14.53         1.91        17.46        12.59        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        86.14        49.35        37.35        86.04        58.85 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
        5.29        41.59        31.23        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.66        14.10        11.15        19.13        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        29.13         0.26         0.43        19.82         9.70 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE 
                            0.3                             0.0 
  AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE 
                         110.50                          223.96 
  AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE 
                          18.87                           18.15 
[1] "0.3 - 110.5 (18.9)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1.1"
D20V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(22Q11.22) MUTATED         2       17       29        0        15
  AMP PEAK 20(22Q11.22) WILD-TYPE       3      118      111        1        36
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 20(22Q11.22) MUTATED          11         12          1        1
  AMP PEAK 20(22Q11.22) WILD-TYPE        62         60         10       25
D20V3, multiclass
            clus
vv           AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE
  STAGE I                                2                               3
  STAGE IA                              17                             118
  STAGE IB                              29                             111
  STAGE II                               0                               1
  STAGE IIA                             15                              36
  STAGE IIB                             11                              62
  STAGE IIIA                            12                              60
  STAGE IIIB                             1                              10
  STAGE IV                               1                              25
[1] 9 2
[1] 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(22Q11.22) MUTATED    26  55   6   1
  AMP PEAK 20(22Q11.22) WILD-TYPE 144 223  40  18
D20V4, multiclass
    clus
vv   AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE
  T1                            26                             144
  T2                            55                             223
  T3                             6                              40
  T4                             1                              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1 N2+N3
  AMP PEAK 20(22Q11.22) MUTATED    56  19    12
  AMP PEAK 20(22Q11.22) WILD-TYPE 276  77    64
D20V5, multiclass
       clus
vv      AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE
  N0                               56                             276
  N1                               19                              77
  N2+N3                            12                              64
[1] 3 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(22Q11.22) MUTATED    56   1
  AMP PEAK 20(22Q11.22) WILD-TYPE 292  24
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(22Q11.22) MUTATED     56    1
  AMP PEAK 20(22Q11.22) WILD-TYPE  292   24
   clus
vv  AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE
  0                            56                             292
  1                             1                              24
[1] 2 2
[1] FALSE
D20V7, binary
                                 cls
clus                                0   1
  AMP PEAK 20(22Q11.22) MUTATED    53  35
  AMP PEAK 20(22Q11.22) WILD-TYPE 222 205
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(22Q11.22) MUTATED     53   35
  AMP PEAK 20(22Q11.22) WILD-TYPE  222  205
        clus
vv       AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE
  FEMALE                            53                             222
  MALE                              35                             205
[1] 2 2
[1] FALSE
D20V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 20(22Q11.22) MUTATED                            2
  AMP PEAK 20(22Q11.22) WILD-TYPE                         17
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 20(22Q11.22) MUTATED                                  13
  AMP PEAK 20(22Q11.22) WILD-TYPE                                94
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(22Q11.22) MUTATED                                                   66
  AMP PEAK 20(22Q11.22) WILD-TYPE                                                253
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 20(22Q11.22) MUTATED                                            0
  AMP PEAK 20(22Q11.22) WILD-TYPE                                          5
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 20(22Q11.22) MUTATED                                               3
  AMP PEAK 20(22Q11.22) WILD-TYPE                                            16
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 20(22Q11.22) MUTATED                                1
  AMP PEAK 20(22Q11.22) WILD-TYPE                              1
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 20(22Q11.22) MUTATED                                    1
  AMP PEAK 20(22Q11.22) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(22Q11.22) MUTATED                              0
  AMP PEAK 20(22Q11.22) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 20(22Q11.22) MUTATED                               1
  AMP PEAK 20(22Q11.22) WILD-TYPE                            22
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 20(22Q11.22) MUTATED                                 0
  AMP PEAK 20(22Q11.22) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 20(22Q11.22) MUTATED                                               0
  AMP PEAK 20(22Q11.22) WILD-TYPE                                             5
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 20(22Q11.22) MUTATED                              1
  AMP PEAK 20(22Q11.22) WILD-TYPE                            9
D20V9, multiclass
                                                    clus
vv                                                   AMP PEAK 20(22Q11.22) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             13
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            66
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  3
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                                  1
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  0
  MUCINOUS (COLLOID) CARCINOMA                                                   1
                                                    clus
vv                                                   AMP PEAK 20(22Q11.22) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             253
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   16
  LUNG CLEAR CELL ADENOCARCINOMA                                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               2
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   22
  LUNG SIGNET RING ADENOCARCINOMA                                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    5
  MUCINOUS (COLLOID) CARCINOMA                                                     9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, binary
                                 cls
clus                                0   1
  AMP PEAK 20(22Q11.22) MUTATED     3  85
  AMP PEAK 20(22Q11.22) WILD-TYPE  18 409
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(22Q11.22) MUTATED      3   85
  AMP PEAK 20(22Q11.22) WILD-TYPE   18  409
     clus
vv    AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE
  NO                              3                              18
  YES                            85                             409
[1] 2 2
[1] FALSE
D20V11, continuous
D20V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 20(22Q11.22) MUTATED    61   1   0   3
  AMP PEAK 20(22Q11.22) WILD-TYPE 282  11   4  23
D20V13, multiclass
    clus
vv   AMP PEAK 20(22Q11.22) MUTATED AMP PEAK 20(22Q11.22) WILD-TYPE
  R0                            61                             282
  R1                             1                              11
  R2                             0                               4
  RX                             3                              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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(22Q11.22) MUTATED                                  0     1
  AMP PEAK 20(22Q11.22) WILD-TYPE                                1     6
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(22Q11.22) MUTATED                           9    67
  AMP PEAK 20(22Q11.22) WILD-TYPE                        42   322
D20V14, multiclass
                                  clus
vv                                 AMP PEAK 20(22Q11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                       67
                                  clus
vv                                 AMP PEAK 20(22Q11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     42
  WHITE                                                        322
[1] 4 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(22Q11.22) MUTATED     1  62
  AMP PEAK 20(22Q11.22) WILD-TYPE   6 320
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(22Q11.22) MUTATED      1   62
  AMP PEAK 20(22Q11.22) WILD-TYPE    6  320
                        clus
vv                       AMP PEAK 20(22Q11.22) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            62
                        clus
vv                       AMP PEAK 20(22Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             320
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(XQ28) MUTATION ANALYSIS
D21V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 21(XQ28) MUTATED    98  48
  AMP PEAK 21(XQ28) WILD-TYPE 239 106
  AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE 
                        146                         345 
  AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE 
                         48                         106 
$`AMP PEAK 21(XQ28) MUTATED`
TCGA-05-4382 TCGA-05-4390 TCGA-05-4397 TCGA-05-4405 TCGA-05-4425 TCGA-05-4426 
       19.96        37.02        24.03        20.05        21.99        26.01 
TCGA-05-4432 TCGA-05-4434 TCGA-05-5423 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 
       25.02        15.02         4.96        22.03         7.40         5.98 
TCGA-35-5375 TCGA-38-4629 TCGA-38-4631 TCGA-38-7271 TCGA-44-2659 TCGA-44-3917 
        8.68        28.41        11.64        26.30        44.94        38.89 
TCGA-44-5644 TCGA-44-6778 TCGA-44-6779 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 
       28.37        61.28        16.44        12.03         7.17        18.87 
TCGA-44-8117 TCGA-44-A47A TCGA-44-A4SU TCGA-49-4488 TCGA-49-4494 TCGA-49-4505 
       12.66        15.32        13.45        28.57        35.54        14.07 
TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR3 
        8.81        29.75        29.26        11.64        22.26        62.24 
TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5045 TCGA-50-5933 TCGA-50-5941 
      123.58       211.82         9.86        71.47        78.67        18.64 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-7109 
       22.55         3.91        25.55        11.05        12.16        10.13 
TCGA-53-7624 TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
       34.29        23.05        48.62        45.21         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6970 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 
       32.65         0.79        15.25        40.54        70.26         0.59 
TCGA-55-7576 TCGA-55-7726 TCGA-55-7907 TCGA-55-7994 TCGA-55-8090 TCGA-55-8092 
        1.32         1.28         0.53        19.82        19.66         5.06 
TCGA-55-8096 TCGA-55-8203 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DF 
       23.64        17.98        21.40        20.58        15.81        20.19 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8399 TCGA-62-A46U TCGA-64-1676 TCGA-64-1677 
       19.99        17.95        88.64        67.96        56.81        20.65 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5815 TCGA-67-3772 TCGA-67-6215 TCGA-69-7764 
       39.09        37.02        28.47        18.84         5.72        13.61 
TCGA-69-7979 TCGA-71-6725 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-7499 
        2.93         2.01        26.30         4.31         5.39        23.51 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7154 TCGA-78-7155 TCGA-78-7161 
        5.69        19.27        35.93        19.50        38.50         7.07 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7542 TCGA-78-8640 
      223.96         8.48        26.53        31.20        10.55       214.62 
TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       77.59        27.09        12.36        16.70        24.49         4.08 
TCGA-86-8075 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8673 TCGA-86-A4P7 
       15.75        23.05        21.47        14.60        14.96        13.64 
TCGA-91-6829 TCGA-91-7771 TCGA-91-8496 TCGA-91-8499 TCGA-93-A4JO TCGA-93-A4JQ 
       41.36        16.18        16.60         1.18         1.08        17.29 
TCGA-95-7043 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 
        1.22        18.67        27.29         2.76        25.48         5.95 
TCGA-97-8172 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M6 TCGA-97-A4M7 
       17.92        14.30        21.60        20.19        18.67        20.68 
TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
        0.20         1.91        12.59        27.19        38.63         2.76 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A55A 
       58.45        86.04        11.05        14.10        19.13         0.26 
TCGA-NJ-A7XG TCGA-S2-AA1A 
        9.70        16.87 

$`AMP PEAK 21(XQ28) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        14.01        45.01         0.00         9.96 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
       47.05         8.02        19.00         2.99        14.96         9.01 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
       29.98        12.00        30.02        26.01        25.02        24.00 
TCGA-05-5420 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 
       15.02        29.00         9.04         2.04         0.46        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
      120.79        37.71        49.05        35.28        44.61        14.73 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 
        4.37        43.53        46.98        13.15        24.36        42.08 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
       42.77         3.19        25.02        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
        6.25        26.56        33.30        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 
       32.45        14.60        19.46        36.07        29.00        17.59 
TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F 
       23.64         3.25         8.55        15.98         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4501 
       11.54        13.64        76.21        28.11        12.66        46.72 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 
       32.84        29.46        55.89        14.63        12.13        17.16 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
       22.26       153.04        63.95        28.90         8.55        40.41 
TCGA-49-AARN TCGA-49-AARR TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       37.32       164.12        20.52        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
       21.47         8.45        15.12        29.03        25.12        42.35 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21        41.69         0.72        25.61         7.59        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6968 TCGA-55-6969 
       30.54        13.94         9.21        38.73        42.51        40.73 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-7283 
       45.34        32.71        60.03        24.99       107.21         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
        7.99         0.20         0.13         3.12        23.18         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        1.12         0.79         1.78        18.64         6.48        17.65 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 
        6.15         0.16        29.72        15.19         3.29        19.73 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
        0.13        15.65         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42         1.45         0.76         0.95         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.49        17.72         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
       17.62         0.49         1.58         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-62-8394 
       22.65        20.71         1.58        19.59         0.92         4.57 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       39.98        42.38        14.60        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       56.71        54.35        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       29.92        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 
       28.41        51.25         1.02        20.05        14.04        12.66 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 
        4.64        13.87         6.64         6.12        22.68         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         2.30        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        4.24        26.73         7.04        52.60        23.38        29.98 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7143 
       15.35         1.32         1.25        39.09        11.18       163.10 
TCGA-78-7145 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 
       27.16        20.58        21.90        39.52        24.99        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7167 TCGA-78-7536 
        5.88        64.90        22.29       104.19        88.14         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8660 
       53.33        10.75        39.35        32.68        39.75        10.55 
TCGA-78-8662 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
      110.50         5.88        31.13        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 
       19.43        19.89         4.57        24.33         0.79        16.08 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       15.65        15.85         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 
        0.62        13.32        13.32         3.81        17.62        26.47 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
       27.68         7.36         1.15        14.27         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7039 
        9.76         4.18         6.12        23.61        19.00         1.12 
TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
        2.86        12.39        15.68        15.65        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 
       19.89        31.69        64.60        63.52        43.79         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.72        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       20.58        21.44        19.76        20.52        17.75        20.84 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R 
       24.56        34.85        36.76         1.45         5.59        21.63 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MP-A4SV 
       14.30         3.81        14.53        17.46        11.87        86.14 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       49.35        37.35        58.85         5.49         5.29        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TJ 
       31.23         2.43        10.09        29.46        14.66        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        62.60         0.13         1.64        29.13 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE 
                       0.07                        0.00 
  AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE 
                     223.96                      164.12 
  AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE 
                      19.00                       17.72 
[1] "0.1 - 224.0 (19.0)" "0.0 - 164.1 (17.7)"
[1] "hr=" "1"  
D21V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(XQ28) MUTATED         1       40       44        0        16
  AMP PEAK 21(XQ28) WILD-TYPE       4       95       96        1        35
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 21(XQ28) MUTATED          24         20          3        9
  AMP PEAK 21(XQ28) WILD-TYPE        49         52          8       17
D21V3, multiclass
            clus
vv           AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE
  STAGE I                            1                           4
  STAGE IA                          40                          95
  STAGE IB                          44                          96
  STAGE II                           0                           1
  STAGE IIA                         16                          35
  STAGE IIB                         24                          49
  STAGE IIIA                        20                          52
  STAGE IIIB                         3                           8
  STAGE IV                           9                          17
[1] 9 2
[1] 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(XQ28) MUTATED    47  93  13   4
  AMP PEAK 21(XQ28) WILD-TYPE 123 185  33  15
D21V4, multiclass
    clus
vv   AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE
  T1                        47                         123
  T2                        93                         185
  T3                        13                          33
  T4                         4                          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 21(XQ28) MUTATED    96  36    23
  AMP PEAK 21(XQ28) WILD-TYPE 236  60    53
D21V5, multiclass
       clus
vv      AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE
  N0                           96                         236
  N1                           36                          60
  N2+N3                        23                          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"
D21V6, binary
                             cls
clus                            0   1
  AMP PEAK 21(XQ28) MUTATED   103   9
  AMP PEAK 21(XQ28) WILD-TYPE 245  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 21(XQ28) MUTATED    103    9
  AMP PEAK 21(XQ28) WILD-TYPE  245   16
   clus
vv  AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE
  0                       103                         245
  1                         9                          16
[1] 2 2
[1] FALSE
D21V7, binary
                             cls
clus                            0   1
  AMP PEAK 21(XQ28) MUTATED    79  78
  AMP PEAK 21(XQ28) WILD-TYPE 196 162
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 21(XQ28) MUTATED     79   78
  AMP PEAK 21(XQ28) WILD-TYPE  196  162
        clus
vv       AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE
  FEMALE                        79                         196
  MALE                          78                         162
[1] 2 2
[1] FALSE
D21V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 21(XQ28) MUTATED                            6
  AMP PEAK 21(XQ28) WILD-TYPE                         13
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 21(XQ28) MUTATED                                  33
  AMP PEAK 21(XQ28) WILD-TYPE                                74
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(XQ28) MUTATED                                                  105
  AMP PEAK 21(XQ28) WILD-TYPE                                                214
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 21(XQ28) MUTATED                                            2
  AMP PEAK 21(XQ28) WILD-TYPE                                          3
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 21(XQ28) MUTATED                                               4
  AMP PEAK 21(XQ28) WILD-TYPE                                            15
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 21(XQ28) MUTATED                                1
  AMP PEAK 21(XQ28) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 21(XQ28) MUTATED                                    1
  AMP PEAK 21(XQ28) WILD-TYPE                                  2
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(XQ28) MUTATED                              0
  AMP PEAK 21(XQ28) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 21(XQ28) MUTATED                               5
  AMP PEAK 21(XQ28) WILD-TYPE                            18
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 21(XQ28) MUTATED                                 0
  AMP PEAK 21(XQ28) WILD-TYPE                               1
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 21(XQ28) MUTATED                                               0
  AMP PEAK 21(XQ28) WILD-TYPE                                             5
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 21(XQ28) MUTATED                              0
  AMP PEAK 21(XQ28) WILD-TYPE                           10
D21V9, multiclass
                                                    clus
vv                                                   AMP PEAK 21(XQ28) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       105
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                 2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                              4
  LUNG CLEAR CELL ADENOCARCINOMA                                             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                         1
  LUNG MUCINOUS ADENOCARCINOMA                                               0
  LUNG PAPILLARY ADENOCARCINOMA                                              5
  LUNG SIGNET RING ADENOCARCINOMA                                            0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                              0
  MUCINOUS (COLLOID) CARCINOMA                                               0
                                                    clus
vv                                                   AMP PEAK 21(XQ28) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                  13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         214
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               15
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 2
  LUNG PAPILLARY ADENOCARCINOMA                                               18
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                5
  MUCINOUS (COLLOID) CARCINOMA                                                10
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, binary
                             cls
clus                            0   1
  AMP PEAK 21(XQ28) MUTATED     8 149
  AMP PEAK 21(XQ28) WILD-TYPE  13 345
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 21(XQ28) MUTATED      8  149
  AMP PEAK 21(XQ28) WILD-TYPE   13  345
     clus
vv    AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE
  NO                          8                          13
  YES                       149                         345
[1] 2 2
[1] FALSE
D21V11, continuous
D21V12, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 21(XQ28) MUTATED   107   5   1   6
  AMP PEAK 21(XQ28) WILD-TYPE 236   7   3  20
D21V13, multiclass
    clus
vv   AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE
  R0                       107                         236
  R1                         5                           7
  R2                         1                           3
  RX                         6                          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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(XQ28) MUTATED                                  0     3
  AMP PEAK 21(XQ28) WILD-TYPE                                1     4
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(XQ28) MUTATED                          15   116
  AMP PEAK 21(XQ28) WILD-TYPE                        36   273
D21V14, multiclass
                                  clus
vv                                 AMP PEAK 21(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               15
  WHITE                                                  116
                                  clus
vv                                 AMP PEAK 21(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 36
  WHITE                                                    273
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V15, binary
                             cls
clus                            0   1
  AMP PEAK 21(XQ28) MUTATED     1 108
  AMP PEAK 21(XQ28) WILD-TYPE   6 274
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 21(XQ28) MUTATED      1  108
  AMP PEAK 21(XQ28) WILD-TYPE    6  274
                        clus
vv                       AMP PEAK 21(XQ28) MUTATED AMP PEAK 21(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             1                           6
  NOT HISPANIC OR LATINO                       108                         274
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED    77  42
  DEL PEAK  1(1P36.11) WILD-TYPE 260 112
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           119                            372 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            42                            112 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 
       50.07         3.98        45.01        37.02         9.96        47.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-5420 
        2.99        14.96        12.00        30.02        21.99        15.02 
TCGA-05-5425 TCGA-05-5429 TCGA-38-4625 TCGA-38-4627 TCGA-44-2666 TCGA-44-3917 
       29.00         9.04        97.74        37.71         3.19        38.89 
TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6779 TCGA-44-7660 
       34.06        33.30        28.37        23.77        16.44        19.46 
TCGA-44-A479 TCGA-44-A47F TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 
       15.98        11.08        28.57        35.54        32.84         8.81 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AARE TCGA-50-5051 TCGA-50-5932 
       17.16        11.64        22.26        40.41        15.72        40.60 
TCGA-50-5935 TCGA-50-5936 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-53-7624 
       21.47         8.45        12.16         6.21        10.13        34.29 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6986 TCGA-55-7283 TCGA-55-7911 
       48.62        45.21         2.86       107.21         1.15        17.65 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8092 TCGA-55-8203 TCGA-55-8205 TCGA-55-8508 
        6.15        19.66         5.06        17.98         1.08         0.49 
TCGA-55-8615 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 
        0.49        20.71        21.40        20.58        19.59        15.81 
TCGA-62-8398 TCGA-62-A46S TCGA-62-A46U TCGA-62-A472 TCGA-64-1677 TCGA-64-5774 
       14.60        54.35        67.96        29.92        20.65        87.98 
TCGA-64-5778 TCGA-64-5815 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 
       42.90        28.47         6.64         6.12        22.68         7.56 
TCGA-69-7978 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
        2.30        23.38        26.30         4.31         1.32         1.25 
TCGA-73-A9RS TCGA-78-7146 TCGA-78-7148 TCGA-78-7153 TCGA-78-7154 TCGA-78-7159 
       11.18         5.69        20.58        24.99        19.50        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7536 TCGA-78-8655 TCGA-86-6562 TCGA-86-6851 
       22.29         7.07         8.02        77.59        12.36         5.88 
TCGA-86-7701 TCGA-86-8054 TCGA-86-8358 TCGA-86-8669 TCGA-86-A4JF TCGA-91-6828 
       31.13        24.49        21.47        30.84        17.62        10.62 
TCGA-91-6830 TCGA-91-7771 TCGA-91-8499 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7567 
        1.97        16.18         1.18        17.29         1.22        18.67 
TCGA-95-7944 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7554 TCGA-97-8172 TCGA-97-8176 
       12.39        18.18        19.89        25.48        17.92        15.39 
TCGA-97-A4M5 TCGA-L9-A743 TCGA-MP-A4T7 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
       20.84        17.46         5.49         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-NJ-A4YQ TCGA-NJ-A7XG TCGA-O1-A52J 
       11.05        11.15        29.13         9.70        59.11 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 
       19.96        14.01         0.00        24.03         8.02        19.00 
TCGA-05-4405 TCGA-05-4418 TCGA-05-4420 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
       20.05         9.01        29.98        26.01        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 TCGA-05-5428 TCGA-05-5715 
       25.02        24.00        15.02         4.96        22.03         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4628 
        0.46         7.40         5.98         8.68       120.79        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       28.41        35.28        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
        4.37        43.53        46.98        13.15        44.94        24.36 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
       42.08        42.77        25.02        37.15        38.24         6.25 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       26.56        12.59        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
       21.63        23.18        63.72        32.45        61.28        14.60 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         3.25         8.55        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 
       11.54        13.64        13.45        76.21        28.11        12.66 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       46.72        14.07        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 
       12.13        29.26        22.26       153.04        63.95        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       28.90         8.55        37.32       123.58       211.82       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
        9.86        20.52        71.47        70.55        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 
       49.28         8.22         9.27        14.27        78.67        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 
       25.55        11.05        41.69         0.72        25.61         7.59 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       27.25        30.54        13.94         9.21        23.05        38.73 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 
       45.34        32.71        60.03        24.99        40.54        70.26 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        0.59         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       23.18         1.28         1.28         1.12         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       18.64         0.53         6.48        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19         3.29        19.73         0.13        23.64        15.65 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.95         0.36         0.26        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        4.80         6.64        17.62         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG 
       16.93        22.65         1.58         0.92        20.19        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 
       17.95         4.57        39.98        42.38        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       47.80        19.53        56.71        72.30        13.61        39.25 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       40.96        56.81        39.09        55.43        37.02        38.37 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        2.04        28.41        51.25         1.02        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7764 
       14.04        12.66         5.72         4.64        13.87        13.61 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        5.42         6.05         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 
        4.24        26.73         7.04         2.01        52.60        29.98 
TCGA-73-4668 TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
       15.35         5.39        39.09        23.51       163.10        27.16 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 
       19.27        35.93        21.90        39.52        38.50        32.09 
TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
        5.88       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
       31.20        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-7711 
      214.62        39.75        10.55       110.50        27.09        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       13.87        20.55        19.43        19.89        16.70         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
       15.85        23.05        14.60         1.15        13.91        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
        0.62        14.96        13.32        13.32         3.81        13.64 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       26.47        41.36        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
       27.68         7.36         1.15        16.60        14.27         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
       19.00         1.12         2.86        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        21.40        31.69        64.60        63.52        43.79 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
        5.95         0.59         0.72        18.67         5.39        18.12 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       19.76        20.52        17.75        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       34.85        36.76         1.45         5.59        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       23.80        18.08        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
        3.81         0.20        14.53         1.91        12.59        11.87 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       37.35        86.04        58.85         5.29        41.59        31.23 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        0.13         1.64         0.26         0.43        19.82        16.87 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.49                           0.00 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        107.21                         223.96 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        17.980                         18.655 
[1] "0.5 - 107.2 (18.0)" "0.0 - 224.0 (18.7)"
[1] "hr=" "1.3"
D22V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.11) MUTATED         0       28       24        0        11
  DEL PEAK  1(1P36.11) WILD-TYPE       5      107      116        1        40
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  1(1P36.11) MUTATED          22         28          4        7
  DEL PEAK  1(1P36.11) WILD-TYPE        51         44          7       19
D22V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                             28                            107
  STAGE IB                             24                            116
  STAGE II                              0                              1
  STAGE IIA                            11                             40
  STAGE IIB                            22                             51
  STAGE IIIA                           28                             44
  STAGE IIIB                            4                              7
  STAGE IV                              7                             19
[1] 9 2
[1] 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    36  64  19   5
  DEL PEAK  1(1P36.11) WILD-TYPE 134 214  27  14
D22V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                           36                            134
  T2                           64                            214
  T3                           19                             27
  T4                            5                             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  1(1P36.11) MUTATED    69  27    27
  DEL PEAK  1(1P36.11) WILD-TYPE 263  69    49
D22V5, multiclass
       clus
vv      DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                              69                            263
  N1                              27                             69
  N2+N3                           27                             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    89   7
  DEL PEAK  1(1P36.11) WILD-TYPE 259  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     89    7
  DEL PEAK  1(1P36.11) WILD-TYPE  259   18
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                           89                            259
  1                            7                             18
[1] 2 2
[1] FALSE
D22V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    60  64
  DEL PEAK  1(1P36.11) WILD-TYPE 215 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     60   64
  DEL PEAK  1(1P36.11) WILD-TYPE  215  176
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           60                            215
  MALE                             64                            176
[1] 2 2
[1] FALSE
D22V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                            7
  DEL PEAK  1(1P36.11) WILD-TYPE                         12
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  1(1P36.11) MUTATED                                  28
  DEL PEAK  1(1P36.11) WILD-TYPE                                79
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.11) MUTATED                                                   78
  DEL PEAK  1(1P36.11) WILD-TYPE                                                241
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  1(1P36.11) MUTATED                                            0
  DEL PEAK  1(1P36.11) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  1(1P36.11) MUTATED                                               3
  DEL PEAK  1(1P36.11) WILD-TYPE                                            16
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                                1
  DEL PEAK  1(1P36.11) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                                    0
  DEL PEAK  1(1P36.11) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                              0
  DEL PEAK  1(1P36.11) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                               2
  DEL PEAK  1(1P36.11) WILD-TYPE                            21
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                                 1
  DEL PEAK  1(1P36.11) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                                               2
  DEL PEAK  1(1P36.11) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                              2
  DEL PEAK  1(1P36.11) WILD-TYPE                            8
D22V9, multiclass
                                                    clus
vv                                                   DEL PEAK  1(1P36.11) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            28
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           78
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 3
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            0
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 2
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK  1(1P36.11) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              79
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            241
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  16
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              3
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  21
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   3
  MUCINOUS (COLLOID) CARCINOMA                                                    8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     6 118
  DEL PEAK  1(1P36.11) WILD-TYPE  15 376
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      6  118
  DEL PEAK  1(1P36.11) WILD-TYPE   15  376
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             6                             15
  YES                          118                            376
[1] 2 2
[1] FALSE
D22V11, continuous
D22V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED    82   4   1   6
  DEL PEAK  1(1P36.11) WILD-TYPE 261   8   3  20
D22V13, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                           82                            261
  R1                            4                              8
  R2                            1                              3
  RX                            6                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.11) MUTATED                                  0     2
  DEL PEAK  1(1P36.11) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED                           8    92
  DEL PEAK  1(1P36.11) WILD-TYPE                        43   297
D22V14, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      92
                                  clus
vv                                 DEL PEAK  1(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    43
  WHITE                                                       297
[1] 4 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
  DEL PEAK  1(1P36.11) MUTATED     2  86
  DEL PEAK  1(1P36.11) WILD-TYPE   5 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      2   86
  DEL PEAK  1(1P36.11) WILD-TYPE    5  296
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            296
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK  2(1P13.1) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.1) MUTATED    97  46
  DEL PEAK  2(1P13.1) WILD-TYPE 240 108
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          143                           348 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           46                           108 
$`DEL PEAK  2(1P13.1) MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4398 
       50.07         3.98        45.01        37.02        24.03        47.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4433 TCGA-05-4434 TCGA-05-5715 
        2.99        14.96        12.00        24.00        15.02         2.04 
TCGA-38-4625 TCGA-38-4628 TCGA-44-2668 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 
       97.74        49.05        25.02        33.30        28.37        23.77 
TCGA-44-A47F TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       11.08        35.54        46.72        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARE 
       29.75        55.89        12.13        17.16        11.64        40.41 
TCGA-49-AARQ TCGA-50-5044 TCGA-50-5051 TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 
      211.82        20.52        15.72        40.60        21.47         8.45 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6594 TCGA-50-6595 TCGA-53-7813 TCGA-53-A4EZ 
       22.55         3.91        12.16         6.21        13.94         9.21 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6971 TCGA-55-6972 TCGA-55-6986 TCGA-55-7283 
       45.21         2.86         0.82        48.49       107.21         1.15 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8090 TCGA-55-8091 
        0.53        17.65        19.82         0.16        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8203 TCGA-55-8205 TCGA-55-8505 TCGA-55-8507 
        5.06         0.13        17.98         1.08         0.95         0.26 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8615 TCGA-55-A48Y TCGA-55-A492 TCGA-55-A4DF 
        0.49         0.10         0.49        20.71        19.59        20.19 
TCGA-62-8402 TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-64-1678 
       49.25        54.35        67.96        72.30        39.25        39.09 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 
       87.98         2.04        42.90        28.41         1.02        20.05 
TCGA-67-3772 TCGA-67-3774 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-71-6725 
       18.84        12.66         6.12        22.68         7.56         2.01 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
       23.38        29.98        26.30         4.31         1.32         1.25 
TCGA-73-7498 TCGA-73-A9RS TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 
       39.09        11.18         5.69        20.58        35.93        24.99 
TCGA-78-7154 TCGA-78-7160 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 
       19.50        22.29       223.96        88.14        26.53        10.75 
TCGA-86-6851 TCGA-86-7701 TCGA-86-8054 TCGA-86-8278 TCGA-86-8668 TCGA-86-8669 
        5.88        31.13        24.49        15.65        13.91        30.84 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6836 TCGA-91-6848 TCGA-91-7771 
        3.81        17.62        10.62        13.71         7.36        16.18 
TCGA-91-8497 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
       14.27         4.18         6.12         1.12         1.22        18.67 
TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7554 TCGA-97-8172 
       15.68        27.29        18.18        19.89        25.48        17.92 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M5 TCGA-J2-8192 TCGA-L9-A444 TCGA-L9-A50W 
       21.60        20.58        20.84        24.30         0.20        14.53 
TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TD TCGA-MP-A4TH TCGA-MP-A4TJ 
       58.45        58.85         5.49        10.09        14.66        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A7XG 
       19.13        73.91         0.13        29.13         9.70 

$`DEL PEAK  2(1P13.1) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4402 TCGA-05-4403 
       19.96        14.01         0.00         9.96         8.02        19.00 
TCGA-05-4405 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       20.05         9.01        29.98        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       26.01        25.02        25.02        15.02         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       22.03         9.04         0.46         7.40         5.98         8.68 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
      120.79        37.71        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        13.15 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 
       44.94        24.36        42.08        42.77         3.19        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       38.24        38.89        34.06         6.25        26.56        12.59 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       63.72        32.45        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
       12.03         7.17        36.07        18.87        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       23.64        12.66         3.25         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-6742 TCGA-49-6744 TCGA-49-6767 
       28.57        12.66        14.07        14.63        29.26        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26       153.04        63.95        62.24        28.90         8.55 
TCGA-49-AARN TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 
       37.32       123.58       164.12         9.86        71.47        70.55 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        31.04        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
       78.67        15.12        18.64        29.03        25.12        42.35 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       25.55        11.05        41.69         0.72        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1592 TCGA-55-1594 
        7.59        27.25        34.29        30.54        23.05        38.73 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       48.62         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       15.25         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 
       32.71        60.03        24.99        40.54        70.26         0.59 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        1.28         1.28         1.12         0.79         1.78        18.64 
TCGA-55-7910 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8096 
        6.48         6.15        29.72        15.19         3.29        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       15.65         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 
        0.76         0.36        17.72         0.30         4.80         6.64 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
       17.62         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       21.40         1.58        20.58         0.92        15.81        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       17.95         4.57        39.98        42.38        14.60        88.64 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 
       47.80        19.53        56.71        13.61        40.96        29.92 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5781 
       56.81        20.65        55.43        37.02        38.37        51.25 
TCGA-64-5815 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       28.47        14.04         5.72         4.64        13.87         6.64 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       13.61         5.42         6.05         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 
       14.01        13.45         4.24        26.73         7.04        52.60 
TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
       15.35         5.39        23.51       163.10        27.16        19.27 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       21.90        39.52        38.50        32.09         5.88        64.90 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7166 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
        7.07       104.19         8.48        31.20         8.02        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7711 TCGA-86-7713 
       10.55       110.50        27.09        12.36        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
       20.55        19.43        19.89        16.70         4.08         4.57 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 
       24.33         0.79        15.75        16.08        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       21.47        14.60         1.15        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
       13.32        13.32        13.64        26.47        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 
       10.19         2.60        12.23        27.68         1.15        16.60 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO 
        1.18         1.45        19.82         9.76        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7944 TCGA-95-7948 TCGA-95-8494 
       19.00        17.29         2.86        12.39        15.65         2.76 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       21.40        31.69        64.60        63.52        43.79         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59         0.72        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       16.41        14.30        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       17.75        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45         5.59        21.63        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A5IP TCGA-L9-A743 
       16.44        19.00        14.30         3.81         1.91        17.46 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       12.59        11.87        27.19        38.63         2.76        86.14 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       49.35        37.35        86.04         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-NJ-A4YF TCGA-NJ-A4YG 
        2.43        29.46        11.05        14.10        71.05        62.60 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
        1.64         0.26         0.43        19.82        59.11        16.87 

  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          0.1                           0.0 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                       223.96                        214.62 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                        18.84                         18.10 
[1] "0.1 - 224.0 (18.8)" "0.0 - 214.6 (18.1)"
[1] "hr=" "1"  
D23V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.1) MUTATED         2       33       35        0        11
  DEL PEAK  2(1P13.1) WILD-TYPE       3      102      105        1        40
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  2(1P13.1) MUTATED          21         31          5       10
  DEL PEAK  2(1P13.1) WILD-TYPE        52         41          6       16
D23V3, multiclass
            clus
vv           DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            33                           102
  STAGE IB                            35                           105
  STAGE II                             0                             1
  STAGE IIA                           11                            40
  STAGE IIB                           21                            52
  STAGE IIIA                          31                            41
  STAGE IIIB                           5                             6
  STAGE IV                            10                            16
[1] 9 2
[1] 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    42  83  14   9
  DEL PEAK  2(1P13.1) WILD-TYPE 128 195  32  10
D23V4, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  T1                          42                           128
  T2                          83                           195
  T3                          14                            32
  T4                           9                            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  2(1P13.1) MUTATED    90  29    29
  DEL PEAK  2(1P13.1) WILD-TYPE 242  67    47
D23V5, multiclass
       clus
vv      DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  N0                             90                           242
  N1                             29                            67
  N2+N3                          29                            47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED    99  10
  DEL PEAK  2(1P13.1) WILD-TYPE 249  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED     99   10
  DEL PEAK  2(1P13.1) WILD-TYPE  249   15
   clus
vv  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  0                          99                           249
  1                          10                            15
[1] 2 2
[1] FALSE
D23V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED    79  69
  DEL PEAK  2(1P13.1) WILD-TYPE 196 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED     79   69
  DEL PEAK  2(1P13.1) WILD-TYPE  196  171
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  FEMALE                          79                           196
  MALE                            69                           171
[1] 2 2
[1] FALSE
D23V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                            8
  DEL PEAK  2(1P13.1) WILD-TYPE                         11
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  2(1P13.1) MUTATED                                  31
  DEL PEAK  2(1P13.1) WILD-TYPE                                76
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.1) MUTATED                                                   88
  DEL PEAK  2(1P13.1) WILD-TYPE                                                231
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  2(1P13.1) MUTATED                                            1
  DEL PEAK  2(1P13.1) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  2(1P13.1) MUTATED                                               7
  DEL PEAK  2(1P13.1) WILD-TYPE                                            12
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                                1
  DEL PEAK  2(1P13.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                                    0
  DEL PEAK  2(1P13.1) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                              0
  DEL PEAK  2(1P13.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                               7
  DEL PEAK  2(1P13.1) WILD-TYPE                            16
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                                 1
  DEL PEAK  2(1P13.1) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                                               2
  DEL PEAK  2(1P13.1) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                              2
  DEL PEAK  2(1P13.1) WILD-TYPE                            8
D23V9, multiclass
                                                    clus
vv                                                   DEL PEAK  2(1P13.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           31
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          88
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                7
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           0
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                7
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                2
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   DEL PEAK  2(1P13.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           231
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 12
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 16
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED     7 141
  DEL PEAK  2(1P13.1) WILD-TYPE  14 353
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      7  141
  DEL PEAK  2(1P13.1) WILD-TYPE   14  353
     clus
vv    DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  NO                            7                            14
  YES                         141                           353
[1] 2 2
[1] FALSE
D23V11, continuous
D23V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P13.1) MUTATED    99   2   2   9
  DEL PEAK  2(1P13.1) WILD-TYPE 244  10   2  17
D23V13, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  R0                          99                           244
  R1                           2                            10
  R2                           2                             2
  RX                           9                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P13.1) MUTATED                                  0     3
  DEL PEAK  2(1P13.1) WILD-TYPE                                1     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.1) MUTATED                          10   114
  DEL PEAK  2(1P13.1) WILD-TYPE                        41   275
D23V14, multiclass
                                  clus
vv                                 DEL PEAK  2(1P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                    114
                                  clus
vv                                 DEL PEAK  2(1P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   41
  WHITE                                                      275
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V15, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED     1 106
  DEL PEAK  2(1P13.1) WILD-TYPE   6 276
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      1  106
  DEL PEAK  2(1P13.1) WILD-TYPE    6  276
                        clus
vv                       DEL PEAK  2(1P13.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         106
                        clus
vv                       DEL PEAK  2(1P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           276
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    30  13
  DEL PEAK  3(2Q22.1) WILD-TYPE 307 141
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           43                           448 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           13                           141 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-05-4415 TCGA-05-4418 TCGA-38-4625 TCGA-44-2659 TCGA-44-5645 TCGA-44-6778 
        2.99         9.01        97.74        44.94        12.59        61.28 
TCGA-44-6779 TCGA-44-8119 TCGA-44-A4SS TCGA-49-AARO TCGA-50-5051 TCGA-50-5936 
       16.44         3.25        13.64       123.58        15.72         8.45 
TCGA-50-5946 TCGA-50-6591 TCGA-53-7624 TCGA-55-6986 TCGA-55-8097 TCGA-55-8508 
       22.55         3.91        34.29       107.21        15.65         0.49 
TCGA-55-A492 TCGA-55-A4DF TCGA-62-8397 TCGA-62-A470 TCGA-64-1676 TCGA-67-3772 
       19.59        20.19        42.38        39.25        56.81        18.84 
TCGA-69-7760 TCGA-71-6725 TCGA-73-4670 TCGA-73-7499 TCGA-78-7150 TCGA-78-7153 
        6.64         2.01         4.31        23.51        21.90        24.99 
TCGA-78-7220 TCGA-78-7536 TCGA-86-7701 TCGA-86-8054 TCGA-86-8074 TCGA-86-8358 
       26.53         8.02        31.13        24.49         0.79        21.47 
TCGA-91-6829 TCGA-91-6848 TCGA-93-8067 TCGA-95-7039 TCGA-97-7554 TCGA-97-8172 
       41.36         7.36         6.12         1.12        25.48        17.92 
TCGA-L9-A444 
        0.20 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       20.05        14.96        29.98        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       26.01        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
        0.46         7.40         5.98         8.68       120.79        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 
       49.05        28.41        35.28        11.64        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       26.30         4.37        43.53        46.98        13.15        24.36 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       42.08        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.89        34.06         6.25        26.56        33.30        28.37 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       23.18        63.72        32.45        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
       12.66         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.75        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 
       11.64        22.26        22.26       153.04        63.95        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR 
       28.90         8.55        40.41        37.32       211.82       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
        9.86        20.52        71.47        70.55        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
       21.47        15.12        18.64        29.03        25.12        42.35 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
       25.55        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       10.13        25.61         7.59        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
        9.21        23.05        38.73        48.62        45.21         2.86 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        0.07        32.65         0.79        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
        0.82        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 
       45.34        32.71        60.03        24.99        40.54        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        0.59         1.15         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        1.32        23.18         1.28         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.78        18.64         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 
       19.73         5.06         0.13        23.64        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.95         0.36         0.26        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 
        4.80         6.64        17.62         0.49         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       20.58         0.92        15.81        19.99        17.95         4.57 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       39.98        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 
       56.71        54.35        67.96        72.30        13.61        40.96 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       29.92        20.65        39.09        55.43        37.02        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       87.98         2.04        42.90        28.41        51.25        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
        1.02        20.05        14.04        12.66         5.72         4.64 
TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
       13.87         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
        4.24        26.73         7.04        52.60        23.38        29.98 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       26.30        15.35         1.32         5.39         1.25        39.09 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
       11.18       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       35.93        39.52        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       88.14        31.20        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       27.09        12.36         5.88        34.39        13.87        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.43        19.89        16.70         4.08         4.57        24.33 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
       15.75        16.08        15.65        15.85        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       13.32        13.32         3.81        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         1.15        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82         9.76         4.18        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.22         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
       15.68        15.65        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       19.89        31.69        64.60        63.52        43.79         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59         0.72        18.67         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R 
       24.56        34.85        36.76         1.45         5.59        21.63 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV 
       14.30         3.81        14.53         1.91        17.46        12.59 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       11.87        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       49.35        37.35        86.04        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       41.59        31.23         2.43        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       14.66        14.10        11.15        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       62.60         0.13         1.64        29.13         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82         9.70        59.11        16.87 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       123.58                        223.96 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        18.84                         18.41 
[1] "0.2 - 123.6 (18.8)" "0.0 - 224.0 (18.4)"
[1] "hr=" "1.1"
D24V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(2Q22.1) MUTATED         0       10       13        0         2
  DEL PEAK  3(2Q22.1) WILD-TYPE       5      125      127        1        49
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  3(2Q22.1) MUTATED           9          7          1        4
  DEL PEAK  3(2Q22.1) WILD-TYPE        64         65         10       22
D24V3, multiclass
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                            10                           125
  STAGE IB                            13                           127
  STAGE II                             0                             1
  STAGE IIA                            2                            49
  STAGE IIB                            9                            64
  STAGE IIIA                           7                            65
  STAGE IIIB                           1                            10
  STAGE IV                             4                            22
[1] 9 2
[1] 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(2Q22.1) MUTATED    12  28   5   1
  DEL PEAK  3(2Q22.1) WILD-TYPE 158 250  41  18
D24V4, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                          12                           158
  T2                          28                           250
  T3                           5                            41
  T4                           1                            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  3(2Q22.1) MUTATED    30   7     8
  DEL PEAK  3(2Q22.1) WILD-TYPE 302  89    68
D24V5, multiclass
       clus
vv      DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  N0                             30                           302
  N1                              7                            89
  N2+N3                           8                            68
[1] 3 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
  DEL PEAK  3(2Q22.1) MUTATED    28   4
  DEL PEAK  3(2Q22.1) WILD-TYPE 320  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     28    4
  DEL PEAK  3(2Q22.1) WILD-TYPE  320   21
   clus
vv  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  0                          28                           320
  1                           4                            21
[1] 2 2
[1] FALSE
D24V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    26  20
  DEL PEAK  3(2Q22.1) WILD-TYPE 249 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     26   20
  DEL PEAK  3(2Q22.1) WILD-TYPE  249  220
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          26                           249
  MALE                            20                           220
[1] 2 2
[1] FALSE
D24V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                            4
  DEL PEAK  3(2Q22.1) WILD-TYPE                         15
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  3(2Q22.1) MUTATED                                   8
  DEL PEAK  3(2Q22.1) WILD-TYPE                                99
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  3(2Q22.1) MUTATED                                                   27
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                292
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  3(2Q22.1) MUTATED                                            0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  3(2Q22.1) MUTATED                                               2
  DEL PEAK  3(2Q22.1) WILD-TYPE                                            17
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                                0
  DEL PEAK  3(2Q22.1) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                                    0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                              0
  DEL PEAK  3(2Q22.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                               3
  DEL PEAK  3(2Q22.1) WILD-TYPE                            20
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                                 0
  DEL PEAK  3(2Q22.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                                               0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                             5
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                              2
  DEL PEAK  3(2Q22.1) WILD-TYPE                            8
D24V9, multiclass
                                                    clus
vv                                                   DEL PEAK  3(2Q22.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          27
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                2
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           0
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                3
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                0
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   DEL PEAK  3(2Q22.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             99
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           292
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 17
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 20
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  5
  MUCINOUS (COLLOID) CARCINOMA                                                   8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     3  43
  DEL PEAK  3(2Q22.1) WILD-TYPE  18 451
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      3   43
  DEL PEAK  3(2Q22.1) WILD-TYPE   18  451
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                            3                            18
  YES                          43                           451
[1] 2 2
[1] FALSE
D24V11, continuous
D24V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(2Q22.1) MUTATED    30   0   0   2
  DEL PEAK  3(2Q22.1) WILD-TYPE 313  12   4  24
D24V13, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  R0                          30                           313
  R1                           0                            12
  R2                           0                             4
  RX                           2                            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2Q22.1) MUTATED                                  0     2
  DEL PEAK  3(2Q22.1) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED                           4    35
  DEL PEAK  3(2Q22.1) WILD-TYPE                        47   354
D24V14, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     35
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   47
  WHITE                                                      354
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V15, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     1  32
  DEL PEAK  3(2Q22.1) WILD-TYPE   6 350
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      1   32
  DEL PEAK  3(2Q22.1) WILD-TYPE    6  350
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          32
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           350
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  4(3P26.2) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(3P26.2) MUTATED   152  74
  DEL PEAK  4(3P26.2) WILD-TYPE 185  80
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                          226                           265 
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                           74                            80 
$`DEL PEAK  4(3P26.2) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07        19.96        45.01        37.02         0.00        24.03 
TCGA-05-4402 TCGA-05-4415 TCGA-05-4420 TCGA-05-4432 TCGA-05-4434 TCGA-05-5425 
        8.02         2.99        29.98        25.02        15.02        29.00 
TCGA-05-5715 TCGA-35-5375 TCGA-38-4627 TCGA-38-4628 TCGA-38-6178 TCGA-44-2657 
        2.04         8.68        37.71        49.05        14.73        13.15 
TCGA-44-2662 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 
       42.08         3.19        25.02        38.89        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 
       12.59        23.77        10.78        27.78        21.63        23.18 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7670 TCGA-44-7671 
       63.72        61.28        16.44        19.46        29.00        17.59 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47F 
       23.64        12.66         3.25         8.55        15.98        11.08 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       46.72        14.07        32.84        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR4 
       29.26        17.16        22.26       153.04        63.95        28.90 
TCGA-49-AARE TCGA-49-AARN TCGA-50-5049 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
       40.41        37.32        70.55        49.28         8.22        14.27 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-6590 
       40.60        21.47        15.12        18.64        25.12        42.35 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       10.13        25.61        34.29        30.54        13.94         9.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6968 TCGA-55-6975 TCGA-55-6982 TCGA-55-6983 
       38.73        45.21        42.51         3.88        32.71        60.03 
TCGA-55-6985 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 
       40.54         0.20         0.13         1.32        23.18         1.28 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8090 
        1.12         0.53         6.48         6.15         0.16        19.66 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8206 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
        5.06         0.13         1.51         0.36         0.26         0.49 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A491 TCGA-55-A492 
        6.64        17.62         0.49         2.17        20.58        19.59 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       20.19        19.99         4.57        42.38        14.60        88.64 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 
       47.80        56.71        13.61        39.25        40.96        56.81 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 
       20.65        39.09        55.43        87.98        28.41        51.25 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 
        1.02        20.05        18.84        13.87        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-71-6725 
        5.42         7.56         2.30         2.93        14.01         2.01 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 
       26.30        15.35         4.31         1.32        39.09        23.51 
TCGA-73-A9RS TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7159 
       11.18         5.69        19.27        20.58        21.90        64.90 
TCGA-78-7160 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 
       22.29        88.14        31.20         8.02        10.55       214.62 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       10.55        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 
       13.87        19.43        19.89        24.49         4.08        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 
        0.79        15.75        23.05        21.47         1.15        30.84 
TCGA-86-8672 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
        0.62         3.81        17.62        41.36         1.97         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-8499 TCGA-91-A4BC TCGA-93-7348 TCGA-93-A4JQ 
       12.23        27.68         1.18         1.45         4.18        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        1.12         1.22        18.67        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 
        2.76        19.89        31.69        64.60        25.48         5.95 
TCGA-97-8174 TCGA-97-8177 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
        5.39        16.41        20.19        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AG TCGA-L9-A50W 
       18.67        20.68         5.59        24.30        16.44        14.53 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 
       12.59        27.19        38.63        86.04        58.85         5.29 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YF 
        2.43        10.09        11.05        14.10        11.15        71.05 
TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
       29.13         0.43         9.70        59.11 

$`DEL PEAK  4(3P26.2) WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        3.98        14.01         9.96        47.05        19.00        20.05 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96         9.01        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 
       26.01        25.02        24.00        15.02         4.96        22.03 
TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 
        9.04         0.46         7.40         5.98        97.74       120.79 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        11.64        44.61        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       43.53        46.98        44.94        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-6146 TCGA-44-6148 
       38.24        34.06         6.25        26.56         9.93        23.15 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       32.45        14.60        12.03         7.17        36.07        18.87 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4507 TCGA-49-4510 
       28.11        28.57        12.66        35.54         8.81        29.46 
TCGA-49-4512 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARO 
       29.75        11.64        22.26        62.24         8.55       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 
      211.82       164.12         9.86        20.52        71.47        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5942 
       60.16        31.04         9.27        78.67         8.45        29.03 
TCGA-50-5946 TCGA-50-6592 TCGA-50-8459 TCGA-50-8460 TCGA-55-1592 TCGA-55-1595 
       22.55        25.55         7.59        27.25        23.05        48.62 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
        2.86         0.07        32.65         0.79        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
        0.82        48.49         5.49         7.79         2.20        45.34 
TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       24.99       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
        3.12         1.28         0.79         1.78        18.64        17.65 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8096 
       19.82        29.72        15.19         3.29        19.73        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65        17.98         1.08         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        1.45         0.76         0.95        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        4.80         1.58         1.61        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 
       21.40         1.58         0.92        15.81        17.95        39.98 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 
       49.25        19.53        54.35        67.96        72.30        29.92 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3773 
       37.02        38.37         2.04        42.90        28.47        14.04 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7974 
       12.66         5.72         4.64         6.64         6.12         6.05 
TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 
       12.56        13.45         4.24        26.73         7.04        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4676 TCGA-73-4677 TCGA-78-7143 TCGA-78-7145 
       23.38        29.98         5.39         1.25       163.10        27.16 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       35.93        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 
        5.88         7.07       104.19       223.96         8.48        26.53 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       53.33        10.75        39.35        32.68        39.75        77.59 
TCGA-78-8662 TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 
      110.50        20.55        16.70         4.57        16.08        15.65 
TCGA-86-8279 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
       15.85        14.60        13.91        27.58        14.96        13.32 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6831 TCGA-91-6836 
       13.32        13.64        26.47        10.62        10.19        13.71 
TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
        7.36         1.15        16.18        16.60        14.27        19.82 
TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7562 
        9.76         6.12        23.61         1.08        19.00         2.86 
TCGA-95-7944 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 
       12.39        21.40        18.18        63.52        43.79         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
        0.72        18.67        17.92        18.12        15.39        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-99-7458 TCGA-99-8025 
       21.60        20.58        20.52        17.75        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         1.45        21.63        23.80        18.08        35.47 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A743 
       19.00        14.30         3.81         0.20         1.91        17.46 
TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       11.87         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK 
        5.49        41.59        31.23        29.46        14.66        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55R 
       73.91        62.60         0.13         1.64         0.26        19.82 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                         0.00                          0.07 
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                       214.62                        223.96 
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                       18.755                        18.080 
[1] "0.0 - 214.6 (18.8)" "0.1 - 224.0 (18.1)"
[1] "hr=" "1.2"
D25V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(3P26.2) MUTATED         1       58       59        1        32
  DEL PEAK  4(3P26.2) WILD-TYPE       4       77       81        0        19
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  4(3P26.2) MUTATED          33         33          4       15
  DEL PEAK  4(3P26.2) WILD-TYPE        40         39          7       11
D25V3, multiclass
            clus
vv           DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                            58                            77
  STAGE IB                            59                            81
  STAGE II                             1                             0
  STAGE IIA                           32                            19
  STAGE IIB                           33                            40
  STAGE IIIA                          33                            39
  STAGE IIIB                           4                             7
  STAGE IV                            15                            11
[1] 9 2
[1] 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(3P26.2) MUTATED    80 136  11   8
  DEL PEAK  4(3P26.2) WILD-TYPE  90 142  35  11
D25V4, multiclass
    clus
vv   DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  T1                          80                            90
  T2                         136                           142
  T3                          11                            35
  T4                           8                            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  4(3P26.2) MUTATED   140  54    36
  DEL PEAK  4(3P26.2) WILD-TYPE 192  42    40
D25V5, multiclass
       clus
vv      DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  N0                            140                           192
  N1                             54                            42
  N2+N3                          36                            40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P26.2) MUTATED   161  14
  DEL PEAK  4(3P26.2) WILD-TYPE 187  11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P26.2) MUTATED    161   14
  DEL PEAK  4(3P26.2) WILD-TYPE  187   11
   clus
vv  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  0                         161                           187
  1                          14                            11
[1] 2 2
[1] FALSE
D25V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P26.2) MUTATED   125 111
  DEL PEAK  4(3P26.2) WILD-TYPE 150 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P26.2) MUTATED    125  111
  DEL PEAK  4(3P26.2) WILD-TYPE  150  129
        clus
vv       DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  FEMALE                         125                           150
  MALE                           111                           129
[1] 2 2
[1] FALSE
D25V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                           11
  DEL PEAK  4(3P26.2) WILD-TYPE                          8
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  4(3P26.2) MUTATED                                  51
  DEL PEAK  4(3P26.2) WILD-TYPE                                56
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(3P26.2) MUTATED                                                  152
  DEL PEAK  4(3P26.2) WILD-TYPE                                                167
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  4(3P26.2) MUTATED                                            0
  DEL PEAK  4(3P26.2) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  4(3P26.2) MUTATED                                               6
  DEL PEAK  4(3P26.2) WILD-TYPE                                            13
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                                1
  DEL PEAK  4(3P26.2) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                                    2
  DEL PEAK  4(3P26.2) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                              0
  DEL PEAK  4(3P26.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                               7
  DEL PEAK  4(3P26.2) WILD-TYPE                            16
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                                 1
  DEL PEAK  4(3P26.2) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                                               1
  DEL PEAK  4(3P26.2) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                              4
  DEL PEAK  4(3P26.2) WILD-TYPE                            6
D25V9, multiclass
                                                    clus
vv                                                   DEL PEAK  4(3P26.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         152
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                6
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                7
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  MUCINOUS (COLLOID) CARCINOMA                                                 4
                                                    clus
vv                                                   DEL PEAK  4(3P26.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           167
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 13
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 16
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  MUCINOUS (COLLOID) CARCINOMA                                                   6
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P26.2) MUTATED     8 228
  DEL PEAK  4(3P26.2) WILD-TYPE  13 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P26.2) MUTATED      8  228
  DEL PEAK  4(3P26.2) WILD-TYPE   13  266
     clus
vv    DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  NO                            8                            13
  YES                         228                           266
[1] 2 2
[1] FALSE
D25V11, continuous
D25V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(3P26.2) MUTATED   152   2   2  11
  DEL PEAK  4(3P26.2) WILD-TYPE 191  10   2  15
D25V13, multiclass
    clus
vv   DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  R0                         152                           191
  R1                           2                            10
  R2                           2                             2
  RX                          11                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(3P26.2) MUTATED                                  1     2
  DEL PEAK  4(3P26.2) WILD-TYPE                                0     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(3P26.2) MUTATED                          28   179
  DEL PEAK  4(3P26.2) WILD-TYPE                        23   210
D25V14, multiclass
                                  clus
vv                                 DEL PEAK  4(3P26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 28
  WHITE                                                    179
                                  clus
vv                                 DEL PEAK  4(3P26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                      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"
D25V15, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P26.2) MUTATED     6 179
  DEL PEAK  4(3P26.2) WILD-TYPE   1 203
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P26.2) MUTATED      6  179
  DEL PEAK  4(3P26.2) WILD-TYPE    1  203
                        clus
vv                       DEL PEAK  4(3P26.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         179
                        clus
vv                       DEL PEAK  4(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           203
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  5(3P21.31) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(3P21.31) MUTATED   162  73
  DEL PEAK  5(3P21.31) WILD-TYPE 175  81
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                           235                            256 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            73                             81 
$`DEL PEAK  5(3P21.31) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4402 
       50.07        19.96        45.01        37.02        24.03         8.02 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4432 TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 
        2.99        29.98        25.02        15.02        15.02        29.00 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4627 TCGA-38-4628 
        2.04         7.40         5.98         8.68        37.71        49.05 
TCGA-38-4630 TCGA-38-6178 TCGA-44-2657 TCGA-44-2662 TCGA-44-3917 TCGA-44-3918 
       35.28        14.73        13.15        42.08        38.89        34.06 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6774 TCGA-44-6776 
       33.30        28.37        23.77        10.78        21.63        63.72 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
       61.28        16.44        19.46        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47F TCGA-49-4501 
       12.66         3.25         8.55        15.98        11.08        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       14.07        32.84         8.81        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR9 
       29.26        17.16        22.26       153.04        63.95         8.55 
TCGA-49-AARE TCGA-49-AARN TCGA-50-5049 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
       40.41        37.32        70.55        49.28         8.22        14.27 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 
       40.60        21.47         8.45        15.12        18.64        25.12 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 
        3.91        11.05        12.16         6.21        41.69         0.72 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       10.13        34.29        30.54        13.94         9.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6975 TCGA-55-6982 TCGA-55-6983 
       45.21         2.86        42.51         3.88        32.71        60.03 
TCGA-55-6985 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 
       40.54         0.20         0.13         1.32        23.18         1.28 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7995 TCGA-55-8090 
        1.12         0.53         6.48         6.15         0.16        19.66 
TCGA-55-8094 TCGA-55-8206 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 
        0.13         1.51         0.36         0.26         0.49         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
       17.62         0.49         1.58         2.17        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 
       20.58        19.59        20.19        19.99         4.57        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46Y TCGA-62-A470 
       14.60        88.64        47.80        56.71        13.61        39.25 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-5774 TCGA-64-5779 
       40.96        56.81        39.09        55.43        87.98        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6217 
       51.25        28.47         1.02        20.05        18.84        13.87 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 
       22.68        13.61         5.42         7.56         2.30         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       14.01        13.45         2.01        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7146 TCGA-78-7147 
        1.32        39.09        23.51        11.18         5.69        19.27 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7159 TCGA-78-7160 TCGA-78-7167 TCGA-78-7220 
       20.58        21.90        64.90        22.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 
       31.20         8.02        10.55       214.62        10.55        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 
       12.36         5.88        31.13        34.39        19.43        19.89 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 
       24.49         4.08        24.33         0.79        15.75        15.65 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-86-A4JF 
       23.05        21.47         1.15        30.84         3.81        17.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       41.36         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BC TCGA-93-7348 TCGA-93-A4JQ TCGA-95-7039 
        7.36         1.18         1.45         4.18        17.29         1.12 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        1.22        18.67        15.68        15.65        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 
       19.89        31.69        64.60        25.48         5.95         5.39 
TCGA-97-8176 TCGA-97-8177 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       15.39        16.41        20.19        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AG 
       18.67        20.68         1.45         5.59        24.30        16.44 
TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SW 
       19.00        14.53        12.59        27.19        38.63        58.45 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF 
       37.35        58.85         5.29         2.43        10.09        11.05 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A7XG 
       14.10        11.15        71.05        29.13         0.43         9.70 
TCGA-O1-A52J 
       59.11 

$`DEL PEAK  5(3P21.31) WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4403 
        3.98        14.01         0.00         9.96        47.05        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       20.05        14.96         9.01        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 
       26.01        26.01        25.02        24.00         4.96        22.03 
TCGA-05-5429 TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 TCGA-38-4631 
        9.04         0.46        97.74       120.79        28.41        11.64 
TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 
       44.61        26.30         4.37        43.53        46.98        44.94 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       24.36        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
        6.25        26.56        12.59         9.93        27.78        23.15 
TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
       23.18        32.45        14.60        12.03         7.17        36.07 
TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       18.87        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4510 
       76.21        28.11        28.57        12.66        35.54        29.46 
TCGA-49-4512 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO 
       29.75        11.64        22.26        62.24        28.90       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 
      211.82       164.12         9.86        20.52        71.47        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5933 TCGA-50-5942 TCGA-50-5946 
       60.16        31.04         9.27        78.67        29.03        22.55 
TCGA-50-6590 TCGA-50-6592 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-55-1592 
       42.35        25.55        25.61         7.59        27.25        23.05 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
       48.62         0.07        32.65         0.79        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
        0.82        48.49         5.49         7.79         2.20        45.34 
TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       24.99       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7574 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
        3.12         1.28         0.79         1.78        18.64        17.65 
TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 
       19.82        29.72        15.19         3.29        19.73         5.06 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 
       23.64        15.65        17.98         1.08         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 TCGA-55-8511 
       15.42         1.45         0.76         0.95        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.10         4.80         1.61        16.93        22.65        20.71 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8402 TCGA-62-A46P 
        0.92        15.81        17.95        39.98        49.25        19.53 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 
       54.35        67.96        72.30        29.92        20.65        37.02 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
       38.37         2.04        42.90        14.04        12.66         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7974 TCGA-69-7980 TCGA-69-8255 
        4.64         6.64         6.12         6.05        12.56         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4676 
       26.73         7.04        52.60        23.38        29.98         5.39 
TCGA-73-4677 TCGA-78-7143 TCGA-78-7145 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
        1.25       163.10        27.16        35.93        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 
       19.50        38.50        32.09         5.88         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 
      223.96         8.48        53.33        10.75        39.35        32.68 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 
       39.75        77.59       110.50        13.87        20.55        16.70 
TCGA-86-8056 TCGA-86-8076 TCGA-86-8279 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 
        4.57        16.08        15.85        14.60        13.91        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
        0.62        14.96        13.32        13.32        13.64        26.47 
TCGA-91-6828 TCGA-91-6836 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       10.62        13.71         1.15        16.18        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       19.82         9.76         6.12        23.61         1.08        19.00 
TCGA-95-7562 TCGA-95-7944 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7552 TCGA-97-7553 
        2.86        12.39        21.40        18.18        63.52        43.79 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 
        0.59         0.72        18.67        17.92        18.12        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-99-7458 TCGA-99-8025 
       21.60        20.58        20.52        17.75        24.56        34.85 
TCGA-99-8028 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 
       36.76        21.63        23.80        18.08        35.47        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N5 
        3.81         0.20         1.91        17.46        11.87         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.14        49.35        86.04         5.49        41.59        31.23 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       29.46        14.66        19.13        73.91        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55R TCGA-S2-AA1A 
        1.64         0.26        19.82        16.87 

  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                        214.62                         223.96 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                         17.62                          18.77 
[1] "0.1 - 214.6 (17.6)" "0.0 - 224.0 (18.8)"
[1] "hr=" "1.1"
D26V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(3P21.31) MUTATED         2       61       59        1        32
  DEL PEAK  5(3P21.31) WILD-TYPE       3       74       81        0        19
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  5(3P21.31) MUTATED          34         37          4       14
  DEL PEAK  5(3P21.31) WILD-TYPE        39         35          7       12
D26V3, multiclass
            clus
vv           DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             61                             74
  STAGE IB                             59                             81
  STAGE II                              1                              0
  STAGE IIA                            32                             19
  STAGE IIB                            34                             39
  STAGE IIIA                           37                             35
  STAGE IIIB                            4                              7
  STAGE IV                             14                             12
[1] 9 2
[1] 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(3P21.31) MUTATED    85 140  12   7
  DEL PEAK  5(3P21.31) WILD-TYPE  85 138  34  12
D26V4, multiclass
    clus
vv   DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  T1                           85                             85
  T2                          140                            138
  T3                           12                             34
  T4                            7                             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  5(3P21.31) MUTATED   144  59    37
  DEL PEAK  5(3P21.31) WILD-TYPE 188  37    39
D26V5, multiclass
       clus
vv      DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  N0                             144                            188
  N1                              59                             37
  N2+N3                           37                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED   169  13
  DEL PEAK  5(3P21.31) WILD-TYPE 179  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED    169   13
  DEL PEAK  5(3P21.31) WILD-TYPE  179   12
   clus
vv  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  0                          169                            179
  1                           13                             12
[1] 2 2
[1] FALSE
D26V7, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED   126 119
  DEL PEAK  5(3P21.31) WILD-TYPE 149 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED    126  119
  DEL PEAK  5(3P21.31) WILD-TYPE  149  121
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  FEMALE                          126                            149
  MALE                            119                            121
[1] 2 2
[1] FALSE
D26V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                           12
  DEL PEAK  5(3P21.31) WILD-TYPE                          7
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  5(3P21.31) MUTATED                                  53
  DEL PEAK  5(3P21.31) WILD-TYPE                                54
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(3P21.31) MUTATED                                                  155
  DEL PEAK  5(3P21.31) WILD-TYPE                                                164
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  5(3P21.31) MUTATED                                            0
  DEL PEAK  5(3P21.31) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  5(3P21.31) MUTATED                                               6
  DEL PEAK  5(3P21.31) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                                1
  DEL PEAK  5(3P21.31) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                                    2
  DEL PEAK  5(3P21.31) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                              0
  DEL PEAK  5(3P21.31) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                               8
  DEL PEAK  5(3P21.31) WILD-TYPE                            15
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                                 1
  DEL PEAK  5(3P21.31) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                                               2
  DEL PEAK  5(3P21.31) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                              5
  DEL PEAK  5(3P21.31) WILD-TYPE                            5
D26V9, multiclass
                                                    clus
vv                                                   DEL PEAK  5(3P21.31) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          155
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 6
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 8
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  5
                                                    clus
vv                                                   DEL PEAK  5(3P21.31) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            164
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  15
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   3
  MUCINOUS (COLLOID) CARCINOMA                                                    5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED    10 235
  DEL PEAK  5(3P21.31) WILD-TYPE  11 259
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED     10  235
  DEL PEAK  5(3P21.31) WILD-TYPE   11  259
     clus
vv    DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  NO                            10                             11
  YES                          235                            259
[1] 2 2
[1] FALSE
D26V11, continuous
D26V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  5(3P21.31) MUTATED   162   3   2   9
  DEL PEAK  5(3P21.31) WILD-TYPE 181   9   2  17
D26V13, multiclass
    clus
vv   DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  R0                          162                            181
  R1                            3                              9
  R2                            2                              2
  RX                            9                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(3P21.31) MUTATED                                  1     2
  DEL PEAK  5(3P21.31) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P21.31) MUTATED                          26   190
  DEL PEAK  5(3P21.31) WILD-TYPE                        25   199
D26V14, multiclass
                                  clus
vv                                 DEL PEAK  5(3P21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     190
                                  clus
vv                                 DEL PEAK  5(3P21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       199
[1] 4 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
  DEL PEAK  5(3P21.31) MUTATED     4 189
  DEL PEAK  5(3P21.31) WILD-TYPE   3 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      4  189
  DEL PEAK  5(3P21.31) WILD-TYPE    3  193
                        clus
vv                       DEL PEAK  5(3P21.31) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          189
                        clus
vv                       DEL PEAK  5(3P21.31) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            193
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  6(3Q11.1) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3Q11.1) MUTATED    91  43
  DEL PEAK  6(3Q11.1) WILD-TYPE 246 111
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                          134                           357 
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                           43                           111 
$`DEL PEAK  6(3Q11.1) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-5420 TCGA-05-5425 
       50.07        45.01        37.02         2.99        15.02        29.00 
TCGA-05-5715 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6774 TCGA-44-6776 
        2.04        23.77        10.78        27.78        21.63        63.72 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
       16.44        19.46        17.59        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47F TCGA-49-4490 TCGA-49-4506 TCGA-49-6742 
        8.55        15.98        11.08        12.66        32.84        14.63 
TCGA-49-6743 TCGA-49-AAQV TCGA-49-AAR0 TCGA-50-5068 TCGA-50-5072 TCGA-50-5932 
       12.13        22.26       153.04        49.28         8.22        40.60 
TCGA-50-5935 TCGA-50-5941 TCGA-50-6591 TCGA-50-6593 TCGA-50-6595 TCGA-50-6597 
       21.47        18.64         3.91        11.05         6.21        41.69 
TCGA-50-6673 TCGA-53-7624 TCGA-55-1592 TCGA-55-5899 TCGA-55-6975 TCGA-55-6982 
        0.72        34.29        23.05         2.86         3.88        32.71 
TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7727 
       60.03        40.54         1.15         0.13         1.32         1.12 
TCGA-55-7910 TCGA-55-8090 TCGA-55-8205 TCGA-55-8206 TCGA-55-8514 TCGA-55-8615 
        6.48        19.66         1.08         1.51         6.64         0.49 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A492 TCGA-55-A4DF TCGA-55-A4DG 
        1.58         2.17        21.40        19.59        20.19        19.99 
TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R 
        4.57        42.38        14.60        88.64        19.53        56.71 
TCGA-62-A46Y TCGA-62-A470 TCGA-64-1678 TCGA-64-5774 TCGA-64-5781 TCGA-67-3770 
       13.61        39.25        39.09        87.98        51.25         1.02 
TCGA-67-3772 TCGA-67-6217 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
       18.84        13.87        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-8253 TCGA-71-6725 TCGA-73-4659 TCGA-73-4675 TCGA-73-7498 
        6.05        14.01         2.01        23.38         1.32        39.09 
TCGA-78-7145 TCGA-78-7148 TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 
       27.16        20.58        22.29         7.07        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       31.20         8.02        10.55        27.09        12.36        31.13 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8073 TCGA-86-8075 TCGA-86-8280 TCGA-86-8585 
       19.89        24.49        24.33        15.75        23.05         1.15 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-7771 TCGA-91-8497 TCGA-91-8499 
       10.19         2.60        27.68        16.18        14.27         1.18 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VP 
        4.18         1.12        18.67        15.65        27.29        19.89 
TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 
       31.69        25.48         5.95        17.92         5.39        16.41 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-A4AG 
       19.76        20.84        18.67         1.45        24.30        16.44 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
        2.43        10.09        11.05        14.10        11.15        19.13 
TCGA-NJ-A55O TCGA-NJ-A7XG 
        0.43         9.70 

$`DEL PEAK  6(3Q11.1) WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
        3.98        19.96        14.01         0.00         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 
       47.05         8.02        19.00        20.05        14.96         9.01 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       29.98        12.00        30.02        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 TCGA-05-5428 
       25.02        25.02        24.00        15.02         4.96        22.03 
TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         0.46         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
      120.79        37.71        49.05        28.41        35.28        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       44.61        14.73        26.30         4.37        43.53        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
       13.15        44.94        24.36        42.08        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       25.02        37.15        38.24        38.89        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6146 TCGA-44-6148 
       26.56        33.30        28.37        12.59         9.93        23.15 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 
       23.18        32.45        61.28        14.60        12.03         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       36.07        18.87        29.00        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 
       13.64        13.45        76.21        28.11        28.57        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       46.72        14.07         8.81        29.46        29.75        55.89 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 
       29.26        17.16        11.64        22.26        63.95        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ 
       28.90         8.55        40.41        37.32       123.58       211.82 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
      164.12         9.86        20.52        71.47        70.55        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       60.16        31.04         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 
       15.12        29.03        25.12        22.55        42.35        25.55 
TCGA-50-6594 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
       12.16        10.13        25.61         7.59        27.25        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 
       13.94         9.21        38.73        48.62        45.21         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6984 
       48.49         5.49         7.79         2.20        45.34        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 
      107.21        70.26         0.59         7.99         0.20         3.12 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       23.18         1.28         1.28         0.79         1.78        18.64 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        0.53        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       15.19         3.29        19.73         5.06         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       15.65        17.98         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        0.76         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 
        0.30         0.10         4.80        17.62         1.61        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
       22.65        20.71         1.58        20.58         0.92        15.81 
TCGA-55-A57B TCGA-62-8395 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U 
       17.95        39.98        49.25        47.80        54.35        67.96 
TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       72.30        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 
       37.02        38.37         2.04        42.90        28.41        28.47 
TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       20.05        14.04        12.66         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 
        6.12         2.30         2.93        12.56        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
       26.73         7.04        52.60        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 
        4.31         5.39         1.25        23.51        11.18       163.10 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 
       19.50        38.50        32.09         5.88        64.90       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
      223.96         8.48        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-6851 
       32.68       214.62        39.75        77.59       110.50         5.88 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 
       34.39        13.87        20.55        19.43        16.70         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 
        4.57         0.79        16.08        15.65        15.85        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       13.32        13.32         3.81        17.62        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 
       10.62        41.36         1.97        13.71        12.23         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 
        1.15        16.60         1.45        19.82         9.76         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       23.61         1.08        19.00        17.29         1.22         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7547 
       12.39        15.68         2.76        21.40        18.18        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 
       63.52        43.79         0.59         0.72        18.67        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       15.39        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.52        17.75        20.68        24.56        34.85        36.76 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
        5.59        21.63        23.80        18.08        35.47        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       14.30         3.81         0.20        14.53         1.91        17.46 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       12.59        11.87        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 
        5.29        41.59        31.23        29.46        14.66        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        59.11        16.87 

  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                       153.04                        223.96 
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                       16.425                        19.000 
[1] "0.1 - 153.0 (16.4)" "0.0 - 224.0 (19.0)"
[1] "hr=" "1.3"
D27V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(3Q11.1) MUTATED         1       34       36        1        11
  DEL PEAK  6(3Q11.1) WILD-TYPE       4      101      104        0        40
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  6(3Q11.1) MUTATED          21         25          3        8
  DEL PEAK  6(3Q11.1) WILD-TYPE        52         47          8       18
D27V3, multiclass
            clus
vv           DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                            34                           101
  STAGE IB                            36                           104
  STAGE II                             1                             0
  STAGE IIA                           11                            40
  STAGE IIB                           21                            52
  STAGE IIIA                          25                            47
  STAGE IIIB                           3                             8
  STAGE IV                             8                            18
[1] 9 2
[1] 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(3Q11.1) MUTATED    44  81   9   6
  DEL PEAK  6(3Q11.1) WILD-TYPE 126 197  37  13
D27V4, multiclass
    clus
vv   DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  T1                          44                           126
  T2                          81                           197
  T3                           9                            37
  T4                           6                            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  6(3Q11.1) MUTATED    85  27    27
  DEL PEAK  6(3Q11.1) WILD-TYPE 247  69    49
D27V5, multiclass
       clus
vv      DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  N0                             85                           247
  N1                             27                            69
  N2+N3                          27                            49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(3Q11.1) MUTATED    99   7
  DEL PEAK  6(3Q11.1) WILD-TYPE 249  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3Q11.1) MUTATED     99    7
  DEL PEAK  6(3Q11.1) WILD-TYPE  249   18
   clus
vv  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  0                          99                           249
  1                           7                            18
[1] 2 2
[1] FALSE
D27V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3Q11.1) MUTATED    78  62
  DEL PEAK  6(3Q11.1) WILD-TYPE 197 178
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3Q11.1) MUTATED     78   62
  DEL PEAK  6(3Q11.1) WILD-TYPE  197  178
        clus
vv       DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  FEMALE                          78                           197
  MALE                            62                           178
[1] 2 2
[1] FALSE
D27V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                            6
  DEL PEAK  6(3Q11.1) WILD-TYPE                         13
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  6(3Q11.1) MUTATED                                  34
  DEL PEAK  6(3Q11.1) WILD-TYPE                                73
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(3Q11.1) MUTATED                                                   83
  DEL PEAK  6(3Q11.1) WILD-TYPE                                                236
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  6(3Q11.1) MUTATED                                            0
  DEL PEAK  6(3Q11.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  6(3Q11.1) MUTATED                                               5
  DEL PEAK  6(3Q11.1) WILD-TYPE                                            14
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                                1
  DEL PEAK  6(3Q11.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                                    1
  DEL PEAK  6(3Q11.1) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                              0
  DEL PEAK  6(3Q11.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                               5
  DEL PEAK  6(3Q11.1) WILD-TYPE                            18
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                                 1
  DEL PEAK  6(3Q11.1) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                                               1
  DEL PEAK  6(3Q11.1) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                              3
  DEL PEAK  6(3Q11.1) WILD-TYPE                            7
D27V9, multiclass
                                                    clus
vv                                                   DEL PEAK  6(3Q11.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          83
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                5
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           1
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                5
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  MUCINOUS (COLLOID) CARCINOMA                                                 3
                                                    clus
vv                                                   DEL PEAK  6(3Q11.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           236
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 14
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 18
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  MUCINOUS (COLLOID) CARCINOMA                                                   7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, binary
                               cls
clus                              0   1
  DEL PEAK  6(3Q11.1) MUTATED     6 134
  DEL PEAK  6(3Q11.1) WILD-TYPE  15 360
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3Q11.1) MUTATED      6  134
  DEL PEAK  6(3Q11.1) WILD-TYPE   15  360
     clus
vv    DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  NO                            6                            15
  YES                         134                           360
[1] 2 2
[1] FALSE
D27V11, continuous
D27V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(3Q11.1) MUTATED    82   3   0   5
  DEL PEAK  6(3Q11.1) WILD-TYPE 261   9   4  21
D27V13, multiclass
    clus
vv   DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  R0                          82                           261
  R1                           3                             9
  R2                           0                             4
  RX                           5                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(3Q11.1) MUTATED                                  0     1
  DEL PEAK  6(3Q11.1) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3Q11.1) MUTATED                          11   112
  DEL PEAK  6(3Q11.1) WILD-TYPE                        40   277
D27V14, multiclass
                                  clus
vv                                 DEL PEAK  6(3Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    112
                                  clus
vv                                 DEL PEAK  6(3Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   40
  WHITE                                                      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"
D27V15, binary
                               cls
clus                              0   1
  DEL PEAK  6(3Q11.1) MUTATED     1 106
  DEL PEAK  6(3Q11.1) WILD-TYPE   6 276
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3Q11.1) MUTATED      1  106
  DEL PEAK  6(3Q11.1) WILD-TYPE    6  276
                        clus
vv                       DEL PEAK  6(3Q11.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         106
                        clus
vv                       DEL PEAK  6(3Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           276
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  7(3Q29) MUTATION ANALYSIS
D28V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  7(3Q29) MUTATED    91  38
  DEL PEAK  7(3Q29) WILD-TYPE 246 116
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                        129                         362 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                         38                         116 
$`DEL PEAK  7(3Q29) MUTATED`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
       50.07        37.02        20.05         2.99        14.96        12.00 
TCGA-05-5420 TCGA-05-5715 TCGA-38-4631 TCGA-44-3917 TCGA-44-5644 TCGA-44-6144 
       15.02         2.04        11.64        38.89        28.37        23.77 
TCGA-44-6774 TCGA-44-6776 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       21.63        63.72        18.87        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47F TCGA-49-4506 TCGA-49-4510 TCGA-49-6742 
        3.25         8.55        11.08        32.84        29.46        14.63 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-50-6673 TCGA-53-7626 
       49.28        40.60        21.47        41.69         0.72        30.54 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6972 TCGA-55-6975 TCGA-55-6982 
        2.86        32.65         0.79        48.49         3.88        32.71 
TCGA-55-6983 TCGA-55-7283 TCGA-55-7573 TCGA-55-7725 TCGA-55-7727 TCGA-55-7815 
       60.03         1.15         0.13         1.28         1.12         1.78 
TCGA-55-7910 TCGA-55-8090 TCGA-55-8094 TCGA-55-8203 TCGA-55-8206 TCGA-55-8507 
        6.48        19.66         0.13        17.98         1.51         0.26 
TCGA-55-8508 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Z TCGA-55-A492 
        0.49         6.64         0.49         1.58        21.40        19.59 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       19.99        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46Y TCGA-62-A470 TCGA-64-1677 TCGA-64-1678 
       19.53        56.71        13.61        39.25        20.65        39.09 
TCGA-64-5774 TCGA-67-3770 TCGA-67-3772 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       87.98         1.02        18.84        22.68        13.61         5.42 
TCGA-69-7974 TCGA-69-8253 TCGA-69-8255 TCGA-73-4659 TCGA-73-4662 TCGA-73-4675 
        6.05        14.01         4.24        23.38        29.98         1.32 
TCGA-73-7498 TCGA-73-A9RS TCGA-78-7147 TCGA-78-7148 TCGA-78-7160 TCGA-78-7161 
       39.09        11.18        19.27        20.58        22.29         7.07 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7539 TCGA-78-8660 TCGA-86-6562 
        8.48        88.14        31.20        10.75        10.55        12.36 
TCGA-86-7701 TCGA-86-7713 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8280 
       31.13        13.87        24.49         4.08        15.75        23.05 
TCGA-91-6828 TCGA-91-6835 TCGA-91-6836 TCGA-91-6847 TCGA-91-7771 TCGA-91-8497 
       10.62         2.60        13.71        27.68        16.18        14.27 
TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 
       18.67        15.65        21.40        19.89        31.69        25.48 
TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M1 TCGA-97-A4M3 
        5.95        17.92         5.39        16.41        19.76        17.75 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 
       20.84        18.67        24.56         1.45        24.30        23.80 
TCGA-J2-A4AG TCGA-L9-A443 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TI 
       16.44         3.81        58.85         5.29         2.43        14.10 
TCGA-MP-A4TJ TCGA-NJ-A55O TCGA-NJ-A7XG 
       11.15         0.43         9.70 

$`DEL PEAK  7(3Q29) WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
        3.98        19.96        14.01        45.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4418 TCGA-05-4420 
       24.03        47.05         8.02        19.00         9.01        29.98 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       24.00        15.02         4.96        29.00        22.03         9.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        0.46         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
       37.71        49.05        28.41        35.28        44.61        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       26.30         4.37        43.53        46.98        13.15        44.94 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       24.36        42.08        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
       38.24        34.06         6.25        26.56        33.30        12.59 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 
       10.78         9.93        27.78        23.15        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       61.28        16.44        14.60        19.46        12.03         7.17 
TCGA-44-7667 TCGA-44-7670 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       36.07        29.00        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       13.64        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 
       35.54        46.72        14.07         8.81        29.75        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV 
       12.13        29.26        17.16        11.64        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
      153.04        63.95        62.24        28.90         8.55        40.41 
TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       37.32       123.58       211.82       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
       71.47        70.55        15.72        60.16        31.04         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        9.27        14.27        78.67         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       11.05        12.16         6.21        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       27.25        34.29        13.94         9.21        23.05        38.73 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       48.62        45.21         0.07        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6984 
        0.82         5.49         7.79         2.20        45.34        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 
       40.54       107.21        70.26         0.59         7.99         0.20 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7728 TCGA-55-7903 
        3.12         1.32        23.18         1.28         0.79        18.64 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        0.53        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
       15.19         3.29        19.73         5.06        23.64        15.65 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.08         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.95         0.36        17.72         0.30         0.10         4.80 
TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
       17.62         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A57B 
        1.58        20.58         0.92        15.81        20.19        17.95 
TCGA-62-8394 TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 
        4.57        47.80        54.35        67.96        72.30        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
       29.92        56.81        55.43        37.02        38.37         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 
       42.90        28.41        51.25        28.47        20.05        14.04 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       12.66         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8453 
        7.56         2.30         2.93        12.56        13.45        26.73 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        7.04         2.01        52.60        26.30        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        5.39         1.25        23.51       163.10        27.16         5.69 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 
       32.09         5.88        64.90       104.19       223.96        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 
        8.02        53.33        39.35        10.55        32.68       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 
       39.75        77.59       110.50        27.09         5.88        34.39 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 
       20.55        19.43        19.89        16.70         4.57        24.33 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 
        0.79        16.08        15.65        15.85        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
        1.15        13.91        30.84        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       13.32        13.32         3.81        17.62        13.64        26.47 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 
       41.36         1.97        10.19        12.23         7.36         1.15 
TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 
        1.22         2.86        12.39        15.68        27.29         2.76 
TCGA-95-A4VN TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 
       18.18        64.60        63.52        43.79         0.59         0.72 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.67        18.12        15.39        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 
       20.19        21.44        20.52        20.68        34.85        36.76 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 
        5.59        21.63        18.08        35.47        19.00        14.30 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
        0.20        14.53         1.91        17.46        12.59        11.87 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       27.19        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD 
       37.35        86.04         5.49        41.59        31.23        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       29.46        11.05        14.66        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R 
       62.60         0.13         1.64        29.13         0.26        19.82 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                       0.13                        0.00 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                      88.64                      223.96 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                      17.59                       19.00 
[1] "0.1 - 88.6 (17.6)"  "0.0 - 224.0 (19.0)"
[1] "hr=" "1.2"
D28V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  7(3Q29) MUTATED         1       31       37        0        16
  DEL PEAK  7(3Q29) WILD-TYPE       4      104      103        1        35
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  7(3Q29) MUTATED          22         21          2        5
  DEL PEAK  7(3Q29) WILD-TYPE        51         51          9       21
D28V3, multiclass
            clus
vv           DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  STAGE I                            1                           4
  STAGE IA                          31                         104
  STAGE IB                          37                         103
  STAGE II                           0                           1
  STAGE IIA                         16                          35
  STAGE IIB                         22                          51
  STAGE IIIA                        21                          51
  STAGE IIIB                         2                           9
  STAGE IV                           5                          21
[1] 9 2
[1] 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(3Q29) MUTATED    42  78  10   5
  DEL PEAK  7(3Q29) WILD-TYPE 128 200  36  14
D28V4, multiclass
    clus
vv   DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  T1                        42                         128
  T2                        78                         200
  T3                        10                          36
  T4                         5                          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  7(3Q29) MUTATED    86  28    21
  DEL PEAK  7(3Q29) WILD-TYPE 246  68    55
D28V5, multiclass
       clus
vv      DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  N0                           86                         246
  N1                           28                          68
  N2+N3                        21                          55
[1] 3 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
  DEL PEAK  7(3Q29) MUTATED    98   4
  DEL PEAK  7(3Q29) WILD-TYPE 250  21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED     98    4
  DEL PEAK  7(3Q29) WILD-TYPE  250   21
   clus
vv  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  0                        98                         250
  1                         4                          21
[1] 2 2
[1] FALSE
D28V7, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED    72  63
  DEL PEAK  7(3Q29) WILD-TYPE 203 177
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED     72   63
  DEL PEAK  7(3Q29) WILD-TYPE  203  177
        clus
vv       DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  FEMALE                        72                         203
  MALE                          63                         177
[1] 2 2
[1] FALSE
D28V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                            5
  DEL PEAK  7(3Q29) WILD-TYPE                         14
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  7(3Q29) MUTATED                                  34
  DEL PEAK  7(3Q29) WILD-TYPE                                73
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  7(3Q29) MUTATED                                                   79
  DEL PEAK  7(3Q29) WILD-TYPE                                                240
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  7(3Q29) MUTATED                                            0
  DEL PEAK  7(3Q29) WILD-TYPE                                          5
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  7(3Q29) MUTATED                                               4
  DEL PEAK  7(3Q29) WILD-TYPE                                            15
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                                0
  DEL PEAK  7(3Q29) WILD-TYPE                              2
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                                    1
  DEL PEAK  7(3Q29) WILD-TYPE                                  2
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                              0
  DEL PEAK  7(3Q29) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                               5
  DEL PEAK  7(3Q29) WILD-TYPE                            18
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                                 1
  DEL PEAK  7(3Q29) WILD-TYPE                               0
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                                               2
  DEL PEAK  7(3Q29) WILD-TYPE                                             3
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  7(3Q29) MUTATED                              4
  DEL PEAK  7(3Q29) WILD-TYPE                            6
D28V9, multiclass
                                                    clus
vv                                                   DEL PEAK  7(3Q29) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        79
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                 0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                              4
  LUNG CLEAR CELL ADENOCARCINOMA                                             0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                         1
  LUNG MUCINOUS ADENOCARCINOMA                                               0
  LUNG PAPILLARY ADENOCARCINOMA                                              5
  LUNG SIGNET RING ADENOCARCINOMA                                            1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                              2
  MUCINOUS (COLLOID) CARCINOMA                                               4
                                                    clus
vv                                                   DEL PEAK  7(3Q29) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                  14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         240
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               15
  LUNG CLEAR CELL ADENOCARCINOMA                                               2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 2
  LUNG PAPILLARY ADENOCARCINOMA                                               18
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                3
  MUCINOUS (COLLOID) CARCINOMA                                                 6
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED     4 131
  DEL PEAK  7(3Q29) WILD-TYPE  17 363
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED      4  131
  DEL PEAK  7(3Q29) WILD-TYPE   17  363
     clus
vv    DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  NO                          4                          17
  YES                       131                         363
[1] 2 2
[1] FALSE
D28V11, continuous
D28V12, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  7(3Q29) MUTATED    87   2   0   3
  DEL PEAK  7(3Q29) WILD-TYPE 256  10   4  23
D28V13, multiclass
    clus
vv   DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  R0                        87                         256
  R1                         2                          10
  R2                         0                           4
  RX                         3                          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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3Q29) MUTATED                                  0     0
  DEL PEAK  7(3Q29) WILD-TYPE                                1     7
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3Q29) MUTATED                          11   106
  DEL PEAK  7(3Q29) WILD-TYPE                        40   283
D28V14, multiclass
                                  clus
vv                                 DEL PEAK  7(3Q29) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                               11
  WHITE                                                  106
                                  clus
vv                                 DEL PEAK  7(3Q29) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 40
  WHITE                                                    283
[1] 4 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
  DEL PEAK  7(3Q29) MUTATED     1 102
  DEL PEAK  7(3Q29) WILD-TYPE   6 280
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED      1  102
  DEL PEAK  7(3Q29) WILD-TYPE    6  280
                        clus
vv                       DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             1                           6
  NOT HISPANIC OR LATINO                       102                         280
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  8(4P16.3) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4P16.3) MUTATED    91  33
  DEL PEAK  8(4P16.3) WILD-TYPE 246 121
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                          124                           367 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           33                           121 
$`DEL PEAK  8(4P16.3) MUTATED`
TCGA-05-4249 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 
       50.07        24.03        47.05         8.02        20.05         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-5420 TCGA-05-5425 TCGA-35-4123 
       14.96        29.98        30.02        15.02        29.00         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4632 TCGA-44-2659 TCGA-44-2666 TCGA-44-5643 
        8.68        97.74        44.61        44.94         3.19        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-7670 TCGA-44-8117 TCGA-44-A479 
       61.28        19.46        36.07        29.00        12.66        15.98 
TCGA-49-4487 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 TCGA-49-6742 TCGA-49-6743 
       28.11        46.72        32.84        29.46        14.63        12.13 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AARE TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
      153.04        63.95        40.41        70.55        15.72        31.04 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6673 TCGA-50-7109 TCGA-53-7626 TCGA-53-A4EZ 
       22.55        42.35         0.72        10.13        30.54         9.21 
TCGA-55-5899 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6985 TCGA-55-7574 
        2.86        42.51        40.73         0.82        40.54         3.12 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7995 
       23.18         1.28         1.78        18.64         6.48         0.16 
TCGA-55-8096 TCGA-55-8203 TCGA-55-8505 TCGA-55-8507 TCGA-55-8514 TCGA-55-8614 
       23.64        17.98         0.95         0.26         6.64        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A4DF 
        0.49         1.58         2.17        21.40        20.58        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8398 TCGA-62-A46V TCGA-62-A472 TCGA-64-1677 
       19.99         4.57        14.60        72.30        29.92        20.65 
TCGA-64-5774 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-69-7760 TCGA-69-7763 
       87.98        28.41        28.47        20.05         6.64        22.68 
TCGA-69-7973 TCGA-69-7979 TCGA-69-8453 TCGA-71-6725 TCGA-73-4659 TCGA-73-4670 
        7.56         2.93        26.73         2.01        23.38         4.31 
TCGA-73-4675 TCGA-78-7143 TCGA-78-7159 TCGA-78-7536 TCGA-78-8640 TCGA-78-8662 
        1.32       163.10        64.90         8.02       214.62       110.50 
TCGA-86-7713 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-A4JF TCGA-91-6830 
       13.87         4.08         0.79        15.75        17.62         1.97 
TCGA-91-6840 TCGA-91-6848 TCGA-91-7771 TCGA-93-A4JO TCGA-95-7043 TCGA-95-7567 
       12.23         7.36        16.18         1.08         1.22        18.67 
TCGA-95-7944 TCGA-95-A4VN TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-8025 
       12.39        18.18        21.60        21.44        19.76        34.85 
TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4T4 
        5.59        18.08        19.00        12.59        38.63        86.04 
TCGA-MP-A4TD TCGA-MP-A4TJ TCGA-NJ-A4YI TCGA-O1-A52J 
       10.09        11.15         0.13        59.11 

$`DEL PEAK  8(4P16.3) WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4403 TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
        9.96        19.00         9.01        12.00        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 
       26.01        25.02        25.02        24.00        15.02         4.96 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-38-4626 
       22.03         9.04         2.04         0.46         7.40       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       37.71        49.05        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 
       26.30         4.37        43.53        46.98        13.15        24.36 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       42.08        42.77        25.02        37.15        38.24        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       34.06         6.25        26.56        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 
       63.72        32.45        16.44        14.60        12.03         7.17 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A 
       18.87        17.59        23.64         3.25         8.55        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
        9.44        11.08        11.54        13.64        13.45        76.21 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 
       28.57        12.66        35.54        14.07         8.81        29.75 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV 
       55.89        29.26        17.16        11.64        22.26        22.26 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ 
       62.24        28.90         8.55        37.32       123.58       211.82 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 
      164.12         9.86        20.52        71.47        60.16        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
        8.22         9.27        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6591 
        8.45        15.12        18.64        29.03        25.12         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-8457 
       25.55        11.05        12.16         6.21        41.69        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
        7.59        27.25        34.29        13.94        23.05        38.73 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6970 
       48.62        45.21         0.07        32.65         0.79        15.25 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       48.49         3.88         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       32.71        60.03        24.99       107.21        70.26         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7725 
        1.15         7.99         0.20         0.13         1.32         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        1.12         0.79         0.53        17.65         6.15        19.82 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
        0.13        15.65         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
       15.42         1.45         0.76         0.36         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
        0.30         0.10         4.80         1.61        16.93        22.65 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B 
       20.71         1.58        19.59         0.92        15.81        17.95 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       39.98        42.38        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       56.71        54.35        67.96        13.61        39.25        40.96 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
       56.81        39.09        55.43        37.02        38.37         2.04 
TCGA-64-5778 TCGA-64-5781 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       42.90        51.25         1.02        18.84        14.04        12.66 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
        5.72         4.64        13.87         6.12        13.61         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        6.05         2.30        12.56        14.01        13.45         4.24 
TCGA-69-A59K TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 
        7.04        52.60        29.98        26.30        15.35         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7145 TCGA-78-7146 
        1.25        39.09        23.51        11.18        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 
       19.50        38.50        32.09         5.88        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       53.33        10.75        39.35        10.55        32.68        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       77.59        10.55        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        20.55        19.43        19.89        16.70        24.49 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        4.57        24.33        16.08        15.65        15.85        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
        0.62        14.96        13.32        13.32         3.81        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62        41.36        10.19         2.60        13.71 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
       27.68         1.15        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP 
       19.82         9.76         4.18         6.12        23.61        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
       17.29         1.12         2.86        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
        2.76        21.40        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       20.58        20.19        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 
       20.68        24.56        36.76         1.45        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       23.80        35.47        16.44        14.30         3.81         0.20 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 
       14.53         1.91        17.46        11.87        27.19         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 
       86.14        58.45        49.35        37.35        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF 
        5.29        41.59        31.23         2.43        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        29.13         0.26         0.43        19.82         9.70 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                       214.62                        223.96 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                       18.655                        18.120 
[1] "0.1 - 214.6 (18.7)" "0.0 - 224.0 (18.1)"
[1] "hr=" "1.3"
D29V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(4P16.3) MUTATED         2       32       39        0        11
  DEL PEAK  8(4P16.3) WILD-TYPE       3      103      101        1        40
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  8(4P16.3) MUTATED          17         19          4        6
  DEL PEAK  8(4P16.3) WILD-TYPE        56         53          7       20
D29V3, multiclass
            clus
vv           DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            32                           103
  STAGE IB                            39                           101
  STAGE II                             0                             1
  STAGE IIA                           11                            40
  STAGE IIB                           17                            56
  STAGE IIIA                          19                            53
  STAGE IIIB                           4                             7
  STAGE IV                             6                            20
[1] 9 2
[1] 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(4P16.3) MUTATED    45  69  12   3
  DEL PEAK  8(4P16.3) WILD-TYPE 125 209  34  16
D29V4, multiclass
    clus
vv   DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  T1                          45                           125
  T2                          69                           209
  T3                          12                            34
  T4                           3                            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  8(4P16.3) MUTATED    81  22    22
  DEL PEAK  8(4P16.3) WILD-TYPE 251  74    54
D29V5, multiclass
       clus
vv      DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  N0                             81                           251
  N1                             22                            74
  N2+N3                          22                            54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED    84   6
  DEL PEAK  8(4P16.3) WILD-TYPE 264  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED     84    6
  DEL PEAK  8(4P16.3) WILD-TYPE  264   19
   clus
vv  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  0                          84                           264
  1                           6                            19
[1] 2 2
[1] FALSE
D29V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED    69  61
  DEL PEAK  8(4P16.3) WILD-TYPE 206 179
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED     69   61
  DEL PEAK  8(4P16.3) WILD-TYPE  206  179
        clus
vv       DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  FEMALE                          69                           206
  MALE                            61                           179
[1] 2 2
[1] FALSE
D29V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                            5
  DEL PEAK  8(4P16.3) WILD-TYPE                         14
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  8(4P16.3) MUTATED                                  26
  DEL PEAK  8(4P16.3) WILD-TYPE                                81
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(4P16.3) MUTATED                                                   88
  DEL PEAK  8(4P16.3) WILD-TYPE                                                231
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  8(4P16.3) MUTATED                                            0
  DEL PEAK  8(4P16.3) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  8(4P16.3) MUTATED                                               1
  DEL PEAK  8(4P16.3) WILD-TYPE                                            18
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                1
  DEL PEAK  8(4P16.3) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                    0
  DEL PEAK  8(4P16.3) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                              1
  DEL PEAK  8(4P16.3) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                               3
  DEL PEAK  8(4P16.3) WILD-TYPE                            20
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                 1
  DEL PEAK  8(4P16.3) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                                               2
  DEL PEAK  8(4P16.3) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                              2
  DEL PEAK  8(4P16.3) WILD-TYPE                            8
D29V9, multiclass
                                                    clus
vv                                                   DEL PEAK  8(4P16.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          88
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                1
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           0
  LUNG MUCINOUS ADENOCARCINOMA                                                 1
  LUNG PAPILLARY ADENOCARCINOMA                                                3
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                2
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   DEL PEAK  8(4P16.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             81
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           231
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 18
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                 20
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED     6 124
  DEL PEAK  8(4P16.3) WILD-TYPE  15 370
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED      6  124
  DEL PEAK  8(4P16.3) WILD-TYPE   15  370
     clus
vv    DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  NO                            6                            15
  YES                         124                           370
[1] 2 2
[1] FALSE
D29V11, continuous
D29V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(4P16.3) MUTATED    83   3   2   8
  DEL PEAK  8(4P16.3) WILD-TYPE 260   9   2  18
D29V13, multiclass
    clus
vv   DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  R0                          83                           260
  R1                           3                             9
  R2                           2                             2
  RX                           8                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(4P16.3) MUTATED                                  0     1
  DEL PEAK  8(4P16.3) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4P16.3) MUTATED                          15    93
  DEL PEAK  8(4P16.3) WILD-TYPE                        36   296
D29V14, multiclass
                                  clus
vv                                 DEL PEAK  8(4P16.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                     93
                                  clus
vv                                 DEL PEAK  8(4P16.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      296
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V15, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED     3  93
  DEL PEAK  8(4P16.3) WILD-TYPE   4 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED      3   93
  DEL PEAK  8(4P16.3) WILD-TYPE    4  289
                        clus
vv                       DEL PEAK  8(4P16.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          93
                        clus
vv                       DEL PEAK  8(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           289
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  9(4Q34.3) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4Q34.3) MUTATED   125  55
  DEL PEAK  9(4Q34.3) WILD-TYPE 212  99
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                          180                           311 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                           55                            99 
$`DEL PEAK  9(4Q34.3) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 
       50.07        19.96        45.01        37.02         0.00        47.05 
TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 
        8.02        20.05         2.99        14.96        29.98        30.02 
TCGA-05-4427 TCGA-05-4432 TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 
       26.01        25.02        15.02        15.02        29.00        22.03 
TCGA-35-4123 TCGA-35-5375 TCGA-38-6178 TCGA-44-2668 TCGA-44-3917 TCGA-44-5643 
        5.98         8.68        14.73        25.02        38.89        33.30 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6778 TCGA-44-7660 
       28.37        23.77        10.78        27.78        61.28        19.46 
TCGA-44-7667 TCGA-44-7670 TCGA-44-A479 TCGA-49-4487 TCGA-49-4501 TCGA-49-4506 
       36.07        29.00        15.98        28.11        46.72        32.84 
TCGA-49-4507 TCGA-49-6743 TCGA-49-AAR0 TCGA-49-AARE TCGA-50-5045 TCGA-50-5049 
        8.81        12.13       153.04        40.41        71.47        70.55 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 
       15.72        31.04         8.22         9.27        14.27         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       15.12        18.64        25.55         6.21         0.72        10.13 
TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
       34.29         9.21        23.05        38.73        48.62        45.21 
TCGA-55-5899 TCGA-55-6968 TCGA-55-6971 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
        2.86        42.51         0.82         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7815 TCGA-55-7910 TCGA-55-8085 
        1.32        23.18         1.28         1.78         6.48        29.72 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8203 TCGA-55-8205 TCGA-55-8505 TCGA-55-8507 
        5.06         0.13        17.98         1.08         0.95         0.26 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y 
        0.49         0.10         6.64         0.49         1.58        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-62-8394 
       21.40         1.58        20.58        19.59        20.19         4.57 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46U TCGA-62-A46Y 
       14.60        88.64        47.80        56.71        67.96        13.61 
TCGA-62-A470 TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-5778 TCGA-64-5779 
       39.25        29.92        20.65        55.43        42.90        28.41 
TCGA-67-3771 TCGA-67-3773 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7979 
       20.05        14.04        22.68        13.61         7.56         2.93 
TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 
        4.24        26.73         2.01        23.38        29.98         4.31 
TCGA-73-4675 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7159 
        1.32        20.58        21.90        39.52        38.50        64.90 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-86-6851 
       88.14        26.53        31.20         8.02        10.75         5.88 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8075 
       34.39        13.87        19.89        16.70         4.08        15.75 
TCGA-86-8279 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 TCGA-86-A4JF TCGA-91-6828 
       15.85        30.84         0.62        13.32        17.62        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 
       41.36         1.97        10.19        12.23        27.68        16.18 
TCGA-91-8499 TCGA-91-A4BC TCGA-93-A4JO TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7567 
        1.18         1.45         1.08        17.29         1.22        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7937 TCGA-97-8175 
       12.39        15.68        18.18        19.89         5.95        18.12 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       21.44        19.76        34.85        36.76         1.45         5.59 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
       18.08        19.00        12.59        11.87        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TF 
        2.76        58.45         5.29        31.23        10.09        11.05 
TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A7XG TCGA-O1-A52J 
       11.15        71.05         0.13        29.13         9.70        59.11 

$`DEL PEAK  9(4Q34.3) WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 TCGA-05-4418 
        3.98        14.01         9.96        24.03        19.00         9.01 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 
       12.00        21.99        26.01        25.02        24.00         4.96 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-38-4625 TCGA-38-4626 
        9.04         2.04         0.46         7.40        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       37.71        49.05        28.41        35.28        11.64        44.61 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       26.30         4.37        43.53        46.98        13.15        44.94 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
       24.36        42.08        42.77         3.19        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6146 TCGA-44-6148 
       34.06         6.25        26.56        12.59         9.93        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        63.72        32.45        16.44        14.60 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       12.03         7.17        18.87        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25         8.55        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        76.21        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 
       14.07        29.46        29.75        55.89        14.63        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       17.16        11.64        22.26        22.26        63.95        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       28.90         8.55        37.32       123.58       211.82       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5055 TCGA-50-5068 TCGA-50-5932 TCGA-50-5933 
        9.86        20.52        60.16        49.28        40.60        78.67 
TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       21.47        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       11.05        12.16        41.69        25.61         7.59        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       30.54        13.94         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
       15.25        48.49         3.88         5.49         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        60.03        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7725 TCGA-55-7727 
       70.26         0.59         1.15         7.99         1.28         1.12 
TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 
        0.79        18.64         0.53        17.65         6.15        19.82 
TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 
        0.16        15.19         3.29        19.66        19.73        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       15.65         1.51         2.17        22.16        15.42         1.45 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8614 
        0.76         0.36        17.72         0.30         4.80        17.62 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A493 TCGA-55-A494 
        1.61         2.17        16.93        22.65         0.92        15.81 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46P 
       19.99        17.95        39.98        42.38        49.25        19.53 
TCGA-62-A46S TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 
       54.35        72.30        40.96        56.81        39.09        37.02 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       38.37        87.98         2.04        51.25        28.47         1.02 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       18.84        12.66         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
        6.12         5.42         6.05         2.30        12.56        14.01 
TCGA-69-8254 TCGA-69-A59K TCGA-73-4658 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 
       13.45         7.04        52.60        26.30        15.35         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
        1.25        39.09        23.51        11.18       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
        5.69        19.27        35.93        24.99        19.50        32.09 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        5.88        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       53.33        39.35        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       77.59        10.55       110.50        27.09        12.36        31.13 
TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       20.55        19.43        24.49         4.57        24.33         0.79 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       16.08        15.65        23.05        21.47        14.60         1.15 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 
       13.91        27.58        14.96        13.32         3.81        13.64 
TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6836 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       26.47         2.60        13.71         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
       14.27        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7562 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
       19.00         1.12         2.86        15.65        27.29         2.76 
TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       21.40        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 
        0.59         0.72        18.67        17.92         5.39        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M2 
       16.41        14.30        21.60        20.58        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-AA5R 
       17.75        20.84        18.67        20.68        24.56        21.63 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
       24.30        23.80        35.47        16.44        14.30         3.81 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MP-A4SV TCGA-MP-A4SY 
        0.20        14.53         1.91        17.46        86.14        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC 
       37.35        86.04        58.85         5.49        41.59         2.43 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG 
       29.46        14.66        14.10        19.13        73.91        62.60 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        1.64         0.26         0.43        19.82        16.87 

  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                         0.00                          0.07 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                       153.04                        223.96 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                        18.03                         18.84 
[1] "0.0 - 153.0 (18.0)" "0.1 - 224.0 (18.8)"
[1] "hr=" "1.1"
D30V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(4Q34.3) MUTATED         2       50       50        0        19
  DEL PEAK  9(4Q34.3) WILD-TYPE       3       85       90        1        32
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  9(4Q34.3) MUTATED          19         32          5       10
  DEL PEAK  9(4Q34.3) WILD-TYPE        54         40          6       16
D30V3, multiclass
            clus
vv           DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            50                            85
  STAGE IB                            50                            90
  STAGE II                             0                             1
  STAGE IIA                           19                            32
  STAGE IIB                           19                            54
  STAGE IIIA                          32                            40
  STAGE IIIB                           5                             6
  STAGE IV                            10                            16
[1] 9 2
[1] 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(4Q34.3) MUTATED    60 108  12   6
  DEL PEAK  9(4Q34.3) WILD-TYPE 110 170  34  13
D30V4, multiclass
    clus
vv   DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  T1                          60                           110
  T2                         108                           170
  T3                          12                            34
  T4                           6                            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  9(4Q34.3) MUTATED   119  29    35
  DEL PEAK  9(4Q34.3) WILD-TYPE 213  67    41
D30V5, multiclass
       clus
vv      DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  N0                            119                           213
  N1                             29                            67
  N2+N3                          35                            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED   132  10
  DEL PEAK  9(4Q34.3) WILD-TYPE 216  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED    132   10
  DEL PEAK  9(4Q34.3) WILD-TYPE  216   15
   clus
vv  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  0                         132                           216
  1                          10                            15
[1] 2 2
[1] FALSE
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED    92  95
  DEL PEAK  9(4Q34.3) WILD-TYPE 183 145
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED     92   95
  DEL PEAK  9(4Q34.3) WILD-TYPE  183  145
        clus
vv       DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  FEMALE                          92                           183
  MALE                            95                           145
[1] 2 2
[1] FALSE
D30V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                            6
  DEL PEAK  9(4Q34.3) WILD-TYPE                         13
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  9(4Q34.3) MUTATED                                  41
  DEL PEAK  9(4Q34.3) WILD-TYPE                                66
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(4Q34.3) MUTATED                                                  119
  DEL PEAK  9(4Q34.3) WILD-TYPE                                                200
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  9(4Q34.3) MUTATED                                            0
  DEL PEAK  9(4Q34.3) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  9(4Q34.3) MUTATED                                               4
  DEL PEAK  9(4Q34.3) WILD-TYPE                                            15
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                                2
  DEL PEAK  9(4Q34.3) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                                    1
  DEL PEAK  9(4Q34.3) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                              0
  DEL PEAK  9(4Q34.3) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                               6
  DEL PEAK  9(4Q34.3) WILD-TYPE                            17
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                                 1
  DEL PEAK  9(4Q34.3) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                                               4
  DEL PEAK  9(4Q34.3) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  9(4Q34.3) MUTATED                              3
  DEL PEAK  9(4Q34.3) WILD-TYPE                            7
D30V9, multiclass
                                                    clus
vv                                                   DEL PEAK  9(4Q34.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           41
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         119
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                4
  LUNG CLEAR CELL ADENOCARCINOMA                                               2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           1
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                6
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                4
  MUCINOUS (COLLOID) CARCINOMA                                                 3
                                                    clus
vv                                                   DEL PEAK  9(4Q34.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           200
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 15
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 17
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  1
  MUCINOUS (COLLOID) CARCINOMA                                                   7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED    11 176
  DEL PEAK  9(4Q34.3) WILD-TYPE  10 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED     11  176
  DEL PEAK  9(4Q34.3) WILD-TYPE   10  318
     clus
vv    DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  NO                           11                            10
  YES                         176                           318
[1] 2 2
[1] FALSE
D30V11, continuous
D30V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(4Q34.3) MUTATED   124   4   2  11
  DEL PEAK  9(4Q34.3) WILD-TYPE 219   8   2  15
D30V13, multiclass
    clus
vv   DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  R0                         124                           219
  R1                           4                             8
  R2                           2                             2
  RX                          11                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(4Q34.3) MUTATED                                  0     4
  DEL PEAK  9(4Q34.3) WILD-TYPE                                1     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q34.3) MUTATED                          20   136
  DEL PEAK  9(4Q34.3) WILD-TYPE                        31   253
D30V14, multiclass
                                  clus
vv                                 DEL PEAK  9(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 20
  WHITE                                                    136
                                  clus
vv                                 DEL PEAK  9(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      253
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V15, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED     5 136
  DEL PEAK  9(4Q34.3) WILD-TYPE   2 246
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED      5  136
  DEL PEAK  9(4Q34.3) WILD-TYPE    2  246
                        clus
vv                       DEL PEAK  9(4Q34.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         136
                        clus
vv                       DEL PEAK  9(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           246
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 10(5Q12.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(5Q12.1) MUTATED   118  47
  DEL PEAK 10(5Q12.1) WILD-TYPE 219 107
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                          165                           326 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                           47                           107 
$`DEL PEAK 10(5Q12.1) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 
       50.07        19.96        45.01         9.96        24.03        47.05 
TCGA-05-4402 TCGA-05-4405 TCGA-05-4417 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 
        8.02        20.05        14.96        30.02        26.01        25.02 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 
       29.00        22.03         2.04         7.40         5.98        97.74 
TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-44-2657 TCGA-44-2659 
       49.05        35.28        11.64        44.61        13.15        44.94 
TCGA-44-3917 TCGA-44-3919 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6774 
       38.89         6.25        23.77        10.78         9.93        21.63 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7670 TCGA-44-8120 TCGA-44-A4SS 
       61.28        19.46         7.17        29.00         8.55        13.64 
TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-6742 TCGA-49-AAR2 TCGA-49-AAR4 
       12.66        14.07         8.81        14.63        63.95        28.90 
TCGA-49-AARE TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5944 
       40.41        71.47        70.55        31.04        49.28        25.12 
TCGA-50-5946 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       22.55        34.29        30.54         9.21        23.05        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6969 TCGA-55-6972 TCGA-55-6975 TCGA-55-6979 
       45.21         2.86        40.73        48.49         3.88         7.79 
TCGA-55-6981 TCGA-55-6985 TCGA-55-7570 TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 
       45.34        40.54         0.20        23.18         1.28         1.12 
TCGA-55-7910 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8094 TCGA-55-8203 
        6.48         6.15        19.82         0.16         0.13        17.98 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 
        0.95         0.36         0.26        17.72         0.30         6.64 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A491 
       17.62         0.49         1.58         2.17        20.71        20.58 
TCGA-55-A492 TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       19.59        17.95         4.57        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       47.80        39.25        40.96        56.81        39.09        55.43 
TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-69-7765 
       38.37        42.90         1.02        20.05        18.84         5.42 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4668 
        2.93        12.56         4.24         7.04         2.01        15.35 
TCGA-73-4670 TCGA-78-7149 TCGA-78-7150 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 
        4.31        35.93        21.90        19.50        64.90        22.29 
TCGA-78-7161 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-8640 TCGA-83-5908 
        7.07        26.53        31.20         8.02       214.62        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 
       12.36         5.88        34.39        13.87        19.43        16.70 
TCGA-86-8074 TCGA-86-8279 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-91-6829 
        0.79        15.85        14.60         1.15         0.62        41.36 
TCGA-91-6840 TCGA-91-8499 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP 
       12.23         1.18         4.18         6.12         1.08        19.00 
TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-97-7937 TCGA-97-8172 
        1.22        18.67        15.68        15.65         5.95        17.92 
TCGA-97-8175 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A743 
       18.12         5.59        18.08        19.00         0.20        17.46 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW 
       12.59        11.87        27.19        38.63        86.14        58.45 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TK 
       86.04        58.85         5.29         2.43        29.46        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ 
       73.91        71.05        29.13 

$`DEL PEAK 10(5Q12.1) WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4403 TCGA-05-4415 
        3.98        14.01        37.02         0.00        19.00         2.99 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
        9.01        29.98        12.00        21.99        26.01        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-35-3615 
       24.00        15.02        15.02         4.96         9.04         0.46 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-6178 TCGA-38-7271 
        8.68       120.79        37.71        28.41        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 
        4.37        43.53        46.98        24.36        42.08        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 
        3.19        25.02        37.15        38.24        34.06        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 
       33.30        28.37        12.59        27.78        23.15        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7667 
       63.72        32.45        16.44        14.60        12.03        36.07 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 
       18.87        17.59        23.64        12.66         3.25        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 
       15.32         9.44        11.08        11.54        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 
       28.11        28.57        35.54        46.72        32.84        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       29.75        55.89        12.13        29.26        17.16        11.64 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARN 
       22.26        22.26       153.04        62.24         8.55        37.32 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5051 
      123.58       211.82       164.12         9.86        20.52        15.72 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       60.16         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-6590 
       21.47         8.45        15.12        18.64        29.03        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 
        3.91        25.55        11.05        12.16         6.21        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 
        0.72        10.13        25.61         7.59        27.25        13.94 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6970 
       48.62         0.07        32.65         0.79        42.51        15.25 
TCGA-55-6971 TCGA-55-6978 TCGA-55-6980 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        0.82         5.49         2.20        32.71        60.03        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
      107.21        70.26         0.59         1.15         7.99         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        3.12         1.32         1.28         0.79         1.78        18.64 
TCGA-55-7907 TCGA-55-7911 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        0.53        17.65        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
       19.73         5.06        23.64        15.65         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 
        2.17        22.16        15.42         1.45         0.76         0.49 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z 
        0.10         4.80         1.61        16.93        22.65        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
        1.58         0.92        15.81        20.19        19.99        39.98 
TCGA-62-8397 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       42.38        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 
       13.61        29.92        20.65        37.02        87.98         2.04 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
       28.41        51.25        28.47        14.04        12.66         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        7.56         6.05         2.30        14.01        13.45        26.73 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 
       52.60        23.38        29.98        26.30         1.32         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
        1.25        39.09        23.51        11.18       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
        5.69        19.27        20.58        39.52        24.99        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       32.09         5.88       104.19       223.96         8.48        88.14 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       53.33        10.75        39.35        10.55        32.68        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 
       77.59        10.55       110.50        31.13        20.55        19.89 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 
       24.49         4.08         4.57        24.33        15.75        16.08 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       15.65        23.05        21.47        13.91        30.84        27.58 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
       14.96        13.32        13.32         3.81        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 
       26.47        10.62         1.97        10.19         2.60        13.71 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JQ TCGA-95-7039 
        1.45        19.82         9.76        23.61        17.29         1.12 
TCGA-95-7562 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN 
        2.86        12.39        27.29         2.76        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        31.69        64.60        63.52        43.79        25.48 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 
        0.59         0.72        18.67         5.39        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 
       20.52        17.75        20.84        18.67        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45        21.63        24.30        23.80 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A5IP 
       35.47        16.44        14.30         3.81        14.53         1.91 
TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA 
        2.76        49.35        37.35         5.49        41.59        31.23 
TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YG 
       10.09        11.05        14.66        14.10        11.15        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.13         1.64         0.26         0.43        19.82         9.70 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                       214.62                        223.96 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                        18.67                         18.41 
[1] "0.1 - 214.6 (18.7)" "0.0 - 224.0 (18.4)"
[1] "hr=" "1.2"
D31V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(5Q12.1) MUTATED         2       42       51        0        19
  DEL PEAK 10(5Q12.1) WILD-TYPE       3       93       89        1        32
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 10(5Q12.1) MUTATED          27         21          4       10
  DEL PEAK 10(5Q12.1) WILD-TYPE        46         51          7       16
D31V3, multiclass
            clus
vv           DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            42                            93
  STAGE IB                            51                            89
  STAGE II                             0                             1
  STAGE IIA                           19                            32
  STAGE IIB                           27                            46
  STAGE IIIA                          21                            51
  STAGE IIIB                           4                             7
  STAGE IV                            10                            16
[1] 9 2
[1] 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(5Q12.1) MUTATED    58  98  12   6
  DEL PEAK 10(5Q12.1) WILD-TYPE 112 180  34  13
D31V4, multiclass
    clus
vv   DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  T1                          58                           112
  T2                          98                           180
  T3                          12                            34
  T4                           6                            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 10(5Q12.1) MUTATED   108  40    23
  DEL PEAK 10(5Q12.1) WILD-TYPE 224  56    53
D31V5, multiclass
       clus
vv      DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  N0                            108                           224
  N1                             40                            56
  N2+N3                          23                            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"
D31V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q12.1) MUTATED   124   9
  DEL PEAK 10(5Q12.1) WILD-TYPE 224  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED    124    9
  DEL PEAK 10(5Q12.1) WILD-TYPE  224   16
   clus
vv  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  0                         124                           224
  1                           9                            16
[1] 2 2
[1] FALSE
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q12.1) MUTATED    89  87
  DEL PEAK 10(5Q12.1) WILD-TYPE 186 153
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED     89   87
  DEL PEAK 10(5Q12.1) WILD-TYPE  186  153
        clus
vv       DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  FEMALE                          89                           186
  MALE                            87                           153
[1] 2 2
[1] FALSE
D31V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                            6
  DEL PEAK 10(5Q12.1) WILD-TYPE                         13
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 10(5Q12.1) MUTATED                                  36
  DEL PEAK 10(5Q12.1) WILD-TYPE                                71
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(5Q12.1) MUTATED                                                  119
  DEL PEAK 10(5Q12.1) WILD-TYPE                                                200
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 10(5Q12.1) MUTATED                                            0
  DEL PEAK 10(5Q12.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 10(5Q12.1) MUTATED                                               2
  DEL PEAK 10(5Q12.1) WILD-TYPE                                            17
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                                0
  DEL PEAK 10(5Q12.1) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                                    2
  DEL PEAK 10(5Q12.1) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                              1
  DEL PEAK 10(5Q12.1) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                               5
  DEL PEAK 10(5Q12.1) WILD-TYPE                            18
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                                 0
  DEL PEAK 10(5Q12.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                                               4
  DEL PEAK 10(5Q12.1) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 10(5Q12.1) MUTATED                              1
  DEL PEAK 10(5Q12.1) WILD-TYPE                            9
D31V9, multiclass
                                                    clus
vv                                                   DEL PEAK 10(5Q12.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           36
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         119
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                2
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 1
  LUNG PAPILLARY ADENOCARCINOMA                                                5
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                4
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   DEL PEAK 10(5Q12.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             71
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           200
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 17
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                 18
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  1
  MUCINOUS (COLLOID) CARCINOMA                                                   9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q12.1) MUTATED     6 170
  DEL PEAK 10(5Q12.1) WILD-TYPE  15 324
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED      6  170
  DEL PEAK 10(5Q12.1) WILD-TYPE   15  324
     clus
vv    DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  NO                            6                            15
  YES                         170                           324
[1] 2 2
[1] FALSE
D31V11, continuous
D31V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(5Q12.1) MUTATED   129   3   1  12
  DEL PEAK 10(5Q12.1) WILD-TYPE 214   9   3  14
D31V13, multiclass
    clus
vv   DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  R0                         129                           214
  R1                           3                             9
  R2                           1                             3
  RX                          12                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(5Q12.1) MUTATED                                  1     4
  DEL PEAK 10(5Q12.1) WILD-TYPE                                0     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(5Q12.1) MUTATED                          20   122
  DEL PEAK 10(5Q12.1) WILD-TYPE                        31   267
D31V14, multiclass
                                  clus
vv                                 DEL PEAK 10(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 20
  WHITE                                                    122
                                  clus
vv                                 DEL PEAK 10(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      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"
D31V15, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q12.1) MUTATED     5 125
  DEL PEAK 10(5Q12.1) WILD-TYPE   2 257
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED      5  125
  DEL PEAK 10(5Q12.1) WILD-TYPE    2  257
                        clus
vv                       DEL PEAK 10(5Q12.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         125
                        clus
vv                       DEL PEAK 10(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           257
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK 11(5Q31.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(5Q31.1) MUTATED   140  58
  DEL PEAK 11(5Q31.1) WILD-TYPE 197  96
  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                          198                           293 
  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                           58                            96 
$`DEL PEAK 11(5Q31.1) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 
       50.07        19.96        45.01         9.96        47.05         8.02 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4430 
       20.05        14.96        29.98        30.02        26.01        25.02 
TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       25.02        29.00        22.03         2.04         7.40         5.98 
TCGA-38-4625 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 
       97.74        49.05        35.28        11.64        44.61        26.30 
TCGA-44-2659 TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
       44.94        38.89        33.30        28.37        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 
        9.93        27.78        21.63        23.18        61.28        16.44 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-8117 TCGA-44-8120 
       19.46         7.17        36.07        29.00        12.66         8.55 
TCGA-44-A4SS TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-4514 
       13.64        28.57        12.66        14.07         8.81        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       14.63        12.13        22.26        63.95        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 
        8.55        40.41       123.58       211.82        71.47        70.55 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 TCGA-50-6593 
       31.04        49.28        18.64        22.55        42.35        11.05 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       10.13        34.29        30.54         9.21        23.05        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6969 TCGA-55-6972 TCGA-55-6975 
       45.21         2.86        42.51        40.73        48.49         3.88 
TCGA-55-6979 TCGA-55-6985 TCGA-55-7281 TCGA-55-7570 TCGA-55-7576 TCGA-55-7724 
        7.79        40.54         0.59         0.20         1.32        23.18 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7994 
        1.28         1.12         0.53         6.48         6.15        19.82 
TCGA-55-8094 TCGA-55-8203 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
        0.13        17.98         0.76         0.95         0.36         0.26 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 
       17.72         0.30         6.64        17.62         0.49         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DG TCGA-55-A57B 
        2.17        20.71        20.58        19.59        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V 
        4.57        39.98        14.60        88.64        49.25        72.30 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 
       39.25        40.96        56.81        55.43        38.37        42.90 
TCGA-64-5779 TCGA-67-3771 TCGA-67-3772 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 
       28.41        20.05        18.84        13.61         5.42         2.93 
TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 TCGA-73-A9RS 
       12.56         4.24         2.01        15.35         4.31        11.18 
TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        5.69        35.93        21.90        64.90        22.29         7.07 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-8640 
       88.14        26.53        31.20         8.02        53.33       214.62 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
       27.09        12.36         5.88        34.39        13.87        19.43 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8279 
       16.70         4.08         4.57        24.33         0.79        15.85 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-91-6829 TCGA-91-6831 
       21.47        14.60         1.15         0.62        41.36        10.19 
TCGA-91-6840 TCGA-91-8499 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JQ 
       12.23         1.18         4.18         6.12         1.08        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
        1.12         1.22         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7937 TCGA-97-8172 TCGA-97-8175 
       15.65        21.40        19.89         5.95        17.92        18.12 
TCGA-99-8025 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV 
       34.85        18.08        19.00         0.20        14.53        12.59 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       27.19        38.63        86.14        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
        5.29         2.43        29.46        19.13        73.91        71.05 

$`DEL PEAK 11(5Q31.1) WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 
        3.98        14.01        37.02         0.00        24.03        19.00 
TCGA-05-4415 TCGA-05-4418 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 
        2.99         9.01        12.00        21.99        26.01        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-35-3615 TCGA-35-5375 
       15.02        15.02         4.96         9.04         0.46         8.68 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-6178 TCGA-38-A44F TCGA-44-2655 
      120.79        37.71        28.41        14.73         4.37        43.53 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
       46.98        13.15        24.36        42.08        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       25.02        37.15        38.24        34.06         6.25        26.56 
TCGA-44-5645 TCGA-44-6148 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 
       12.59        23.15        63.72        32.45        14.60        12.03 
TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
       18.87        17.59        23.64         3.25        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        9.44        11.08        11.54        13.45        76.21        28.11 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 
       35.54        46.72        32.84        29.46        29.75        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AARN TCGA-49-AARR 
       17.16        11.64        22.26       153.04        37.32       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 
        9.86        20.52        15.72        60.16         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
       14.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 
       29.03        25.12         3.91        25.55        12.16         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 
       41.69         0.72        25.61         7.59        27.25        13.94 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6970 TCGA-55-6971 
       48.62         0.07        32.65         0.79        15.25         0.82 
TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        5.49         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 
      107.21        70.26         1.15         7.99         0.13         3.12 
TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7995 
        1.28         0.79         1.78        18.64        17.65         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       29.72        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       23.64        15.65         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 
       15.42         1.45         0.49         0.10         4.80         1.61 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       16.93        22.65        21.40         1.58         0.92        15.81 
TCGA-55-A4DF TCGA-62-8397 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       20.19        42.38        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46Y TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 
       67.96        13.61        29.92        20.65        39.09        37.02 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 
       87.98         2.04        51.25        28.47         1.02        14.04 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       12.66         5.72         4.64        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 
       22.68         7.56         6.05         2.30        14.01        13.45 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
       26.73         7.04        52.60        23.38        29.98        26.30 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 
        1.32         5.39         1.25        39.09        23.51       163.10 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       27.16        19.27        20.58        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       38.50        32.09         5.88       104.19       223.96         8.48 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       10.75        39.35        10.55        32.68        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
       10.55       110.50        31.13        20.55        19.89        24.49 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8668 TCGA-86-8669 
       15.75        16.08        15.65        23.05        13.91        30.84 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
       27.58        14.96        13.32        13.32         3.81        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 
       13.64        26.47        10.62         1.97         2.60        13.71 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       27.68         7.36         1.15        16.18        16.60        14.27 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-8039 
        1.45        19.82         9.76        23.61        19.00        27.29 
TCGA-95-8494 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        18.18        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 
       25.48         0.59         0.72        18.67         5.39        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       24.56        36.76         1.45         5.59        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A5IP 
       23.80        35.47        16.44        14.30         3.81         1.91 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       17.46        11.87         2.76        58.45        49.35        37.35 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       41.59        31.23        10.09        11.05        14.66        14.10 
TCGA-MP-A4TJ TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       11.15        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.43        19.82         9.70        59.11        16.87 

  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                       214.62                        223.96 
  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE 
                        18.92                         17.65 
[1] "0.1 - 214.6 (18.9)" "0.0 - 224.0 (17.6)"
[1] "hr=" "1.2"
D32V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(5Q31.1) MUTATED         3       48       59        0        21
  DEL PEAK 11(5Q31.1) WILD-TYPE       2       87       81        1        30
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 11(5Q31.1) MUTATED          32         29          4       11
  DEL PEAK 11(5Q31.1) WILD-TYPE        41         43          7       15
D32V3, multiclass
            clus
vv           DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            48                            87
  STAGE IB                            59                            81
  STAGE II                             0                             1
  STAGE IIA                           21                            30
  STAGE IIB                           32                            41
  STAGE IIIA                          29                            43
  STAGE IIIB                           4                             7
  STAGE IV                            11                            15
[1] 9 2
[1] 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(5Q31.1) MUTATED    67 116  17   7
  DEL PEAK 11(5Q31.1) WILD-TYPE 103 162  29  12
D32V4, multiclass
    clus
vv   DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  T1                          67                           103
  T2                         116                           162
  T3                          17                            29
  T4                           7                            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(5Q31.1) MUTATED   131  43    30
  DEL PEAK 11(5Q31.1) WILD-TYPE 201  53    46
D32V5, multiclass
       clus
vv      DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  N0                            131                           201
  N1                             43                            53
  N2+N3                          30                            46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q31.1) MUTATED   137  10
  DEL PEAK 11(5Q31.1) WILD-TYPE 211  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q31.1) MUTATED    137   10
  DEL PEAK 11(5Q31.1) WILD-TYPE  211   15
   clus
vv  DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  0                         137                           211
  1                          10                            15
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q31.1) MUTATED   103 104
  DEL PEAK 11(5Q31.1) WILD-TYPE 172 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q31.1) MUTATED    103  104
  DEL PEAK 11(5Q31.1) WILD-TYPE  172  136
        clus
vv       DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  FEMALE                         103                           172
  MALE                           104                           136
[1] 2 2
[1] FALSE
D32V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                            8
  DEL PEAK 11(5Q31.1) WILD-TYPE                         11
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 11(5Q31.1) MUTATED                                  46
  DEL PEAK 11(5Q31.1) WILD-TYPE                                61
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(5Q31.1) MUTATED                                                  135
  DEL PEAK 11(5Q31.1) WILD-TYPE                                                184
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 11(5Q31.1) MUTATED                                            0
  DEL PEAK 11(5Q31.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 11(5Q31.1) MUTATED                                               3
  DEL PEAK 11(5Q31.1) WILD-TYPE                                            16
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                                1
  DEL PEAK 11(5Q31.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                                    2
  DEL PEAK 11(5Q31.1) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                              1
  DEL PEAK 11(5Q31.1) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                               7
  DEL PEAK 11(5Q31.1) WILD-TYPE                            16
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                                 0
  DEL PEAK 11(5Q31.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                                               3
  DEL PEAK 11(5Q31.1) WILD-TYPE                                             2
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 11(5Q31.1) MUTATED                              1
  DEL PEAK 11(5Q31.1) WILD-TYPE                            9
D32V9, multiclass
                                                    clus
vv                                                   DEL PEAK 11(5Q31.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         135
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                3
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 1
  LUNG PAPILLARY ADENOCARCINOMA                                                7
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                3
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   DEL PEAK 11(5Q31.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           184
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 16
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                 16
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  2
  MUCINOUS (COLLOID) CARCINOMA                                                   9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q31.1) MUTATED     8 199
  DEL PEAK 11(5Q31.1) WILD-TYPE  13 295
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q31.1) MUTATED      8  199
  DEL PEAK 11(5Q31.1) WILD-TYPE   13  295
     clus
vv    DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  NO                            8                            13
  YES                         199                           295
[1] 2 2
[1] FALSE
D32V11, continuous
D32V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(5Q31.1) MUTATED   144   3   1  14
  DEL PEAK 11(5Q31.1) WILD-TYPE 199   9   3  12
D32V13, multiclass
    clus
vv   DEL PEAK 11(5Q31.1) MUTATED DEL PEAK 11(5Q31.1) WILD-TYPE
  R0                         144                           199
  R1                           3                             9
  R2                           1                             3
  RX                          14                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(5Q31.1) MUTATED                                  1     3
  DEL PEAK 11(5Q31.1) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(5Q31.1) MUTATED                          27   146
  DEL PEAK 11(5Q31.1) WILD-TYPE                        24   243
D32V14, multiclass
                                  clus
vv                                 DEL PEAK 11(5Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    146
                                  clus
vv                                 DEL PEAK 11(5Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      243
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V15, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q31.1) MUTATED     6 147
  DEL PEAK 11(5Q31.1) WILD-TYPE   1 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q31.1) MUTATED      6  147
  DEL PEAK 11(5Q31.1) WILD-TYPE    1  235
                        clus
vv                       DEL PEAK 11(5Q31.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         147
                        clus
vv                       DEL PEAK 11(5Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           235
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK 12(6Q11.1) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(6Q11.1) MUTATED    79  48
  DEL PEAK 12(6Q11.1) WILD-TYPE 258 106
  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                          127                           364 
  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                           48                           106 
$`DEL PEAK 12(6Q11.1) MUTATED`
TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 TCGA-05-4405 TCGA-05-4415 TCGA-35-3615 
        3.98        37.02         0.00        20.05         2.99         0.46 
TCGA-35-4123 TCGA-38-4631 TCGA-44-2659 TCGA-44-5644 TCGA-44-6778 TCGA-44-6779 
        5.98        11.64        44.94        28.37        61.28        16.44 
TCGA-44-7667 TCGA-44-A47F TCGA-44-A4SU TCGA-49-4488 TCGA-49-4494 TCGA-49-4507 
       36.07        11.08        13.45        28.57        35.54         8.81 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARE 
       55.89        29.26        17.16        11.64       153.04        40.41 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5932 TCGA-50-5935 TCGA-50-5939 
       15.72        31.04        49.28        40.60        21.47        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6594 TCGA-53-7626 
       18.64        29.03        22.55        42.35        12.16        30.54 
TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6981 
        9.21         0.07        42.51         0.82        48.49        45.34 
TCGA-55-6983 TCGA-55-6984 TCGA-55-7283 TCGA-55-7724 TCGA-55-7815 TCGA-55-7914 
       60.03        24.99         1.15        23.18         1.78         6.15 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8207 TCGA-55-8302 
        3.29        19.66        19.73        17.98         2.17         0.76 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-A48X TCGA-55-A490 
        0.36         0.49         0.30         0.10        22.65         1.58 
TCGA-55-A493 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U 
        0.92        14.60        49.25        19.53        56.71        67.96 
TCGA-62-A472 TCGA-64-1677 TCGA-64-5775 TCGA-64-5781 TCGA-67-3771 TCGA-67-6216 
       29.92        20.65         2.04        51.25        20.05         4.64 
TCGA-69-7974 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 
        6.05        14.01        13.45        26.73         7.04        23.38 
TCGA-73-4666 TCGA-73-4675 TCGA-78-7146 TCGA-78-7152 TCGA-78-7153 TCGA-78-7158 
       26.30         1.32         5.69        39.52        24.99         5.88 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-83-5908 
       26.53        31.20         8.02        53.33        39.35        27.09 
TCGA-86-6562 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8074 TCGA-86-8280 
       12.36        31.13        20.55        19.43         0.79        23.05 
TCGA-86-8359 TCGA-86-A456 TCGA-91-6831 TCGA-93-7347 TCGA-93-7348 TCGA-95-7567 
       14.60        13.32        10.19         9.76         4.18        18.67 
TCGA-95-7944 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7554 TCGA-97-8177 
       12.39         2.76        19.89        64.60        25.48        16.41 
TCGA-97-8547 TCGA-97-A4M0 TCGA-99-7458 TCGA-99-8025 TCGA-J2-8192 TCGA-L9-A443 
       21.60        21.44        24.56        34.85        24.30         3.81 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 
       27.19        38.63        86.14        49.35        37.35        58.85 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YP 
        2.43        10.09        11.05        73.91         0.13         1.64 
TCGA-NJ-A4YQ 
       29.13 

$`DEL PEAK 12(6Q11.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4396 TCGA-05-4397 
       50.07        19.96        14.01        45.01         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 
       47.05         8.02        19.00        14.96         9.01        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
       12.00        30.02        21.99        26.01        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       25.02        24.00        15.02        15.02         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 
       22.03         9.04         2.04         7.40         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 
      120.79        37.71        49.05        28.41        35.28        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        13.15 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       24.36        42.08        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       38.24        38.89        34.06         6.25        26.56        33.30 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 
       21.63        23.18        63.72        32.45        14.60        19.46 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
       12.03         7.17        18.87        29.00        17.59        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.66         3.25         8.55        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4501 
       11.54        13.64        76.21        28.11        12.66        46.72 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 
       14.07        32.84        29.46        29.75        14.63        12.13 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26        22.26        63.95        62.24        28.90         8.55 
TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       37.32       123.58       211.82       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       71.47        70.55        60.16         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       78.67         8.45        25.12         3.91        25.55        11.05 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 
       27.25        34.29        13.94        23.05        38.73        48.62 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
       45.21         2.86        32.65         0.79        40.73        15.25 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6982 TCGA-55-6985 
        3.88         5.49         7.79         2.20        32.71        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
      107.21        70.26         0.59         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
        3.12         1.32         1.28         1.28         1.12         0.79 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
       18.64         0.53         6.48        17.65        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       29.72        15.19         5.06         0.13        23.64        15.65 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
        1.08         1.51        22.16        15.42         1.45         0.95 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.26        17.72         4.80         6.64        17.62         0.49 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
        1.58         1.61         2.17        16.93        20.71        21.40 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B 
       20.58        19.59        15.81        20.19        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46S 
        4.57        39.98        42.38        88.64        47.80        54.35 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 
       72.30        13.61        39.25        40.96        56.81        39.09 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
       55.43        37.02        38.37        87.98        42.90        28.41 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
       28.47         1.02        18.84        14.04        12.66         5.72 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       13.87         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 
        7.56         2.30         2.93        12.56         4.24         2.01 
TCGA-73-4658 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
       52.60        29.98        15.35         4.31         5.39         1.25 
TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
       39.09        23.51        11.18       163.10        27.16        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       20.58        35.93        21.90        19.50        38.50        32.09 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       88.14        10.75        10.55        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
       77.59        10.55       110.50         5.88        34.39        13.87 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       19.89        16.70        24.49         4.08         4.57        24.33 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 
       15.75        16.08        15.65        15.85        21.47         1.15 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       13.91        30.84        27.58         0.62        14.96        13.32 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
        3.81        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
       19.82         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        1.12         1.22         2.86        15.68        15.65        27.29 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       21.40        18.18        31.69        63.52        43.79         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
        0.59         0.72        18.67        17.92         5.39        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 
       15.39        14.30        20.58        20.19        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 
       17.75        20.84        18.67        20.68        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        21.63        23.80        18.08        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       19.00        14.30         0.20        14.53         1.91        17.46 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 
       12.59        11.87         2.76        58.45        86.04         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI 
        5.29        41.59        31.23        29.46        14.66        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A55A TCGA-NJ-A55O 
       11.15        19.13        71.05        62.60         0.26         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82         9.70        59.11        16.87 

  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                         0.00                          0.13 
  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                       153.04                        223.96 
  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE 
                       19.730                        17.835 
[1] "0.0 - 153.0 (19.7)" "0.1 - 224.0 (17.8)"
[1] "hr=" "1.3"
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(6Q11.1) MUTATED         0       26       36        0        15
  DEL PEAK 12(6Q11.1) WILD-TYPE       5      109      104        1        36
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 12(6Q11.1) MUTATED          15         33          3        5
  DEL PEAK 12(6Q11.1) WILD-TYPE        58         39          8       21
D33V3, multiclass
            clus
vv           DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                            26                           109
  STAGE IB                            36                           104
  STAGE II                             0                             1
  STAGE IIA                           15                            36
  STAGE IIB                           15                            58
  STAGE IIIA                          33                            39
  STAGE IIIB                           3                             8
  STAGE IV                             5                            21
[1] 9 2
[1] 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(6Q11.1) MUTATED    41  75  13   5
  DEL PEAK 12(6Q11.1) WILD-TYPE 129 203  33  14
D33V4, multiclass
    clus
vv   DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  T1                          41                           129
  T2                          75                           203
  T3                          13                            33
  T4                           5                            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 12(6Q11.1) MUTATED    75  26    32
  DEL PEAK 12(6Q11.1) WILD-TYPE 257  70    44
D33V5, multiclass
       clus
vv      DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  N0                             75                           257
  N1                             26                            70
  N2+N3                          32                            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                               cls
clus                              0   1
  DEL PEAK 12(6Q11.1) MUTATED    90   5
  DEL PEAK 12(6Q11.1) WILD-TYPE 258  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q11.1) MUTATED     90    5
  DEL PEAK 12(6Q11.1) WILD-TYPE  258   20
   clus
vv  DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  0                          90                           258
  1                           5                            20
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(6Q11.1) MUTATED    78  56
  DEL PEAK 12(6Q11.1) WILD-TYPE 197 184
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q11.1) MUTATED     78   56
  DEL PEAK 12(6Q11.1) WILD-TYPE  197  184
        clus
vv       DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  FEMALE                          78                           197
  MALE                            56                           184
[1] 2 2
[1] FALSE
D33V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                            3
  DEL PEAK 12(6Q11.1) WILD-TYPE                         16
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 12(6Q11.1) MUTATED                                  30
  DEL PEAK 12(6Q11.1) WILD-TYPE                                77
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(6Q11.1) MUTATED                                                   85
  DEL PEAK 12(6Q11.1) WILD-TYPE                                                234
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 12(6Q11.1) MUTATED                                            2
  DEL PEAK 12(6Q11.1) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 12(6Q11.1) MUTATED                                               4
  DEL PEAK 12(6Q11.1) WILD-TYPE                                            15
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                                0
  DEL PEAK 12(6Q11.1) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                                    0
  DEL PEAK 12(6Q11.1) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                              0
  DEL PEAK 12(6Q11.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                               7
  DEL PEAK 12(6Q11.1) WILD-TYPE                            16
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                                 0
  DEL PEAK 12(6Q11.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                                               0
  DEL PEAK 12(6Q11.1) WILD-TYPE                                             5
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 12(6Q11.1) MUTATED                              3
  DEL PEAK 12(6Q11.1) WILD-TYPE                            7
D33V9, multiclass
                                                    clus
vv                                                   DEL PEAK 12(6Q11.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          85
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                4
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           0
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                7
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                0
  MUCINOUS (COLLOID) CARCINOMA                                                 3
                                                    clus
vv                                                   DEL PEAK 12(6Q11.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           234
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 15
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 16
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  5
  MUCINOUS (COLLOID) CARCINOMA                                                   7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, binary
                               cls
clus                              0   1
  DEL PEAK 12(6Q11.1) MUTATED     8 126
  DEL PEAK 12(6Q11.1) WILD-TYPE  13 368
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q11.1) MUTATED      8  126
  DEL PEAK 12(6Q11.1) WILD-TYPE   13  368
     clus
vv    DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  NO                            8                            13
  YES                         126                           368
[1] 2 2
[1] FALSE
D33V11, continuous
D33V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(6Q11.1) MUTATED    92   1   1   6
  DEL PEAK 12(6Q11.1) WILD-TYPE 251  11   3  20
D33V13, multiclass
    clus
vv   DEL PEAK 12(6Q11.1) MUTATED DEL PEAK 12(6Q11.1) WILD-TYPE
  R0                          92                           251
  R1                           1                            11
  R2                           1                             3
  RX                           6                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(6Q11.1) MUTATED                                  0     1
  DEL PEAK 12(6Q11.1) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q11.1) MUTATED                          12   105
  DEL PEAK 12(6Q11.1) WILD-TYPE                        39   284
D33V14, multiclass
                                  clus
vv                                 DEL PEAK 12(6Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                    105
                                  clus
vv                                 DEL PEAK 12(6Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   39
  WHITE                                                      284
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V15, binary
                               cls
clus                              0   1
  DEL PEAK 12(6Q11.1) MUTATED     1  96
  DEL PEAK 12(6Q11.1) WILD-TYPE   6 286
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q11.1) MUTATED      1   96
  DEL PEAK 12(6Q11.1) WILD-TYPE    6  286
                        clus
vv                       DEL PEAK 12(6Q11.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          96
                        clus
vv                       DEL PEAK 12(6Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           286
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 13(6Q22.31) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 13(6Q22.31) MUTATED   158  81
  DEL PEAK 13(6Q22.31) WILD-TYPE 179  73
  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                           239                            252 
  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                            81                             73 
$`DEL PEAK 13(6Q22.31) MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4405 
        3.98        19.96        37.02         0.00         9.96        20.05 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-5425 
        2.99        29.98        21.99        26.01        25.02        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 TCGA-38-4631 TCGA-38-4632 
       22.03         9.04         0.46         5.98        11.64        44.61 
TCGA-38-6178 TCGA-44-2659 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 
       14.73        44.94         3.19        25.02        38.89        34.06 
TCGA-44-5644 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       28.37        21.63        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7670 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SU 
       14.60        29.00        12.66         8.55        11.08        13.45 
TCGA-49-4486 TCGA-49-4488 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 
       76.21        28.57        35.54        14.07         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
       29.75        55.89        29.26        17.16        11.64       153.04 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-50-5051 TCGA-50-5068 
        8.55        40.41        37.32       123.58        15.72        49.28 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 
       40.60        78.67        21.47        18.64        29.03        22.55 
TCGA-50-6590 TCGA-50-6593 TCGA-50-6594 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       42.35        11.05        12.16        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 
        9.21        23.05        48.62        45.21         0.07        32.65 
TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6981 TCGA-55-6983 TCGA-55-6985 
       42.51         0.82        48.49        45.34        60.03        40.54 
TCGA-55-6986 TCGA-55-7283 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7815 
      107.21         1.15         1.32        23.18         1.28         1.78 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 
       18.64        17.65         6.15        19.82        29.72         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8207 
       19.66        19.73         0.13        15.65        17.98         2.17 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8615 
        0.76         0.36         0.49         0.30         0.10         0.49 
TCGA-55-8616 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A490 TCGA-55-A494 TCGA-62-8395 
        1.58        22.65        20.71         1.58        15.81        39.98 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       14.60        49.25        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
       72.30        13.61        39.25        29.92        20.65        39.09 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       37.02        87.98         2.04        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3773 TCGA-67-6216 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 
       20.05        14.04         4.64         6.64        22.68        13.61 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         2.30         2.93        14.01        13.45 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 
       26.73         7.04        52.60        23.38        26.30         1.32 
TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7146 TCGA-78-7149 TCGA-78-7152 
       39.09        23.51        11.18         5.69        35.93        39.52 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 
       24.99        32.09         5.88        64.90         7.07       104.19 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 
       88.14        31.20         8.02        53.33        39.35        10.55 
TCGA-78-7633 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       32.68        77.59        27.09        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8075 
       13.87        20.55        19.43        16.70        24.49        15.75 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8672 
       15.65        15.85        23.05        21.47        14.60         0.62 
TCGA-86-8674 TCGA-86-A456 TCGA-91-6831 TCGA-91-7771 TCGA-91-A4BD TCGA-93-7347 
       13.32        13.32        10.19        16.18        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 
        4.18         6.12         1.22        18.67        12.39        15.65 
TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 
        2.76        18.18        19.89        64.60        25.48         5.95 
TCGA-97-7938 TCGA-97-8174 TCGA-97-8176 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M2 
        0.59         5.39        15.39        21.60        21.44        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 
       17.75        20.84        20.68        24.56        34.85         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
       24.30        23.80        19.00         3.81         0.20        14.53 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       12.59        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
       49.35        37.35        58.85         2.43        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       11.05        14.10        11.15        19.13        73.91        71.05 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A7XG 
        0.13         1.64        29.13         0.26         9.70 

$`DEL PEAK 13(6Q22.31) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4389 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
       50.07        14.01        45.01        24.03        47.05         8.02 
TCGA-05-4403 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 
       19.00        14.96         9.01        12.00        30.02        26.01 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5715 
       25.02        24.00        15.02        15.02         4.96         2.04 
TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        7.40         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       28.41        35.28        26.30         4.37        43.53        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 
       13.15        24.36        42.08        42.77        37.15        38.24 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
        6.25        26.56        33.30        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-7660 TCGA-44-7661 
        9.93        27.78        23.15        23.18        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
        7.17        36.07        18.87        17.59        23.64         3.25 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4487 
       15.98        15.32         9.44        11.54        13.64        28.11 
TCGA-49-4490 TCGA-49-4501 TCGA-49-4506 TCGA-49-6742 TCGA-49-6743 TCGA-49-6767 
       12.66        46.72        32.84        14.63        12.13        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARQ TCGA-49-AARR 
       22.26        63.95        62.24        28.90       211.82       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
        9.86        20.52        71.47        70.55        60.16        31.04 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 
        8.22         9.27        14.27         8.45        15.12        25.12 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
        3.91        25.55         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-55-1594 TCGA-55-5899 TCGA-55-6712 
       25.61         7.59        27.25        38.73         2.86         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 
       40.73        15.25         3.88         5.49         7.79         2.20 
TCGA-55-6982 TCGA-55-6984 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 
       32.71        24.99        70.26         0.59         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 
        0.13         3.12         1.28         1.12         0.79         0.53 
TCGA-55-7910 TCGA-55-7995 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 
        6.48         0.16        15.19         5.06        23.64         1.08 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 
        1.51        22.16        15.42         1.45         0.95         0.26 
TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 
       17.72         4.80         6.64        17.62         1.61         2.17 
TCGA-55-8621 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF 
       16.93        21.40        20.58        19.59         0.92        20.19 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46O 
       19.99        17.95         4.57        42.38        88.64        47.80 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 
       40.96        56.81        55.43        38.37        42.90         1.02 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 TCGA-69-7761 TCGA-69-7765 
       18.84        12.66         5.72        13.87         6.12         5.42 
TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
       12.56         4.24         2.01        29.98        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
        5.39         1.25       163.10        27.16        19.27        20.58 
TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 
       21.90        19.50        38.50        22.29       223.96         8.48 
TCGA-78-7220 TCGA-78-7539 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 
       26.53        10.75       214.62        39.75        10.55       110.50 
TCGA-86-6851 TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
        5.88        19.89         4.08         4.57        24.33         0.79 
TCGA-86-8076 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
       16.08         1.15        13.91        30.84        27.58        14.96 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
        3.81        17.62        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
        1.97         2.60        13.71        12.23        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-93-A4JN 
        1.15        16.60        14.27         1.18         1.45        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 
        1.08        19.00        17.29         1.12         2.86        15.68 
TCGA-95-8039 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
       27.29        21.40        31.69        63.52        43.79         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
       18.67        17.92        18.12        16.41        14.30        20.58 
TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R 
       20.19        19.76        18.67        36.76         1.45        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A743 
       18.08        35.47        16.44        14.30         1.91        17.46 
TCGA-L9-A8F4 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       11.87        86.04         5.49         5.29        41.59        31.23 
TCGA-MP-A4TH TCGA-NJ-A4YG TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       14.66        62.60         0.43        19.82        59.11        16.87 

  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                          0.00                           0.13 
  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                        153.04                         223.96 
  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE 
                         19.82                          17.11 
[1] "0.0 - 153.0 (19.8)" "0.1 - 224.0 (17.1)"
[1] "hr=" "1.1"
D34V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(6Q22.31) MUTATED         1       56       69        0        29
  DEL PEAK 13(6Q22.31) WILD-TYPE       4       79       71        1        22
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 13(6Q22.31) MUTATED          33         42          7       13
  DEL PEAK 13(6Q22.31) WILD-TYPE        40         30          4       13
D34V3, multiclass
            clus
vv           DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             56                             79
  STAGE IB                             69                             71
  STAGE II                              0                              1
  STAGE IIA                            29                             22
  STAGE IIB                            33                             40
  STAGE IIIA                           42                             30
  STAGE IIIB                            7                              4
  STAGE IV                             13                             13
[1] 9 2
[1] 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(6Q22.31) MUTATED    75 139  25  11
  DEL PEAK 13(6Q22.31) WILD-TYPE  95 139  21   8
D34V4, multiclass
    clus
vv   DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  T1                           75                             95
  T2                          139                            139
  T3                           25                             21
  T4                           11                              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 13(6Q22.31) MUTATED   155  50    41
  DEL PEAK 13(6Q22.31) WILD-TYPE 177  46    35
D34V5, multiclass
       clus
vv      DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  N0                             155                            177
  N1                              50                             46
  N2+N3                           41                             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                                cls
clus                               0   1
  DEL PEAK 13(6Q22.31) MUTATED   170  13
  DEL PEAK 13(6Q22.31) WILD-TYPE 178  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(6Q22.31) MUTATED    170   13
  DEL PEAK 13(6Q22.31) WILD-TYPE  178   12
   clus
vv  DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  0                          170                            178
  1                           13                             12
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                               0   1
  DEL PEAK 13(6Q22.31) MUTATED   127 124
  DEL PEAK 13(6Q22.31) WILD-TYPE 148 116
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(6Q22.31) MUTATED    127  124
  DEL PEAK 13(6Q22.31) WILD-TYPE  148  116
        clus
vv       DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  FEMALE                          127                            148
  MALE                            124                            116
[1] 2 2
[1] FALSE
D34V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                            9
  DEL PEAK 13(6Q22.31) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 13(6Q22.31) MUTATED                                  61
  DEL PEAK 13(6Q22.31) WILD-TYPE                                46
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(6Q22.31) MUTATED                                                  150
  DEL PEAK 13(6Q22.31) WILD-TYPE                                                169
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 13(6Q22.31) MUTATED                                            2
  DEL PEAK 13(6Q22.31) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 13(6Q22.31) MUTATED                                               8
  DEL PEAK 13(6Q22.31) WILD-TYPE                                            11
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                                1
  DEL PEAK 13(6Q22.31) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                                    1
  DEL PEAK 13(6Q22.31) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                              0
  DEL PEAK 13(6Q22.31) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                              13
  DEL PEAK 13(6Q22.31) WILD-TYPE                            10
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                                 1
  DEL PEAK 13(6Q22.31) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                                               2
  DEL PEAK 13(6Q22.31) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 13(6Q22.31) MUTATED                              3
  DEL PEAK 13(6Q22.31) WILD-TYPE                            7
D34V9, multiclass
                                                    clus
vv                                                   DEL PEAK 13(6Q22.31) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          150
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 8
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                13
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   DEL PEAK 13(6Q22.31) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            169
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  11
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  10
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   3
  MUCINOUS (COLLOID) CARCINOMA                                                    7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, binary
                                cls
clus                               0   1
  DEL PEAK 13(6Q22.31) MUTATED    12 239
  DEL PEAK 13(6Q22.31) WILD-TYPE   9 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(6Q22.31) MUTATED     12  239
  DEL PEAK 13(6Q22.31) WILD-TYPE    9  255
     clus
vv    DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  NO                            12                              9
  YES                          239                            255
[1] 2 2
[1] FALSE
D34V11, continuous
D34V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 13(6Q22.31) MUTATED   177   5   1  10
  DEL PEAK 13(6Q22.31) WILD-TYPE 166   7   3  16
D34V13, multiclass
    clus
vv   DEL PEAK 13(6Q22.31) MUTATED DEL PEAK 13(6Q22.31) WILD-TYPE
  R0                          177                            166
  R1                            5                              7
  R2                            1                              3
  RX                           10                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(6Q22.31) MUTATED                                  0     4
  DEL PEAK 13(6Q22.31) WILD-TYPE                                1     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(6Q22.31) MUTATED                          23   193
  DEL PEAK 13(6Q22.31) WILD-TYPE                        28   196
D34V14, multiclass
                                  clus
vv                                 DEL PEAK 13(6Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     193
                                  clus
vv                                 DEL PEAK 13(6Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    28
  WHITE                                                       196
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V15, binary
                                cls
clus                               0   1
  DEL PEAK 13(6Q22.31) MUTATED     5 181
  DEL PEAK 13(6Q22.31) WILD-TYPE   2 201
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(6Q22.31) MUTATED      5  181
  DEL PEAK 13(6Q22.31) WILD-TYPE    2  201
                        clus
vv                       DEL PEAK 13(6Q22.31) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          181
                        clus
vv                       DEL PEAK 13(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            201
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 14(6Q26) MUTATION ANALYSIS
D35V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 14(6Q26) MUTATED   163  82
  DEL PEAK 14(6Q26) WILD-TYPE 174  72
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                        245                         246 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                         82                          72 
$`DEL PEAK 14(6Q26) MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4405 
        3.98        19.96        45.01        37.02         0.00        20.05 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4434 
        2.99        29.98        21.99        26.01        25.02        15.02 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 
       29.00        22.03         9.04         0.46         5.98        97.74 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 
       11.64        44.61        14.73        46.98        44.94        42.08 
TCGA-44-2666 TCGA-44-3917 TCGA-44-3918 TCGA-44-5644 TCGA-44-5645 TCGA-44-6147 
        3.19        38.89        34.06        28.37        12.59        27.78 
TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7670 
       21.63        32.45        61.28        16.44        14.60        29.00 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 
       12.66         8.55        11.08        13.45        76.21        28.57 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       35.54        14.07         8.81        29.46        29.75        55.89 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AAR9 TCGA-49-AARE 
       29.26        17.16        11.64       153.04         8.55        40.41 
TCGA-49-AARN TCGA-49-AARO TCGA-50-5051 TCGA-50-5068 TCGA-50-5932 TCGA-50-5933 
       37.32       123.58        15.72        49.28        40.60        78.67 
TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6594 
       21.47        18.64        29.03        22.55        42.35        12.16 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       10.13        34.29        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6971 
       48.62        45.21         0.07        32.65        42.51         0.82 
TCGA-55-6972 TCGA-55-6981 TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 TCGA-55-7576 
       48.49        45.34        60.03        40.54         1.15         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 
       23.18         1.28         1.78        18.64        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
       19.82         0.16        29.72         3.29        19.66        19.73 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8207 TCGA-55-8302 
        5.06         0.13        15.65        17.98         2.17         0.76 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8615 TCGA-55-A48X 
        0.36         0.49         0.30         0.10         0.49        22.65 
TCGA-55-A48Y TCGA-55-A494 TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O 
       20.71        15.81        39.98        14.60        49.25        47.80 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       56.71        54.35        67.96        72.30        13.61        39.25 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 
       29.92        56.81        20.65        39.09        37.02        87.98 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 
        2.04        28.41        51.25        28.47        20.05        14.04 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 
        4.64         6.64        22.68        13.61         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K 
        2.30         2.93        14.01        13.45        26.73         7.04 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
        2.01        52.60        23.38        26.30         4.31         1.32 
TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7146 TCGA-78-7149 TCGA-78-7152 
       39.09        23.51        11.18         5.69        35.93        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 
       24.99        19.50        32.09         5.88        64.90       104.19 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
       88.14        26.53        31.20         8.02        53.33        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       10.55        32.68        77.59        27.09        12.36        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 
       34.39        13.87        20.55        19.43        16.70        24.49 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8671 
       15.75        15.65        15.85        23.05        14.60        27.58 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-91-6831 TCGA-91-6849 TCGA-91-7771 
        0.62        13.32        13.32        10.19         1.15        16.18 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JQ TCGA-95-7043 
        1.18        19.82         9.76         4.18        17.29         1.22 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP 
       18.67        12.39        15.65         2.76        18.18        19.89 
TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8174 TCGA-97-8176 
       64.60        25.48         5.95         0.59         5.39        15.39 
TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       21.60        20.19        21.44        20.52        17.75        20.84 
TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       20.68        34.85        36.76         5.59        24.30        23.80 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N4 
       19.00         3.81         0.20        14.53        12.59        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 
        2.76        86.14        58.45        49.35        37.35        58.85 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
        2.43        29.46        11.05        14.10        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       73.91        71.05         0.13         1.64         0.26 

$`DEL PEAK 14(6Q26) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
       50.07        14.01         9.96        24.03        47.05         8.02 
TCGA-05-4403 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 
       19.00        14.96         9.01        12.00        30.02        26.01 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5715 TCGA-35-4122 
       25.02        24.00        15.02         4.96         2.04         7.40 
TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
        8.68       120.79        37.71        49.05        28.41        35.28 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 
       26.30         4.37        43.53        13.15        24.36        42.77 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       25.02        37.15        38.24         6.25        26.56        33.30 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 
       23.77        10.78         9.93        23.15        23.18        63.72 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 
       19.46        12.03         7.17        36.07        18.87        17.59 
TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       23.64         3.25        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-49-4487 TCGA-49-4490 TCGA-49-4501 TCGA-49-4506 TCGA-49-6742 
       13.64        28.11        12.66        46.72        32.84        14.63 
TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       12.13        22.26        22.26        63.95        62.24        28.90 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      211.82       164.12         9.86        20.52        71.47        70.55 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 
       60.16        31.04         8.22         9.27        14.27         8.45 
TCGA-50-5939 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 
       15.12        25.12         3.91        25.55        11.05         6.21 
TCGA-50-6597 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-55-1594 
       41.69         0.72        25.61         7.59        27.25        38.73 
TCGA-55-5899 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6975 TCGA-55-6978 
        2.86         0.79        40.73        15.25         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6982 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 
        7.79         2.20        32.71        24.99       107.21        70.26 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7726 
        0.59         7.99         0.20         0.13         3.12         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-8087 TCGA-55-8096 
        1.12         0.79         0.53         6.48        15.19        23.64 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
        1.08         1.51        22.16        15.42         1.45         0.95 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
        0.26        17.72         4.80         6.64        17.62         1.58 
TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        1.61         2.17        16.93        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       19.59         0.92        20.19        19.99        17.95         4.57 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46P TCGA-62-A471 TCGA-64-1679 TCGA-64-1681 
       42.38        88.64        19.53        40.96        55.43        38.37 
TCGA-64-5778 TCGA-67-3770 TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-67-6217 
       42.90         1.02        18.84        12.66         5.72        13.87 
TCGA-69-7761 TCGA-69-7765 TCGA-69-7980 TCGA-69-8255 TCGA-73-4662 TCGA-73-4668 
        6.12         5.42        12.56         4.24        29.98        15.35 
TCGA-73-4676 TCGA-73-4677 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
        5.39         1.25       163.10        27.16        19.27        20.58 
TCGA-78-7150 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7166 
       21.90        38.50        22.29         7.07       223.96         8.48 
TCGA-78-7539 TCGA-78-8640 TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 
       10.75       214.62        39.75        10.55       110.50         5.88 
TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 
       19.89         4.08         4.57        24.33         0.79        16.08 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 
       21.47         1.15        13.91        30.84        14.96         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 
        2.60        13.71        12.23        27.68         7.36        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       14.27         1.45         6.12        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VK TCGA-97-7546 
        1.12         2.86        15.68        27.29        21.40        31.69 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 
       63.52        43.79         0.72        18.67        17.92        18.12 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 
       16.41        14.30        20.58        19.76        18.67        24.56 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
        1.45        21.63        18.08        35.47        16.44        14.30 
TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MP-A4T4 TCGA-MP-A4T7 
        1.91        17.46        11.87        27.19        86.04         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TH TCGA-NJ-A4YG 
        5.29        41.59        31.23        10.09        14.66        62.60 
TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       29.13         0.43        19.82         9.70        59.11        16.87 

  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                       0.00                        0.13 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                     153.04                      223.96 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                     19.890                      16.735 
[1] "0.0 - 153.0 (19.9)" "0.1 - 224.0 (16.7)"
[1] "hr=" "1"  
D35V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(6Q26) MUTATED         1       63       68        0        27
  DEL PEAK 14(6Q26) WILD-TYPE       4       72       72        1        24
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 14(6Q26) MUTATED          34         41          6       15
  DEL PEAK 14(6Q26) WILD-TYPE        39         31          5       11
D35V3, multiclass
            clus
vv           DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  STAGE I                            1                           4
  STAGE IA                          63                          72
  STAGE IB                          68                          72
  STAGE II                           0                           1
  STAGE IIA                         27                          24
  STAGE IIB                         34                          39
  STAGE IIIA                        41                          31
  STAGE IIIB                         6                           5
  STAGE IV                          15                          11
[1] 9 2
[1] 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(6Q26) MUTATED    81 139  26   9
  DEL PEAK 14(6Q26) WILD-TYPE  89 139  20  10
D35V4, multiclass
    clus
vv   DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  T1                        81                          89
  T2                       139                         139
  T3                        26                          20
  T4                         9                          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 14(6Q26) MUTATED   158  49    42
  DEL PEAK 14(6Q26) WILD-TYPE 174  47    34
D35V5, multiclass
       clus
vv      DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  N0                          158                         174
  N1                           49                          47
  N2+N3                        42                          34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q26) MUTATED   171  15
  DEL PEAK 14(6Q26) WILD-TYPE 177  10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED    171   15
  DEL PEAK 14(6Q26) WILD-TYPE  177   10
   clus
vv  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  0                       171                         177
  1                        15                          10
[1] 2 2
[1] FALSE
D35V7, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q26) MUTATED   132 124
  DEL PEAK 14(6Q26) WILD-TYPE 143 116
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED    132  124
  DEL PEAK 14(6Q26) WILD-TYPE  143  116
        clus
vv       DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  FEMALE                       132                         143
  MALE                         124                         116
[1] 2 2
[1] FALSE
D35V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                           10
  DEL PEAK 14(6Q26) WILD-TYPE                          9
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 14(6Q26) MUTATED                                  61
  DEL PEAK 14(6Q26) WILD-TYPE                                46
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(6Q26) MUTATED                                                  154
  DEL PEAK 14(6Q26) WILD-TYPE                                                165
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 14(6Q26) MUTATED                                            2
  DEL PEAK 14(6Q26) WILD-TYPE                                          3
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 14(6Q26) MUTATED                                               6
  DEL PEAK 14(6Q26) WILD-TYPE                                            13
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                                1
  DEL PEAK 14(6Q26) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                                    1
  DEL PEAK 14(6Q26) WILD-TYPE                                  2
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                              0
  DEL PEAK 14(6Q26) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                              15
  DEL PEAK 14(6Q26) WILD-TYPE                             8
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                                 1
  DEL PEAK 14(6Q26) WILD-TYPE                               0
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                                               2
  DEL PEAK 14(6Q26) WILD-TYPE                                             3
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 14(6Q26) MUTATED                              3
  DEL PEAK 14(6Q26) WILD-TYPE                            7
D35V9, multiclass
                                                    clus
vv                                                   DEL PEAK 14(6Q26) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       154
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                 2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                              6
  LUNG CLEAR CELL ADENOCARCINOMA                                             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                         1
  LUNG MUCINOUS ADENOCARCINOMA                                               0
  LUNG PAPILLARY ADENOCARCINOMA                                             15
  LUNG SIGNET RING ADENOCARCINOMA                                            1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                              2
  MUCINOUS (COLLOID) CARCINOMA                                               3
                                                    clus
vv                                                   DEL PEAK 14(6Q26) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         165
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               13
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 2
  LUNG PAPILLARY ADENOCARCINOMA                                                8
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                3
  MUCINOUS (COLLOID) CARCINOMA                                                 7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q26) MUTATED    13 243
  DEL PEAK 14(6Q26) WILD-TYPE   8 251
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED     13  243
  DEL PEAK 14(6Q26) WILD-TYPE    8  251
     clus
vv    DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  NO                         13                           8
  YES                       243                         251
[1] 2 2
[1] FALSE
D35V11, continuous
D35V12, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 14(6Q26) MUTATED   179   4   2   9
  DEL PEAK 14(6Q26) WILD-TYPE 164   8   2  17
D35V13, multiclass
    clus
vv   DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  R0                       179                         164
  R1                         4                           8
  R2                         2                           2
  RX                         9                          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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(6Q26) MUTATED                                  0     4
  DEL PEAK 14(6Q26) WILD-TYPE                                1     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(6Q26) MUTATED                          24   197
  DEL PEAK 14(6Q26) WILD-TYPE                        27   192
D35V14, multiclass
                                  clus
vv                                 DEL PEAK 14(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               24
  WHITE                                                  197
                                  clus
vv                                 DEL PEAK 14(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V15, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q26) MUTATED     5 188
  DEL PEAK 14(6Q26) WILD-TYPE   2 194
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED      5  188
  DEL PEAK 14(6Q26) WILD-TYPE    2  194
                        clus
vv                       DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             5                           2
  NOT HISPANIC OR LATINO                       188                         194
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 15(8P23.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(8P23.2) MUTATED   162  81
  DEL PEAK 15(8P23.2) WILD-TYPE 175  73
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          243                           248 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                           81                            73 
$`DEL PEAK 15(8P23.2) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4402 
       50.07        45.01        37.02         0.00        47.05         8.02 
TCGA-05-4420 TCGA-05-4425 TCGA-05-4427 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 
       29.98        21.99        26.01        24.00        29.00        22.03 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        7.40         5.98        97.74        37.71        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2662 
       35.28        11.64        14.73        46.98        13.15        42.08 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       42.77         3.19        25.02        38.89        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7660 
        9.93        21.63        23.18        32.45        16.44        19.46 
TCGA-44-7662 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
        7.17        29.00        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 
       15.98        28.11        28.57        12.66        46.72        14.07 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV 
       29.46        29.75        12.13        11.64        22.26        22.26 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-50-5045 TCGA-50-5049 
       28.90         8.55        37.32       123.58        71.47        70.55 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       31.04        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 
       78.67        15.12        18.64         3.91        11.05        12.16 
TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
       41.69         0.72        10.13        34.29        30.54         9.21 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 
       23.05        38.73        48.62        45.21         2.86        42.51 
TCGA-55-6969 TCGA-55-6975 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       40.73         3.88         7.79         2.20        45.34        32.71 
TCGA-55-6985 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
       40.54         1.15         0.20         0.13         3.12         1.32 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
        1.28         1.12        18.64         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 
       29.72         5.06        23.64        15.65         1.08         2.17 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8614 TCGA-55-8616 
        1.45         0.76         0.36        17.72        17.62         1.58 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B 
       20.71         1.58        20.58         0.92        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R 
        4.57        39.98        42.38        49.25        47.80        56.71 
TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
       67.96        29.92        56.81        20.65        39.09        55.43 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       38.37         2.04        42.90        28.47         1.02        20.05 
TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       18.84        13.87         6.64         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 
       12.56         4.24        26.73         7.04         2.01        29.98 
TCGA-73-4668 TCGA-73-4670 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7150 
       15.35         4.31        39.09        23.51        11.18        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7159 TCGA-78-7167 TCGA-78-7536 
       39.52        24.99        38.50        64.90        88.14         8.02 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 TCGA-86-6851 TCGA-86-7713 
       10.55       214.62        10.55       110.50         5.88        13.87 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 
       19.43        19.89        24.49         4.08         0.79        15.75 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-A456 
       15.85        23.05         1.15        13.91        30.84        13.32 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
        3.81        17.62        13.64        13.71        27.68         7.36 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 
        1.18        19.82         6.12        17.29         1.12         1.22 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 
        2.86        18.67        12.39        15.68        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 
        2.76        21.40        18.18        31.69        25.48         5.95 
TCGA-97-7938 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-99-7458 
        0.59        21.60        21.44        17.75        20.68        24.56 
TCGA-99-8032 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
        1.45        24.30        23.80        18.08        35.47        19.00 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
        0.20        14.53         1.91        12.59        11.87        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
        2.76        86.14        58.45        86.04         5.49        41.59 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-NJ-A4YI 
       31.23         2.43        11.05        11.15        71.05         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-O1-A52J 
       29.13         0.43        59.11 

$`DEL PEAK 15(8P23.2) WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 
        3.98        19.96        14.01         9.96        24.03        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 
       20.05         2.99        14.96         9.01        12.00        30.02 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       26.01        25.02        25.02        15.02        15.02         4.96 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4632 
        9.04         2.04         0.46         8.68       120.79        44.61 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 TCGA-44-2661 TCGA-44-3396 
       26.30         4.37        43.53        44.94        24.36        37.15 
TCGA-44-3398 TCGA-44-6147 TCGA-44-6148 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 
       38.24        27.78        23.15        63.72        61.28        14.60 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-A47A TCGA-44-A47B 
       12.03        36.07        18.87        17.59        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 
       11.08        11.54        13.64        13.45        76.21        35.54 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 
       32.84         8.81        55.89        14.63        29.26        17.16 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR 
      153.04        63.95        62.24        40.41       211.82       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5935 TCGA-50-5936 
        9.86        20.52        15.72        60.16        21.47         8.45 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 
       29.03        25.12        22.55        42.35        25.55         6.21 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-55-6543 TCGA-55-6642 
       25.61         7.59        27.25        13.94         0.07        32.65 
TCGA-55-6712 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6983 
        0.79        15.25         0.82        48.49         5.49        60.03 
TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7724 
       24.99       107.21        70.26         0.59         7.99        23.18 
TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        1.28         0.79         1.78         0.53         6.48        17.65 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8203 
       15.19         3.29        19.66        19.73         0.13        17.98 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
        1.51        22.16        15.42         0.95         0.26         0.49 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8619 
        0.30         0.10         4.80         6.64         0.49         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A492 TCGA-55-A494 
        2.17        16.93        22.65        21.40        19.59        15.81 
TCGA-55-A4DF TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46V 
       20.19        14.60        88.64        19.53        54.35        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 
       13.61        39.25        40.96        37.02        87.98        28.41 
TCGA-64-5781 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 
       51.25        14.04        12.66         5.72         4.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-8253 TCGA-69-8254 
       22.68        13.61         5.42         7.56        14.01        13.45 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       52.60        23.38        26.30         1.32         5.39         1.25 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       19.50        32.09         5.88        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
      223.96         8.48        26.53        31.20        53.33        10.75 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 
       39.35        32.68        39.75        77.59        27.09        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 
       31.13        34.39        20.55        16.70         4.57        24.33 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 TCGA-86-8359 TCGA-86-8671 TCGA-86-8672 
       16.08        15.65        21.47        14.60        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       14.96        13.32        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       10.19         2.60        12.23         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
       14.27         1.45         9.76         4.18        23.61         1.08 
TCGA-93-A4JP TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
       19.00        19.89        64.60        63.52        43.79         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 
       14.30        20.58        20.19        19.76        20.52        20.84 
TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AG 
       18.67        34.85        36.76         5.59        21.63        16.44 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4SY TCGA-MP-A4T2 
       14.30         3.81        17.46        27.19        49.35        37.35 
TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI 
       58.85         5.29        10.09        29.46        14.66        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55R 
       19.13        73.91        62.60         1.64         0.26        19.82 
TCGA-NJ-A7XG TCGA-S2-AA1A 
        9.70        16.87 

  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                         0.00                          0.07 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                       214.62                        223.96 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                        18.67                         17.95 
[1] "0.0 - 214.6 (18.7)" "0.1 - 224.0 (18.0)"
[1] "hr=" "1.2"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(8P23.2) MUTATED         3       63       70        1        28
  DEL PEAK 15(8P23.2) WILD-TYPE       2       72       70        0        23
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 15(8P23.2) MUTATED          43         34          4       10
  DEL PEAK 15(8P23.2) WILD-TYPE        30         38          7       16
D36V3, multiclass
            clus
vv           DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            63                            72
  STAGE IB                            70                            70
  STAGE II                             1                             0
  STAGE IIA                           28                            23
  STAGE IIB                           43                            30
  STAGE IIIA                          34                            38
  STAGE IIIB                           4                             7
  STAGE IV                            10                            16
[1] 9 2
[1] 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(8P23.2) MUTATED    84 143  23   6
  DEL PEAK 15(8P23.2) WILD-TYPE  86 135  23  13
D36V4, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  T1                          84                            86
  T2                         143                           135
  T3                          23                            23
  T4                           6                            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 15(8P23.2) MUTATED   165  48    38
  DEL PEAK 15(8P23.2) WILD-TYPE 167  48    38
D36V5, multiclass
       clus
vv      DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  N0                            165                           167
  N1                             48                            48
  N2+N3                          38                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.2) MUTATED   176  10
  DEL PEAK 15(8P23.2) WILD-TYPE 172  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED    176   10
  DEL PEAK 15(8P23.2) WILD-TYPE  172   15
   clus
vv  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  0                         176                           172
  1                          10                            15
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.2) MUTATED   149 107
  DEL PEAK 15(8P23.2) WILD-TYPE 126 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED    149  107
  DEL PEAK 15(8P23.2) WILD-TYPE  126  133
        clus
vv       DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  FEMALE                         149                           126
  MALE                           107                           133
[1] 2 2
[1] FALSE
D36V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                            8
  DEL PEAK 15(8P23.2) WILD-TYPE                         11
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 15(8P23.2) MUTATED                                  47
  DEL PEAK 15(8P23.2) WILD-TYPE                                60
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 15(8P23.2) MUTATED                                                  170
  DEL PEAK 15(8P23.2) WILD-TYPE                                                149
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 15(8P23.2) MUTATED                                            1
  DEL PEAK 15(8P23.2) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 15(8P23.2) MUTATED                                               8
  DEL PEAK 15(8P23.2) WILD-TYPE                                            11
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                                2
  DEL PEAK 15(8P23.2) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                                    3
  DEL PEAK 15(8P23.2) WILD-TYPE                                  0
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                              1
  DEL PEAK 15(8P23.2) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                               9
  DEL PEAK 15(8P23.2) WILD-TYPE                            14
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                                 1
  DEL PEAK 15(8P23.2) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                                               4
  DEL PEAK 15(8P23.2) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                              2
  DEL PEAK 15(8P23.2) WILD-TYPE                            8
D36V9, multiclass
                                                    clus
vv                                                   DEL PEAK 15(8P23.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           47
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         170
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                8
  LUNG CLEAR CELL ADENOCARCINOMA                                               2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           3
  LUNG MUCINOUS ADENOCARCINOMA                                                 1
  LUNG PAPILLARY ADENOCARCINOMA                                                9
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                4
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   DEL PEAK 15(8P23.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           149
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 11
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             0
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                 14
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  1
  MUCINOUS (COLLOID) CARCINOMA                                                   8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.2) MUTATED    11 245
  DEL PEAK 15(8P23.2) WILD-TYPE  10 249
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED     11  245
  DEL PEAK 15(8P23.2) WILD-TYPE   10  249
     clus
vv    DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  NO                           11                            10
  YES                         245                           249
[1] 2 2
[1] FALSE
D36V11, continuous
D36V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(8P23.2) MUTATED   165   6   2  16
  DEL PEAK 15(8P23.2) WILD-TYPE 178   6   2  10
D36V13, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  R0                         165                           178
  R1                           6                             6
  R2                           2                             2
  RX                          16                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(8P23.2) MUTATED                                  1     5
  DEL PEAK 15(8P23.2) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(8P23.2) MUTATED                          25   194
  DEL PEAK 15(8P23.2) WILD-TYPE                        26   195
D36V14, multiclass
                                  clus
vv                                 DEL PEAK 15(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 25
  WHITE                                                    194
                                  clus
vv                                 DEL PEAK 15(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      195
[1] 4 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 15(8P23.2) MUTATED     6 196
  DEL PEAK 15(8P23.2) WILD-TYPE   1 186
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED      6  196
  DEL PEAK 15(8P23.2) WILD-TYPE    1  186
                        clus
vv                       DEL PEAK 15(8P23.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         196
                        clus
vv                       DEL PEAK 15(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           186
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 16(8P11.21) MUTATION ANALYSIS
D37V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(8P11.21) MUTATED    81  36
  DEL PEAK 16(8P11.21) WILD-TYPE 256 118
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                           117                            374 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                            36                            118 
$`DEL PEAK 16(8P11.21) MUTATED`
TCGA-05-4249 TCGA-05-4402 TCGA-05-4420 TCGA-05-4425 TCGA-38-4631 TCGA-38-6178 
       50.07         8.02        29.98        21.99        11.64        14.73 
TCGA-44-2657 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6775 TCGA-44-6777 
       13.15        28.37        23.77        10.78        23.18        32.45 
TCGA-44-7662 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A4SU TCGA-49-4487 
        7.17        23.64         8.55        15.98        13.45        28.11 
TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-6742 TCGA-49-6743 
       12.66        46.72        14.07         8.81        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-49-AARQ TCGA-50-5049 
       29.26        17.16        11.64        37.32       211.82        70.55 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5939 TCGA-50-6591 TCGA-50-6597 TCGA-53-7813 
       40.60        78.67        15.12         3.91        41.69        13.94 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6972 TCGA-55-6975 TCGA-55-6979 TCGA-55-6985 
       48.62        45.21        48.49         3.88         7.79        40.54 
TCGA-55-7283 TCGA-55-7573 TCGA-55-7726 TCGA-55-7994 TCGA-55-8097 TCGA-55-8302 
        1.15         0.13         1.28        19.82        15.65         0.76 
TCGA-55-8506 TCGA-55-8510 TCGA-55-8615 TCGA-55-A490 TCGA-55-A4DG TCGA-62-8394 
        0.36        17.72         0.49         1.58        19.99         4.57 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46U TCGA-62-A472 TCGA-64-1678 
       49.25        47.80        56.71        67.96        29.92        39.09 
TCGA-64-1679 TCGA-67-3770 TCGA-67-6217 TCGA-69-7978 TCGA-69-7980 TCGA-69-A59K 
       55.43         1.02        13.87         2.30        12.56         7.04 
TCGA-71-6725 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-7498 TCGA-73-7499 
        2.01        29.98        15.35         4.31        39.09        23.51 
TCGA-73-A9RS TCGA-78-7146 TCGA-78-7161 TCGA-78-8640 TCGA-86-7711 TCGA-86-7953 
       11.18         5.69         7.07       214.62        34.39        19.43 
TCGA-86-8054 TCGA-86-8074 TCGA-86-8280 TCGA-86-8359 TCGA-86-8668 TCGA-86-A456 
       24.49         0.79        23.05        14.60        13.91        13.32 
TCGA-86-A4JF TCGA-91-6847 TCGA-91-7771 TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 
       17.62        27.68        16.18        17.29         1.12         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK 
       18.67        12.39        15.68        27.29         2.76        21.40 
TCGA-97-7546 TCGA-97-7938 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M3 TCGA-97-A4M7 
       31.69         0.59        21.60        21.44        17.75        20.68 
TCGA-99-8025 TCGA-J2-8192 TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 
       34.85        24.30        19.00        14.53         1.91        11.87 
TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
       38.63        58.45        86.04         5.49         5.29        41.59 
TCGA-MP-A4TC TCGA-NJ-A4YQ TCGA-O1-A52J 
        2.43        29.13        59.11 

$`DEL PEAK 16(8P11.21) WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        9.96        24.03        47.05        19.00        20.05         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 
       14.96         9.01        12.00        30.02        26.01        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
       25.02        25.02        24.00        15.02        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
       29.00        22.03         9.04         2.04         0.46         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       28.41        35.28        44.61        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 
       46.98        44.94        24.36        42.08        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       25.02        37.15        38.24        38.89        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       26.56        33.30        12.59         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       21.63        63.72        61.28        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 
       12.03        36.07        18.87        29.00        17.59        12.66 
TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
        3.25        15.32         9.44        11.08        11.54        13.64 
TCGA-49-4486 TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 
       76.21        28.57        35.54        32.84        29.46        29.75 
TCGA-49-4514 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 
       55.89        22.26        22.26       153.04        63.95        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V 
       28.90         8.55        40.41       123.58       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47        15.72        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 TCGA-50-5936 TCGA-50-5941 
        8.22         9.27        14.27        21.47         8.45        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 
       29.03        25.12        22.55        42.35        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       12.16         6.21         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 
       27.25        34.29        30.54         9.21        23.05        38.73 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
        2.86         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       15.25         0.82         5.49         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 
       60.03        24.99       107.21        70.26         0.59         7.99 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 
        0.20         3.12         1.32        23.18         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8203 TCGA-55-8205 
       19.73         5.06         0.13        23.64        17.98         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
        1.51         2.17        22.16        15.42         1.45         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.26         0.49         0.30         0.10         4.80         6.64 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
       17.62         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       20.71        21.40        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       20.19        17.95        39.98        42.38        14.60        88.64 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       19.53        54.35        72.30        13.61        39.25        40.96 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        20.65        37.02        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       14.04        12.66         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 
       22.68        13.61         5.42         7.56         6.05         2.93 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-73-4658 TCGA-73-4659 
       14.01        13.45         4.24        26.73        52.60        23.38 
TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-78-7143 TCGA-78-7145 
       26.30         1.32         5.39         1.25       163.10        27.16 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       19.50        38.50        32.09         5.88        64.90        22.29 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
      104.19       223.96         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59        10.55       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
        5.88        31.13        13.87        20.55        19.89        16.70 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57        24.33        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       15.85        21.47         1.15        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       14.96        13.32         3.81        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        7.36         1.15        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
       19.82         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JP TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 
       19.00         1.22        15.65        18.18        19.89        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
       63.52        43.79        25.48         5.95         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       17.92         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 
       20.58        20.19        19.76        20.52        20.84        18.67 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 
       24.56        36.76         1.45         5.59        21.63        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       18.08        35.47        16.44        14.30         3.81         0.20 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY 
       17.46        12.59        27.19         2.76        86.14        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
       37.35        58.85        31.23        10.09        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       14.66        14.10        11.15        19.13        73.91        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64         0.26         0.43        19.82 
TCGA-NJ-A7XG TCGA-S2-AA1A 
        9.70        16.87 

  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                        214.62                         223.96 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                        17.290                         18.755 
[1] "0.1 - 214.6 (17.3)" "0.0 - 224.0 (18.8)"
[1] "hr=" "1"  
D37V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(8P11.21) MUTATED         3       29       27        0        13
  DEL PEAK 16(8P11.21) WILD-TYPE       2      106      113        1        38
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 16(8P11.21) MUTATED          23         18          3        6
  DEL PEAK 16(8P11.21) WILD-TYPE        50         54          8       20
D37V3, multiclass
            clus
vv           DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             29                            106
  STAGE IB                             27                            113
  STAGE II                              0                              1
  STAGE IIA                            13                             38
  STAGE IIB                            23                             50
  STAGE IIIA                           18                             54
  STAGE IIIB                            3                              8
  STAGE IV                              6                             20
[1] 9 2
[1] 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(8P11.21) MUTATED    37  66  16   3
  DEL PEAK 16(8P11.21) WILD-TYPE 133 212  30  16
D37V4, multiclass
    clus
vv   DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  T1                           37                            133
  T2                           66                            212
  T3                           16                             30
  T4                            3                             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 16(8P11.21) MUTATED    74  25    20
  DEL PEAK 16(8P11.21) WILD-TYPE 258  71    56
D37V5, multiclass
       clus
vv      DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  N0                              74                            258
  N1                              25                             71
  N2+N3                           20                             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"
D37V6, binary
                                cls
clus                               0   1
  DEL PEAK 16(8P11.21) MUTATED    78   6
  DEL PEAK 16(8P11.21) WILD-TYPE 270  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED     78    6
  DEL PEAK 16(8P11.21) WILD-TYPE  270   19
   clus
vv  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  0                           78                            270
  1                            6                             19
[1] 2 2
[1] FALSE
D37V7, binary
                                cls
clus                               0   1
  DEL PEAK 16(8P11.21) MUTATED    78  44
  DEL PEAK 16(8P11.21) WILD-TYPE 197 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED     78   44
  DEL PEAK 16(8P11.21) WILD-TYPE  197  196
        clus
vv       DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  FEMALE                           78                            197
  MALE                             44                            196
[1] 2 2
[1] FALSE
D37V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                            4
  DEL PEAK 16(8P11.21) WILD-TYPE                         15
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 16(8P11.21) MUTATED                                  25
  DEL PEAK 16(8P11.21) WILD-TYPE                                82
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(8P11.21) MUTATED                                                   79
  DEL PEAK 16(8P11.21) WILD-TYPE                                                240
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 16(8P11.21) MUTATED                                            1
  DEL PEAK 16(8P11.21) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 16(8P11.21) MUTATED                                               5
  DEL PEAK 16(8P11.21) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                                2
  DEL PEAK 16(8P11.21) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                                    2
  DEL PEAK 16(8P11.21) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                              0
  DEL PEAK 16(8P11.21) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                               3
  DEL PEAK 16(8P11.21) WILD-TYPE                            20
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                                 0
  DEL PEAK 16(8P11.21) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                                               0
  DEL PEAK 16(8P11.21) WILD-TYPE                                             5
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                              1
  DEL PEAK 16(8P11.21) WILD-TYPE                            9
D37V9, multiclass
                                                    clus
vv                                                   DEL PEAK 16(8P11.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           79
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 5
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 3
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 0
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   DEL PEAK 16(8P11.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            240
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  14
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  20
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   5
  MUCINOUS (COLLOID) CARCINOMA                                                    9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, binary
                                cls
clus                               0   1
  DEL PEAK 16(8P11.21) MUTATED     4 118
  DEL PEAK 16(8P11.21) WILD-TYPE  17 376
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED      4  118
  DEL PEAK 16(8P11.21) WILD-TYPE   17  376
     clus
vv    DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  NO                             4                             17
  YES                          118                            376
[1] 2 2
[1] FALSE
D37V11, continuous
D37V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 16(8P11.21) MUTATED    73   4   1  11
  DEL PEAK 16(8P11.21) WILD-TYPE 270   8   3  15
D37V13, multiclass
    clus
vv   DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  R0                           73                            270
  R1                            4                              8
  R2                            1                              3
  RX                           11                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(8P11.21) MUTATED                                  1     4
  DEL PEAK 16(8P11.21) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(8P11.21) MUTATED                          11    93
  DEL PEAK 16(8P11.21) WILD-TYPE                        40   296
D37V14, multiclass
                                  clus
vv                                 DEL PEAK 16(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      93
                                  clus
vv                                 DEL PEAK 16(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    40
  WHITE                                                       296
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V15, binary
                                cls
clus                               0   1
  DEL PEAK 16(8P11.21) MUTATED     2  96
  DEL PEAK 16(8P11.21) WILD-TYPE   5 286
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED      2   96
  DEL PEAK 16(8P11.21) WILD-TYPE    5  286
                        clus
vv                       DEL PEAK 16(8P11.21) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           96
                        clus
vv                       DEL PEAK 16(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            286
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 17(9P23) MUTATION ANALYSIS
D38V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 17(9P23) MUTATED   178  96
  DEL PEAK 17(9P23) WILD-TYPE 159  58
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                        274                         217 
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                         96                          58 
$`DEL PEAK 17(9P23) MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07         3.98        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 
        9.96         8.02        20.05         2.99         9.01        29.98 
TCGA-05-4424 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       30.02        25.02        24.00        15.02         4.96        29.00 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 
        9.04         2.04         7.40        37.71        49.05        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 
       11.64        44.61        14.73         4.37        43.53        13.15 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2668 TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 
       44.94        24.36        25.02        38.89        33.30        28.37 
TCGA-44-6144 TCGA-44-6146 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 
       23.77         9.93        32.45        61.28        16.44         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 
       36.07        18.87        29.00        17.59        12.66         8.55 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        76.21        28.11        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 
       46.72        14.07         8.81        29.46        55.89        14.63 
TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 
       12.13        22.26        22.26       153.04        63.95        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-50-5044 TCGA-50-5055 
       28.90         8.55        37.32       123.58        20.52        60.16 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 
       21.47         8.45        15.12        25.12        22.55        25.55 
TCGA-50-6593 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 
       11.05        41.69         0.72        10.13         7.59        27.25 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 
       30.54        13.94         9.21        23.05        38.73        45.21 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 
        2.86        32.65         0.79         0.82         3.88         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 
       45.34        32.71        40.54       107.21         0.59         1.15 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 
        0.20         0.13         1.32        23.18         1.28         0.53 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
        3.29        19.66        19.73         5.06         0.13        15.65 
TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       17.98         1.51         2.17         0.95         0.36         0.26 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48X TCGA-55-A490 
       17.72         0.10        17.62         0.49        22.65         1.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 
       19.59         0.92        19.99        17.95        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46V TCGA-62-A46Y 
       14.60        88.64        49.25        47.80        72.30        13.61 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       40.96        29.92        39.09        55.43        37.02        38.37 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 
       51.25        28.47         1.02        20.05        18.84        12.66 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7974 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-73-4662 TCGA-73-4666 
        6.05        13.45         4.24        26.73        29.98        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 
       15.35         4.31         1.32        23.51        11.18       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       27.16         5.69        19.27        20.58        35.93        21.90 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
       32.09        22.29         7.07         8.48        88.14        26.53 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 
       39.35        10.55        32.68       214.62        77.59        10.55 
TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
      110.50         5.88        34.39        13.87        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
       16.70        24.49         4.08         4.57         0.79        15.75 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8672 
       15.85        23.05        21.47         1.15        13.91         0.62 
TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       13.32        41.36         1.97         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 TCGA-93-7348 
       27.68         7.36         1.15        14.27         1.18         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-95-7562 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 
        6.12        23.61         2.86        18.67        27.29         2.76 
TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 
       21.40        19.89         5.95         0.59         0.72         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 
       21.44        19.76        18.67        20.68         1.45         5.59 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV 
       24.30        18.08        16.44        14.53        17.46        12.59 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       11.87        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       49.35        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI 
       10.09        29.46        19.13        73.91        71.05         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
       29.13         0.43         9.70        59.11 

$`DEL PEAK 17(9P23) WILD-TYPE`
TCGA-05-4382 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 
       19.96        24.03        47.05        19.00        14.96        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4434 TCGA-05-5428 
       21.99        26.01        26.01        25.02        15.02        22.03 
TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 
        0.46         5.98         8.68        97.74       120.79        28.41 
TCGA-38-7271 TCGA-44-2656 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 
       26.30        46.98        42.08        42.77         3.19        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6145 
       38.24        34.06         6.25        26.56        12.59        10.78 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-7659 
       27.78        23.15        21.63        23.18        63.72        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
       19.46        12.03        23.64         3.25        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-49-4488 TCGA-49-4506 TCGA-49-4512 
        9.44        11.08        11.54        28.57        32.84        29.75 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR 
       29.26        17.16        11.64        40.41       211.82       164.12 
TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5941 
        9.86        71.47        70.55        15.72        31.04        18.64 
TCGA-50-5942 TCGA-50-6590 TCGA-50-6591 TCGA-50-6594 TCGA-50-6595 TCGA-50-8457 
       29.03        42.35         3.91        12.16         6.21        25.61 
TCGA-53-7624 TCGA-55-1595 TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       34.29        48.62         0.07        42.51        40.73        15.25 
TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 TCGA-55-6983 TCGA-55-6984 TCGA-55-6987 
       48.49         5.49         7.79        60.03        24.99        70.26 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        7.99         3.12         1.28         1.12         0.79         1.78 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
       18.64         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 
       29.72        15.19        23.64         1.08        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 
        1.45         0.76         0.49         0.30         4.80         6.64 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
        1.58         1.61         2.17        16.93        20.71        21.40 
TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-A46P TCGA-62-A46R 
       20.58        15.81        20.19         4.57        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 TCGA-64-1676 TCGA-64-1677 TCGA-64-5774 
       54.35        67.96        39.25        56.81        20.65        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-67-3773 TCGA-67-6215 TCGA-69-7765 
        2.04        42.90        28.41        14.04         5.72         5.42 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-A59K 
        7.56         2.30         2.93        12.56        14.01         7.04 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
        2.01        52.60        23.38         5.39         1.25        39.09 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 
       39.52        24.99        19.50        38.50         5.88        64.90 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
      104.19       223.96        31.20         8.02        53.33        10.75 
TCGA-78-8648 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7714 TCGA-86-8073 
       39.75        27.09        12.36        31.13        20.55        24.33 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
       16.08        15.65        14.60        30.84        27.58        14.96 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32         3.81        17.62        13.64        26.47        10.62 
TCGA-91-6831 TCGA-91-7771 TCGA-91-8496 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       10.19        16.18        16.60         1.45        19.82         9.76 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 
        1.08        19.00        17.29         1.12         1.22        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       15.68        15.65        18.18        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       43.79        25.48        18.67        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R 
       17.75        20.84        24.56        34.85        36.76        21.63 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 
       23.80        35.47        19.00        14.30         3.81         0.20 
TCGA-L9-A5IP TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH 
        1.91        37.35        86.04         2.43        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55R 
       14.10        11.15        62.60         1.64         0.26        19.82 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                       0.00                        0.07 
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                     214.62                      223.96 
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                      18.10                       18.64 
[1] "0.0 - 214.6 (18.1)" "0.1 - 224.0 (18.6)"
[1] "hr=" "1.3"
D38V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(9P23) MUTATED         2       68       71        1        32
  DEL PEAK 17(9P23) WILD-TYPE       3       67       69        0        19
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 17(9P23) MUTATED          44         43          7       15
  DEL PEAK 17(9P23) WILD-TYPE        29         29          4       11
D38V3, multiclass
            clus
vv           DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  STAGE I                            2                           3
  STAGE IA                          68                          67
  STAGE IB                          71                          69
  STAGE II                           1                           0
  STAGE IIA                         32                          19
  STAGE IIB                         44                          29
  STAGE IIIA                        43                          29
  STAGE IIIB                         7                           4
  STAGE IV                          15                          11
[1] 9 2
[1] 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(9P23) MUTATED    91 154  26  12
  DEL PEAK 17(9P23) WILD-TYPE  79 124  20   7
D38V4, multiclass
    clus
vv   DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  T1                        91                          79
  T2                       154                         124
  T3                        26                          20
  T4                        12                           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
  DEL PEAK 17(9P23) MUTATED   169  67    43
  DEL PEAK 17(9P23) WILD-TYPE 163  29    33
D38V5, multiclass
       clus
vv      DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  N0                          169                         163
  N1                           67                          29
  N2+N3                        43                          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"
D38V6, binary
                             cls
clus                            0   1
  DEL PEAK 17(9P23) MUTATED   192  15
  DEL PEAK 17(9P23) WILD-TYPE 156  10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(9P23) MUTATED    192   15
  DEL PEAK 17(9P23) WILD-TYPE  156   10
   clus
vv  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  0                       192                         156
  1                        15                          10
[1] 2 2
[1] FALSE
D38V7, binary
                             cls
clus                            0   1
  DEL PEAK 17(9P23) MUTATED   146 138
  DEL PEAK 17(9P23) WILD-TYPE 129 102
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(9P23) MUTATED    146  138
  DEL PEAK 17(9P23) WILD-TYPE  129  102
        clus
vv       DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  FEMALE                       146                         129
  MALE                         138                         102
[1] 2 2
[1] FALSE
D38V8, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                           13
  DEL PEAK 17(9P23) WILD-TYPE                          6
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 17(9P23) MUTATED                                  61
  DEL PEAK 17(9P23) WILD-TYPE                                46
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(9P23) MUTATED                                                  175
  DEL PEAK 17(9P23) WILD-TYPE                                                144
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 17(9P23) MUTATED                                            2
  DEL PEAK 17(9P23) WILD-TYPE                                          3
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 17(9P23) MUTATED                                              11
  DEL PEAK 17(9P23) WILD-TYPE                                             8
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                                1
  DEL PEAK 17(9P23) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                                    3
  DEL PEAK 17(9P23) WILD-TYPE                                  0
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                              1
  DEL PEAK 17(9P23) WILD-TYPE                            1
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                               9
  DEL PEAK 17(9P23) WILD-TYPE                            14
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                                 0
  DEL PEAK 17(9P23) WILD-TYPE                               1
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                                               3
  DEL PEAK 17(9P23) WILD-TYPE                                             2
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 17(9P23) MUTATED                              5
  DEL PEAK 17(9P23) WILD-TYPE                            5
D38V9, multiclass
                                                    clus
vv                                                   DEL PEAK 17(9P23) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       175
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                 2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                             11
  LUNG CLEAR CELL ADENOCARCINOMA                                             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                         3
  LUNG MUCINOUS ADENOCARCINOMA                                               1
  LUNG PAPILLARY ADENOCARCINOMA                                              9
  LUNG SIGNET RING ADENOCARCINOMA                                            0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                              3
  MUCINOUS (COLLOID) CARCINOMA                                               5
                                                    clus
vv                                                   DEL PEAK 17(9P23) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         144
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                8
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           0
  LUNG MUCINOUS ADENOCARCINOMA                                                 1
  LUNG PAPILLARY ADENOCARCINOMA                                               14
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                2
  MUCINOUS (COLLOID) CARCINOMA                                                 5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, binary
                             cls
clus                            0   1
  DEL PEAK 17(9P23) MUTATED    12 272
  DEL PEAK 17(9P23) WILD-TYPE   9 222
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(9P23) MUTATED     12  272
  DEL PEAK 17(9P23) WILD-TYPE    9  222
     clus
vv    DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  NO                         12                           9
  YES                       272                         222
[1] 2 2
[1] FALSE
D38V11, continuous
D38V12, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 17(9P23) MUTATED   187   5   2  18
  DEL PEAK 17(9P23) WILD-TYPE 156   7   2   8
D38V13, multiclass
    clus
vv   DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  R0                       187                         156
  R1                         5                           7
  R2                         2                           2
  RX                        18                           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                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(9P23) MUTATED                                  1     3
  DEL PEAK 17(9P23) WILD-TYPE                                0     4
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(9P23) MUTATED                          29   213
  DEL PEAK 17(9P23) WILD-TYPE                        22   176
D38V14, multiclass
                                  clus
vv                                 DEL PEAK 17(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               29
  WHITE                                                  213
                                  clus
vv                                 DEL PEAK 17(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                    176
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V15, binary
                             cls
clus                            0   1
  DEL PEAK 17(9P23) MUTATED     4 205
  DEL PEAK 17(9P23) WILD-TYPE   3 177
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(9P23) MUTATED      4  205
  DEL PEAK 17(9P23) WILD-TYPE    3  177
                        clus
vv                       DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  HISPANIC OR LATINO                             4                           3
  NOT HISPANIC OR LATINO                       205                         177
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 18(9P21.3) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(9P21.3) MUTATED   179  98
  DEL PEAK 18(9P21.3) WILD-TYPE 158  56
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          277                           214 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                           98                            56 
$`DEL PEAK 18(9P21.3) MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4418 
        9.96         8.02        19.00        20.05         2.99         9.01 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
       29.98        30.02        25.02        24.00        15.02         4.96 
TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-38-4625 TCGA-38-4627 
       29.00         9.04         2.04         7.40        97.74        37.71 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F 
       49.05        28.41        11.64        44.61        14.73         4.37 
TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-3917 TCGA-44-5643 
       43.53        13.15        44.94        24.36        38.89        33.30 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6146 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       28.37        23.77         9.93        32.45        61.28        16.44 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 
        7.17        36.07        18.87        29.00        17.59        12.66 
TCGA-44-8120 TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 
        8.55        13.64        13.45        76.21        28.11        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       35.54        46.72        14.07        32.84         8.81        29.46 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6767 TCGA-49-AAQV 
       55.89        14.63        12.13        17.16        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO 
      153.04        63.95        62.24        28.90         8.55       123.58 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-5946 
       78.67        21.47         8.45        15.12        25.12        22.55 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 
       25.55        11.05        41.69         0.72        10.13         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
       27.25        34.29        30.54        13.94        23.05        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6975 
       45.21         2.86        32.65         0.79         0.82         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        2.20        45.34        32.71        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 
        0.59         1.15         7.99         0.20         0.13         1.32 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7907 TCGA-55-7914 TCGA-55-8089 TCGA-55-8090 
       23.18         1.28         0.53         6.15         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 
       19.73         5.06         0.13        15.65        17.98         1.51 
TCGA-55-8207 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 
        2.17         0.95         0.36         0.26        17.72         0.10 
TCGA-55-8614 TCGA-55-A48X TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DG 
       17.62        22.65         1.58        19.59         0.92        19.99 
TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       17.95        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       47.80        72.30        13.61        40.96        29.92        56.81 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5781 TCGA-64-5815 
       39.09        55.43        37.02        38.37        51.25        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6216 TCGA-67-6217 
        1.02        20.05        18.84        12.66         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7974 TCGA-69-7980 
        6.64         6.12        22.68        13.61         6.05        12.56 
TCGA-69-8255 TCGA-69-8453 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        4.24        26.73        29.98        15.35         4.31         1.32 
TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       23.51        11.18       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 
       20.58        35.93        21.90        32.09        22.29         7.07 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.48        88.14        26.53        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 
      214.62        77.59        10.55        12.36         5.88        34.39 
TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       13.87        19.89        16.70        24.49         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 
        0.79        15.75        15.85        23.05        21.47         1.15 
TCGA-86-8668 TCGA-86-8672 TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.91         0.62        13.32        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8497 
        2.60        12.23        27.68         7.36         1.15        14.27 
TCGA-91-8499 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JQ TCGA-95-7562 
        1.18         4.18         6.12        23.61        17.29         2.86 
TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7547 
       18.67        27.29         2.76        21.40        19.89        64.60 
TCGA-97-7552 TCGA-97-7937 TCGA-97-7938 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
       63.52         5.95         0.59         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       16.41        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD 
       18.67        20.68         1.45         5.59        24.30        18.08 
TCGA-J2-A4AG TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
       16.44        14.53        17.46        12.59        11.87        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T6 
       38.63         2.76        86.14        58.45        49.35        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49         5.29        41.59        31.23        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A7XG 
       11.05        19.13        73.91         0.13        29.13         9.70 
TCGA-O1-A52J 
       59.11 

$`DEL PEAK 18(9P21.3) WILD-TYPE`
TCGA-05-4390 TCGA-05-4397 TCGA-05-4398 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 
       37.02        24.03        47.05        14.96        12.00        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4434 TCGA-05-5428 TCGA-35-3615 
       26.01        26.01        25.02        15.02        22.03         0.46 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4630 TCGA-38-7271 TCGA-44-2656 
        5.98         8.68       120.79        35.28        26.30        46.98 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       42.08        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 
       34.06         6.25        26.56        12.59        10.78        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 
       23.15        21.63        23.18        63.72        14.60        19.46 
TCGA-44-7661 TCGA-44-7672 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       12.03        23.64         3.25        15.98        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-49-4488 TCGA-49-4512 TCGA-49-6744 TCGA-49-6761 
       11.08        11.54        28.57        29.75        29.26        11.64 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       40.41        37.32       211.82       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5941 TCGA-50-5942 
       71.47        70.55        15.72        31.04        18.64        29.03 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6594 TCGA-50-6595 TCGA-50-8457 TCGA-53-A4EZ 
       42.35         3.91        12.16         6.21        25.61         9.21 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
       48.62         0.07        42.51        40.73        15.25        48.49 
TCGA-55-6978 TCGA-55-6979 TCGA-55-6983 TCGA-55-6984 TCGA-55-7574 TCGA-55-7725 
        5.49         7.79        60.03        24.99         3.12         1.28 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        1.12         0.79         1.78        18.64         6.48        17.65 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8205 
       19.82         0.16        29.72        15.19        23.64         1.08 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8511 
       22.16        15.42         1.45         0.76         0.49         0.30 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        4.80         6.64         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A494 TCGA-55-A4DF 
       16.93        20.71        21.40        20.58        15.81        20.19 
TCGA-62-8394 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 
        4.57        19.53        56.71        54.35        67.96        39.25 
TCGA-64-1677 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-67-3773 
       20.65        87.98         2.04        42.90        28.41        14.04 
TCGA-67-6215 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
        5.72         5.42         7.56         2.30         2.93        14.01 
TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
       13.45         7.04         2.01        52.60        23.38        26.30 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        5.39         1.25        39.09        39.52        24.99        19.50 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 
       38.50         5.88        64.90       104.19       223.96        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-8648 TCGA-78-8662 TCGA-83-5908 
        8.02        53.33        10.75        39.75       110.50        27.09 
TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 
       31.13        20.55        19.43        24.33        16.08        15.65 
TCGA-86-8359 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 
       14.60        30.84        27.58        14.96        13.32         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6836 TCGA-91-7771 
       17.62        13.64        26.47        10.62        13.71        16.18 
TCGA-91-8496 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JO TCGA-93-A4JP 
       16.60         1.45        19.82         9.76         1.08        19.00 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VN 
        1.12         1.22        12.39        15.68        15.65        18.18 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       31.69        43.79        25.48         0.72        18.67        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 
       20.19        20.52        17.75        20.84        24.56        34.85 
TCGA-99-8028 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 
       36.76        21.63        23.80        35.47        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A5IP TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TC 
        3.81         0.20         1.91        37.35        86.04         2.43 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP 
       14.66        14.10        11.15        71.05        62.60         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        0.26         0.43        19.82        16.87 

  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                         0.00                          0.07 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                       214.62                        223.96 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                       18.080                        18.655 
[1] "0.0 - 214.6 (18.1)" "0.1 - 224.0 (18.7)"
[1] "hr=" "1.3"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(9P21.3) MUTATED         3       67       72        1        33
  DEL PEAK 18(9P21.3) WILD-TYPE       2       68       68        0        18
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 18(9P21.3) MUTATED          48         45          6       15
  DEL PEAK 18(9P21.3) WILD-TYPE        25         27          5       11
D39V3, multiclass
            clus
vv           DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            67                            68
  STAGE IB                            72                            68
  STAGE II                             1                             0
  STAGE IIA                           33                            18
  STAGE IIB                           48                            25
  STAGE IIIA                          45                            27
  STAGE IIIB                           6                             5
  STAGE IV                            15                            11
[1] 9 2
[1] 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(9P21.3) MUTATED    90 161  27  11
  DEL PEAK 18(9P21.3) WILD-TYPE  80 117  19   8
D39V4, multiclass
    clus
vv   DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  T1                          90                            80
  T2                         161                           117
  T3                          27                            19
  T4                          11                             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 18(9P21.3) MUTATED   173  68    45
  DEL PEAK 18(9P21.3) WILD-TYPE 159  28    31
D39V5, multiclass
       clus
vv      DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  N0                            173                           159
  N1                             68                            28
  N2+N3                          45                            31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED   198  15
  DEL PEAK 18(9P21.3) WILD-TYPE 150  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED    198   15
  DEL PEAK 18(9P21.3) WILD-TYPE  150   10
   clus
vv  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  0                         198                           150
  1                          15                            10
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED   142 148
  DEL PEAK 18(9P21.3) WILD-TYPE 133  92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED    142  148
  DEL PEAK 18(9P21.3) WILD-TYPE  133   92
        clus
vv       DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  FEMALE                         142                           133
  MALE                           148                            92
[1] 2 2
[1] FALSE
D39V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                           12
  DEL PEAK 18(9P21.3) WILD-TYPE                          7
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 18(9P21.3) MUTATED                                  60
  DEL PEAK 18(9P21.3) WILD-TYPE                                47
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(9P21.3) MUTATED                                                  181
  DEL PEAK 18(9P21.3) WILD-TYPE                                                138
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 18(9P21.3) MUTATED                                            3
  DEL PEAK 18(9P21.3) WILD-TYPE                                          2
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 18(9P21.3) MUTATED                                              12
  DEL PEAK 18(9P21.3) WILD-TYPE                                             7
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                                1
  DEL PEAK 18(9P21.3) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                                    3
  DEL PEAK 18(9P21.3) WILD-TYPE                                  0
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                              1
  DEL PEAK 18(9P21.3) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                               9
  DEL PEAK 18(9P21.3) WILD-TYPE                            14
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                                 0
  DEL PEAK 18(9P21.3) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                                               4
  DEL PEAK 18(9P21.3) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                              4
  DEL PEAK 18(9P21.3) WILD-TYPE                            6
D39V9, multiclass
                                                    clus
vv                                                   DEL PEAK 18(9P21.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         181
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               12
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           3
  LUNG MUCINOUS ADENOCARCINOMA                                                 1
  LUNG PAPILLARY ADENOCARCINOMA                                                9
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                4
  MUCINOUS (COLLOID) CARCINOMA                                                 4
                                                    clus
vv                                                   DEL PEAK 18(9P21.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             47
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           138
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  7
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             0
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                 14
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  1
  MUCINOUS (COLLOID) CARCINOMA                                                   6
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED    11 279
  DEL PEAK 18(9P21.3) WILD-TYPE  10 215
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED     11  279
  DEL PEAK 18(9P21.3) WILD-TYPE   10  215
     clus
vv    DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  NO                           11                            10
  YES                         279                           215
[1] 2 2
[1] FALSE
D39V11, continuous
D39V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(9P21.3) MUTATED   193   5   2  17
  DEL PEAK 18(9P21.3) WILD-TYPE 150   7   2   9
D39V13, multiclass
    clus
vv   DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  R0                         193                           150
  R1                           5                             7
  R2                           2                             2
  RX                          17                             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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(9P21.3) MUTATED                                  1     3
  DEL PEAK 18(9P21.3) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(9P21.3) MUTATED                          27   218
  DEL PEAK 18(9P21.3) WILD-TYPE                        24   171
D39V14, multiclass
                                  clus
vv                                 DEL PEAK 18(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    218
                                  clus
vv                                 DEL PEAK 18(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      171
[1] 4 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 18(9P21.3) MUTATED     4 207
  DEL PEAK 18(9P21.3) WILD-TYPE   3 175
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      4  207
  DEL PEAK 18(9P21.3) WILD-TYPE    3  175
                        clus
vv                       DEL PEAK 18(9P21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         207
                        clus
vv                       DEL PEAK 18(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           175
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 19(9Q21.11) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(9Q21.11) MUTATED   162  84
  DEL PEAK 19(9Q21.11) WILD-TYPE 175  70
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                           246                            245 
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                            84                             70 
$`DEL PEAK 19(9Q21.11) MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4402 
       50.07         3.98        19.96        45.01        37.02         8.02 
TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-5420 
        2.99         9.01        29.98        30.02        25.02        15.02 
TCGA-05-5425 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
       29.00         2.04         7.40         8.68        97.74        37.71 
TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-A44F 
       49.05        35.28        11.64        44.61        14.73         4.37 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-3917 TCGA-44-5644 
       13.15        44.94        24.36        42.08        38.89        28.37 
TCGA-44-6144 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       23.77        21.63        32.45        61.28        16.44        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 
        7.17        36.07        18.87        29.00        17.59        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 
        3.25         8.55        15.98        13.64        13.45        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       28.57        12.66        35.54        46.72        14.07        32.84 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV 
       29.46        55.89        14.63        12.13        22.26        22.26 
TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO TCGA-50-5055 
      153.04        63.95        62.24        28.90       123.58        60.16 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       49.28         8.22        14.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 
        8.45        15.12        25.12        11.05        12.16        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
        0.72        10.13         7.59        27.25        34.29        13.94 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
       23.05        38.73        45.21         2.86        32.65         0.79 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 
        0.82         3.88         2.20        45.34        32.71        40.54 
TCGA-55-6986 TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 
      107.21         1.15         0.20         0.13        23.18         1.28 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 
        0.53        17.65         6.15        19.82        29.72         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 
       19.66        19.73         0.13        15.65        17.98         1.51 
TCGA-55-8207 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        2.17         1.45         0.95         0.26         0.49        17.72 
TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48X TCGA-55-A492 
        0.10         6.64        17.62         0.49        22.65        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8397 
        0.92        15.81        20.19        19.99        17.95        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46V 
       14.60        88.64        49.25        47.80        56.71        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
       13.61        39.25        56.81        39.09        55.43        38.37 
TCGA-64-5774 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 
       87.98        28.41         1.02        20.05        18.84        12.66 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 
        4.64        13.87         6.64         6.12        22.68         7.56 
TCGA-69-7974 TCGA-69-7980 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 
        6.05        12.56         4.24        26.73         7.04        23.38 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
       15.35         4.31         1.32        11.18       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7161 
        5.69        19.27        20.58        35.93        21.90         7.07 
TCGA-78-7167 TCGA-78-7536 TCGA-78-7633 TCGA-78-8640 TCGA-78-8660 TCGA-86-7711 
       88.14         8.02        32.68       214.62        10.55        34.39 
TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8075 TCGA-86-8279 
       13.87        19.89        16.70         4.08        15.75        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 
       23.05        21.47         1.15        13.91        30.84         0.62 
TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       13.32        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-93-7348 TCGA-93-A4JQ 
       27.68         7.36        16.18         1.18         4.18        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 
        1.12         1.22        18.67        15.65        27.29         2.76 
TCGA-95-A4VP TCGA-97-7937 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       19.89         5.95         5.39        15.39        16.41        21.60 
TCGA-97-8552 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
       20.58        18.67        20.68         1.45         5.59        24.30 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
       18.08        16.44        12.59        11.87        27.19        38.63 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
       86.14        58.45        49.35        58.85         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TJ 
       41.59        31.23        10.09        29.46        11.05        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A7XG TCGA-O1-A52J 
       73.91        71.05         0.13        29.13         9.70        59.11 

$`DEL PEAK 19(9Q21.11) WILD-TYPE`
TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       14.01         0.00         9.96        24.03        47.05        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
       20.05        14.96        12.00        21.99        26.01        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00        15.02         4.96        22.03         9.04 
TCGA-35-3615 TCGA-35-4123 TCGA-38-4626 TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 
        0.46         5.98       120.79        28.41        26.30        43.53 
TCGA-44-2656 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       46.98        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 
       34.06         6.25        26.56        33.30        12.59        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-7659 
        9.93        27.78        23.15        23.18        63.72        14.60 
TCGA-44-7661 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
       12.03        23.64        15.32         9.44        11.08        11.54 
TCGA-49-4486 TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
       76.21         8.81        29.75        29.26        17.16        11.64 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
        8.55        40.41        37.32       211.82       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5930 
       20.52        71.47        70.55        15.72        31.04         9.27 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       18.64        29.03        22.55        42.35         3.91        25.55 
TCGA-50-6595 TCGA-50-8457 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6543 
        6.21        25.61        30.54         9.21        48.62         0.07 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 
       42.51        40.73        15.25        48.49         5.49         7.79 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7574 
       60.03        24.99        70.26         0.59         7.99         3.12 
TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
        1.32         1.28         1.12         0.79         1.78        18.64 
TCGA-55-7910 TCGA-55-7995 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8205 
        6.48         0.16        15.19         5.06        23.64         1.08 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 TCGA-55-8511 TCGA-55-8513 
       22.16        15.42         0.76         0.36         0.30         4.80 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
        1.58         1.61         2.17        16.93        20.71        21.40 
TCGA-55-A490 TCGA-55-A491 TCGA-62-8394 TCGA-62-8395 TCGA-62-A46P TCGA-62-A46S 
        1.58        20.58         4.57        39.98        19.53        54.35 
TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 TCGA-64-5775 
       67.96        40.96        29.92        20.65        37.02         2.04 
TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-6215 TCGA-69-7764 
       42.90        51.25        28.47        14.04         5.72        13.61 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 
        5.42         2.30         2.93        14.01        13.45         2.01 
TCGA-73-4658 TCGA-73-4662 TCGA-73-4666 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       52.60        29.98        26.30         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       23.51        39.52        24.99        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
        5.88        64.90        22.29       104.19       223.96         8.48 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53        31.20        53.33        10.75        39.35        10.55 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       31.13        20.55        19.43        24.49         4.57        24.33 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 TCGA-86-8671 TCGA-86-8673 
        0.79        16.08        15.65        14.60        27.58        14.96 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32         3.81        17.62        13.64        26.47        10.62 
TCGA-91-6836 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
       13.71         1.15        16.60        14.27         1.45        19.82 
TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7562 
        9.76         6.12        23.61         1.08        19.00         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 
       12.39        15.68        21.40        18.18        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        43.79        25.48         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       17.92        18.12        14.30        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.52        17.75        20.84        24.56        34.85        36.76 
TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       21.63        23.80        35.47        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N5 TCGA-MP-A4T2 
        0.20        14.53         1.91        17.46         2.76        37.35 
TCGA-MP-A4T4 TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YG 
       86.04         2.43        14.66        14.10        19.13        62.60 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        1.64         0.26         0.43        19.82        16.87 

  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                           0.1                            0.0 
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                        214.62                         223.96 
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                        17.965                         18.670 
[1] "0.1 - 214.6 (18.0)" "0.0 - 224.0 (18.7)"
[1] "hr=" "1.1"
D40V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(9Q21.11) MUTATED         3       63       71        1        26
  DEL PEAK 19(9Q21.11) WILD-TYPE       2       72       69        0        25
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 19(9Q21.11) MUTATED          38         40          4       10
  DEL PEAK 19(9Q21.11) WILD-TYPE        35         32          7       16
D40V3, multiclass
            clus
vv           DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             63                             72
  STAGE IB                             71                             69
  STAGE II                              1                              0
  STAGE IIA                            26                             25
  STAGE IIB                            38                             35
  STAGE IIIA                           40                             32
  STAGE IIIB                            4                              7
  STAGE IV                             10                             16
[1] 9 2
[1] 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(9Q21.11) MUTATED    83 142  24   6
  DEL PEAK 19(9Q21.11) WILD-TYPE  87 136  22  13
D40V4, multiclass
    clus
vv   DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  T1                           83                             87
  T2                          142                            136
  T3                           24                             22
  T4                            6                             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 19(9Q21.11) MUTATED   162  52    38
  DEL PEAK 19(9Q21.11) WILD-TYPE 170  44    38
D40V5, multiclass
       clus
vv      DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  N0                             162                            170
  N1                              52                             44
  N2+N3                           38                             38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q21.11) MUTATED   169  10
  DEL PEAK 19(9Q21.11) WILD-TYPE 179  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q21.11) MUTATED    169   10
  DEL PEAK 19(9Q21.11) WILD-TYPE  179   15
   clus
vv  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  0                          169                            179
  1                           10                             15
[1] 2 2
[1] FALSE
D40V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q21.11) MUTATED   133 123
  DEL PEAK 19(9Q21.11) WILD-TYPE 142 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q21.11) MUTATED    133  123
  DEL PEAK 19(9Q21.11) WILD-TYPE  142  117
        clus
vv       DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  FEMALE                          133                            142
  MALE                            123                            117
[1] 2 2
[1] FALSE
D40V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                           11
  DEL PEAK 19(9Q21.11) WILD-TYPE                          8
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 19(9Q21.11) MUTATED                                  43
  DEL PEAK 19(9Q21.11) WILD-TYPE                                64
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 19(9Q21.11) MUTATED                                                  168
  DEL PEAK 19(9Q21.11) WILD-TYPE                                                151
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 19(9Q21.11) MUTATED                                            1
  DEL PEAK 19(9Q21.11) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 19(9Q21.11) MUTATED                                              10
  DEL PEAK 19(9Q21.11) WILD-TYPE                                             9
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                                1
  DEL PEAK 19(9Q21.11) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                                    3
  DEL PEAK 19(9Q21.11) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                              0
  DEL PEAK 19(9Q21.11) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                              10
  DEL PEAK 19(9Q21.11) WILD-TYPE                            13
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                                 1
  DEL PEAK 19(9Q21.11) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                                               3
  DEL PEAK 19(9Q21.11) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                              5
  DEL PEAK 19(9Q21.11) WILD-TYPE                            5
D40V9, multiclass
                                                    clus
vv                                                   DEL PEAK 19(9Q21.11) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            43
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          168
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                10
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                10
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  5
                                                    clus
vv                                                   DEL PEAK 19(9Q21.11) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              64
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            151
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   9
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              0
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  13
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  MUCINOUS (COLLOID) CARCINOMA                                                    5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q21.11) MUTATED     8 248
  DEL PEAK 19(9Q21.11) WILD-TYPE  13 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q21.11) MUTATED      8  248
  DEL PEAK 19(9Q21.11) WILD-TYPE   13  246
     clus
vv    DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  NO                             8                             13
  YES                          248                            246
[1] 2 2
[1] FALSE
D40V11, continuous
D40V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 19(9Q21.11) MUTATED   171   6   2  11
  DEL PEAK 19(9Q21.11) WILD-TYPE 172   6   2  15
D40V13, multiclass
    clus
vv   DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  R0                          171                            172
  R1                            6                              6
  R2                            2                              2
  RX                           11                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(9Q21.11) MUTATED                                  1     2
  DEL PEAK 19(9Q21.11) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(9Q21.11) MUTATED                          26   197
  DEL PEAK 19(9Q21.11) WILD-TYPE                        25   192
D40V14, multiclass
                                  clus
vv                                 DEL PEAK 19(9Q21.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     197
                                  clus
vv                                 DEL PEAK 19(9Q21.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V15, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q21.11) MUTATED     4 192
  DEL PEAK 19(9Q21.11) WILD-TYPE   3 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q21.11) MUTATED      4  192
  DEL PEAK 19(9Q21.11) WILD-TYPE    3  190
                        clus
vv                       DEL PEAK 19(9Q21.11) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          192
                        clus
vv                       DEL PEAK 19(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            190
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 20(10P15.3) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(10P15.3) MUTATED    73  50
  DEL PEAK 20(10P15.3) WILD-TYPE 264 104
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           123                            368 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                            50                            104 
$`DEL PEAK 20(10P15.3) MUTATED`
TCGA-05-4402 TCGA-05-5429 TCGA-05-5715 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 
        8.02         9.04         2.04        37.71        49.05        35.28 
TCGA-38-4631 TCGA-38-6178 TCGA-44-2657 TCGA-44-2662 TCGA-44-2666 TCGA-44-3398 
       11.64        14.73        13.15        42.08         3.19        38.24 
TCGA-44-3919 TCGA-44-5644 TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7660 
        6.25        28.37        23.18        63.72        16.44        19.46 
TCGA-44-7669 TCGA-44-7670 TCGA-44-8119 TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 
       18.87        29.00         3.25        13.45        28.57        12.66 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-6742 TCGA-49-AAR2 
       46.72        14.07        29.46        29.75        14.63        63.95 
TCGA-49-AAR9 TCGA-49-AARQ TCGA-50-5931 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 
        8.55       211.82        14.27         3.91        11.05        12.16 
TCGA-50-6597 TCGA-53-7624 TCGA-53-7626 TCGA-55-6642 TCGA-55-6980 TCGA-55-6981 
       41.69        34.29        30.54        32.65         2.20        45.34 
TCGA-55-6982 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7726 TCGA-55-7994 
       32.71       107.21         0.59         1.15         1.28        19.82 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8514 
       19.73         0.13         0.95         0.36         0.26         6.64 
TCGA-55-8614 TCGA-55-A48X TCGA-55-A490 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8402 
       17.62        22.65         1.58        20.19         4.57        49.25 
TCGA-62-A46Y TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
       13.61        55.43        38.37        87.98         2.04        28.41 
TCGA-67-3771 TCGA-67-3772 TCGA-69-7973 TCGA-69-7974 TCGA-69-8453 TCGA-69-A59K 
       20.05        18.84         7.56         6.05        26.73         7.04 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-78-7150 TCGA-78-7155 TCGA-78-7167 
       23.38        26.30         1.32        21.90        38.50        88.14 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-8640 TCGA-78-8655 TCGA-83-5908 
       26.53         8.02        39.35       214.62        77.59        27.09 
TCGA-86-6851 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 
        5.88        19.89        24.49         4.08         0.79        15.75 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8669 TCGA-91-6828 TCGA-91-6831 
       15.65        23.05        14.60        30.84        10.62        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JQ 
        2.60        12.23         7.36         4.18        23.61        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-8494 TCGA-97-7546 
        1.22         2.86        15.68        15.65         2.76        31.69 
TCGA-97-8547 TCGA-97-A4M1 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG 
       21.60        19.76        20.68        24.30        18.08        16.44 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TJ TCGA-MP-A4TK 
       49.35        37.35        58.85        41.59        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A55A 
       73.91         0.13         0.26 

$`DEL PEAK 20(10P15.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4405 
        0.00         9.96        24.03        47.05        19.00        20.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
        2.99        14.96         9.01        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       21.99        26.01        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-3615 
       15.02        15.02         4.96        29.00        22.03         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 
        7.40         5.98         8.68        97.74       120.79        28.41 
TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 
       44.61        26.30         4.37        43.53        46.98        44.94 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 
       24.36        42.77        25.02        37.15        38.89        34.06 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       26.56        33.30        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
       27.78        23.15        21.63        32.45        61.28        14.60 
TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       12.03         7.17        36.07        17.59        23.64        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        8.55        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 
       13.64        76.21        28.11        35.54        32.84         8.81 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 
       55.89        12.13        29.26        17.16        11.64        22.26 
TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARN 
       22.26       153.04        62.24        28.90        40.41        37.32 
TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      123.58       164.12         9.86        20.52        71.47        70.55 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        31.04        49.28         8.22         9.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 
       29.03        25.12        22.55        42.35        25.55         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 
        0.72        10.13        25.61         7.59        27.25        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
        9.21        23.05        38.73        48.62        45.21         2.86 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
        0.07         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6983 TCGA-55-6984 
       48.49         3.88         5.49         7.79        60.03        24.99 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
       40.54        70.26         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        1.32        23.18         1.28         1.12         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
       18.64         0.53         6.48        17.65         6.15         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 
       29.72        15.19         3.29        19.66         5.06        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
       15.42         1.45         0.76         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        0.10         4.80         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
       16.93        20.71        21.40        20.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        19.99        17.95        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       88.64        47.80        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       72.30        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       39.09        37.02        42.90        51.25        28.47         1.02 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        12.66         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 
        6.12        22.68        13.61         5.42         2.30         2.93 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 
       12.56        14.01        13.45         4.24         2.01        52.60 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       29.98        15.35         4.31         5.39         1.25        39.09 
TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       23.51        11.18       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
       20.58        35.93        39.52        24.99        19.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 TCGA-78-7633 
        8.48        31.20        53.33        10.75        10.55        32.68 
TCGA-78-8648 TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       39.75        10.55       110.50        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 
       13.87        20.55        19.43        16.70         4.57        24.33 
TCGA-86-8076 TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
       16.08        15.85        21.47         1.15        13.91        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
        0.62        14.96        13.32        13.32         3.81        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6836 TCGA-91-6847 
       13.64        26.47        41.36         1.97        13.71        27.68 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
        1.15        16.18        16.60        14.27         1.18         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       19.82         9.76         6.12         1.08        19.00         1.12 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       18.67        12.39        27.29        21.40        18.18        19.89 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 
       16.41        14.30        20.58        20.19        21.44        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       17.75        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E5 
        1.45         5.59        21.63        23.80        35.47        19.00 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       14.30         3.81         0.20        14.53         1.91        17.46 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       12.59        11.87        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.45        86.04         5.49         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-NJ-A4YF 
       10.09        29.46        11.05        14.66        14.10        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       62.60         1.64        29.13         0.43        19.82         9.70 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                        214.62                         223.96 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                         18.84                          18.41 
[1] "0.1 - 214.6 (18.8)" "0.0 - 224.0 (18.4)"
[1] "hr=" "1.4"
D41V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(10P15.3) MUTATED         1       29       31        0        15
  DEL PEAK 20(10P15.3) WILD-TYPE       4      106      109        1        36
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 20(10P15.3) MUTATED          17         25          1        7
  DEL PEAK 20(10P15.3) WILD-TYPE        56         47         10       19
D41V3, multiclass
            clus
vv           DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             29                            106
  STAGE IB                             31                            109
  STAGE II                              0                              1
  STAGE IIA                            15                             36
  STAGE IIB                            17                             56
  STAGE IIIA                           25                             47
  STAGE IIIB                            1                             10
  STAGE IV                              7                             19
[1] 9 2
[1] 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(10P15.3) MUTATED    43  69  12   2
  DEL PEAK 20(10P15.3) WILD-TYPE 127 209  34  17
D41V4, multiclass
    clus
vv   DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  T1                           43                            127
  T2                           69                            209
  T3                           12                             34
  T4                            2                             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 20(10P15.3) MUTATED    75  25    24
  DEL PEAK 20(10P15.3) WILD-TYPE 257  71    52
D41V5, multiclass
       clus
vv      DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  N0                              75                            257
  N1                              25                             71
  N2+N3                           24                             52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED    79   7
  DEL PEAK 20(10P15.3) WILD-TYPE 269  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED     79    7
  DEL PEAK 20(10P15.3) WILD-TYPE  269   18
   clus
vv  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  0                           79                            269
  1                            7                             18
[1] 2 2
[1] FALSE
D41V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED    80  46
  DEL PEAK 20(10P15.3) WILD-TYPE 195 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED     80   46
  DEL PEAK 20(10P15.3) WILD-TYPE  195  194
        clus
vv       DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  FEMALE                           80                            195
  MALE                             46                            194
[1] 2 2
[1] FALSE
D41V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                            6
  DEL PEAK 20(10P15.3) WILD-TYPE                         13
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 20(10P15.3) MUTATED                                  18
  DEL PEAK 20(10P15.3) WILD-TYPE                                89
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(10P15.3) MUTATED                                                   89
  DEL PEAK 20(10P15.3) WILD-TYPE                                                230
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 20(10P15.3) MUTATED                                            1
  DEL PEAK 20(10P15.3) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 20(10P15.3) MUTATED                                               5
  DEL PEAK 20(10P15.3) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                                0
  DEL PEAK 20(10P15.3) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                                    1
  DEL PEAK 20(10P15.3) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                              0
  DEL PEAK 20(10P15.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                               3
  DEL PEAK 20(10P15.3) WILD-TYPE                            20
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                                 1
  DEL PEAK 20(10P15.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                                               0
  DEL PEAK 20(10P15.3) WILD-TYPE                                             5
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                              2
  DEL PEAK 20(10P15.3) WILD-TYPE                            8
D41V9, multiclass
                                                    clus
vv                                                   DEL PEAK 20(10P15.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           89
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 5
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 3
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 0
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 20(10P15.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              89
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            230
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  14
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  20
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   5
  MUCINOUS (COLLOID) CARCINOMA                                                    8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED     5 121
  DEL PEAK 20(10P15.3) WILD-TYPE  16 373
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED      5  121
  DEL PEAK 20(10P15.3) WILD-TYPE   16  373
     clus
vv    DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  NO                             5                             16
  YES                          121                            373
[1] 2 2
[1] FALSE
D41V11, continuous
D41V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 20(10P15.3) MUTATED    87   3   1   7
  DEL PEAK 20(10P15.3) WILD-TYPE 256   9   3  19
D41V13, multiclass
    clus
vv   DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  R0                           87                            256
  R1                            3                              9
  R2                            1                              3
  RX                            7                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(10P15.3) MUTATED                                  0     0
  DEL PEAK 20(10P15.3) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10P15.3) MUTATED                          10   105
  DEL PEAK 20(10P15.3) WILD-TYPE                        41   284
D41V14, multiclass
                                  clus
vv                                 DEL PEAK 20(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                     105
                                  clus
vv                                 DEL PEAK 20(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       284
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V15, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED     4  97
  DEL PEAK 20(10P15.3) WILD-TYPE   3 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED      4   97
  DEL PEAK 20(10P15.3) WILD-TYPE    3  285
                        clus
vv                       DEL PEAK 20(10P15.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           97
                        clus
vv                       DEL PEAK 20(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            285
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 21(10Q26.3) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(10Q26.3) MUTATED    95  54
  DEL PEAK 21(10Q26.3) WILD-TYPE 242 100
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                           149                            342 
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                            54                            100 
$`DEL PEAK 21(10Q26.3) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4420 
       45.01        37.02        24.03        47.05         8.02        29.98 
TCGA-05-4424 TCGA-05-4430 TCGA-05-5429 TCGA-05-5715 TCGA-38-4628 TCGA-38-4631 
       30.02        25.02         9.04         2.04        49.05        11.64 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       46.98        13.15        42.08        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       37.15        38.24        38.89        34.06         6.25        26.56 
TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 TCGA-44-6775 TCGA-44-7660 TCGA-44-7662 
       12.59         9.93        27.78        23.18        19.46         7.17 
TCGA-44-7669 TCGA-44-7670 TCGA-44-A4SU TCGA-49-4487 TCGA-49-4494 TCGA-49-4505 
       18.87        29.00        13.45        28.11        35.54        14.07 
TCGA-49-6742 TCGA-49-AAR0 TCGA-49-AARE TCGA-49-AARQ TCGA-50-5049 TCGA-50-5931 
       14.63       153.04        40.41       211.82        70.55        14.27 
TCGA-50-5941 TCGA-50-5944 TCGA-50-6591 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       18.64        25.12         3.91        41.69         0.72        10.13 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6971 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       23.05         2.86         0.82         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6986 TCGA-55-7281 TCGA-55-7994 TCGA-55-8091 TCGA-55-8092 
       32.71       107.21         0.59        19.82        19.73         5.06 
TCGA-55-8094 TCGA-55-8206 TCGA-55-8207 TCGA-55-8505 TCGA-55-8508 TCGA-55-8514 
        0.13         1.51         2.17         0.95         0.49         6.64 
TCGA-55-8614 TCGA-55-A48X TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       17.62        22.65        20.19        19.99        17.95         4.57 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46U TCGA-62-A46Y TCGA-64-1676 TCGA-64-1679 
       49.25        19.53        67.96        13.61        56.81        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-67-3770 TCGA-67-3772 TCGA-69-7978 
       38.37        87.98        42.90         1.02        18.84         2.30 
TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 
        2.93         4.24         7.04         2.01        26.30        15.35 
TCGA-73-A9RS TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 TCGA-78-7220 TCGA-78-7535 
       11.18        19.27        19.50        38.50        26.53        31.20 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 
       39.35        10.55       214.62        77.59        10.55        27.09 
TCGA-86-6851 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 
        5.88        19.89        16.70         4.08         0.79        15.75 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8669 TCGA-86-A4JF 
       15.65        23.05        21.47        14.60        30.84        17.62 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 
       10.62        41.36         2.60        13.71        12.23         7.36 
TCGA-91-8499 TCGA-93-7348 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 
        1.18         4.18         1.22         2.86        12.39        15.68 
TCGA-95-7948 TCGA-97-7546 TCGA-97-7554 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M1 
       15.65        31.69        25.48        18.12        21.60        19.76 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A443 TCGA-MN-A4N5 
       20.68        24.30        18.08        16.44         3.81         2.76 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TF 
       49.35        37.35        86.04        58.85        41.59        11.05 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-O1-A52J 
       11.15        19.13         0.13        29.13        59.11 

$`DEL PEAK 21(10Q26.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        19.96        14.01         0.00         9.96 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 
       19.00        20.05         2.99        14.96         9.01        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 
       21.99        26.01        26.01        25.02        24.00        15.02 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-3615 TCGA-35-4122 
       15.02         4.96        29.00        22.03         0.46         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
        5.98         8.68        97.74       120.79        37.71        28.41 
TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       35.28        44.61        14.73        26.30         4.37        43.53 
TCGA-44-2659 TCGA-44-2661 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
       44.94        24.36        33.30        28.37        23.77        10.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        63.72        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 
       14.60        12.03        36.07        17.59        23.64        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F 
        3.25         8.55        15.98        15.32         9.44        11.08 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 
       11.54        13.64        76.21        28.57        12.66        46.72 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       32.84         8.81        29.46        29.75        55.89        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 
       29.26        17.16        11.64        22.26        22.26        63.95 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARR 
       62.24        28.90         8.55        37.32       123.58       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
        9.86        20.52        71.47        15.72        60.16        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 
       49.28         8.22         9.27        40.60        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 
        8.45        15.12        29.03        22.55        42.35        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       11.05        12.16         6.21        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
       34.29        30.54        13.94         9.21        38.73        48.62 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       45.21         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6983 TCGA-55-6984 
       15.25        48.49         3.88         5.49        60.03        24.99 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
       40.54        70.26         1.15         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 
        3.12         1.32        23.18         1.28         1.28         1.12 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
        6.15         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 
       23.64        15.65        17.98         1.08        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 
        1.45         0.76         0.36         0.26        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        0.10         4.80         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 
       16.93        20.71        21.40         1.58        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
        0.92        15.81        39.98        42.38        14.60        88.64 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 
       47.80        56.71        54.35        72.30        39.25        40.96 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 
       29.92        20.65        39.09        37.02         2.04        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
       51.25        28.47        20.05        14.04        12.66         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        4.64        13.87         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        5.42         7.56         6.05        12.56        14.01        13.45 
TCGA-69-8453 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 TCGA-73-4675 
       26.73        52.60        23.38        29.98         4.31         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
        5.39         1.25        39.09        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
      223.96         8.48        88.14         8.02        53.33        10.75 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8662 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       32.68        39.75       110.50        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       13.87        20.55        19.43        24.49         4.57        24.33 
TCGA-86-8076 TCGA-86-8279 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
       16.08        15.85         1.15        13.91        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32         3.81        13.64        26.47 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6847 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
        1.97        10.19        27.68         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN 
       14.27         1.45        19.82         9.76         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 
        1.08        19.00        17.29         1.12        18.67        27.29 
TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
        2.76        21.40        18.18        19.89        64.60        63.52 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       43.79         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4LX 
        5.39        15.39        16.41        14.30        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       21.44        20.52        17.75        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 
       34.85        36.76         1.45         5.59        21.63        23.80 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
       35.47        19.00        14.30         0.20        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV 
       17.46        12.59        11.87        27.19        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       58.45         5.49         5.29        31.23         2.43        10.09 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       29.46        14.66        14.10        73.91        71.05        62.60 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        1.64         0.26         0.43        19.82         9.70        16.87 

  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                        214.62                         223.96 
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                        19.130                         17.835 
[1] "0.1 - 214.6 (19.1)" "0.0 - 224.0 (17.8)"
[1] "hr=" "1.2"
D42V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(10Q26.3) MUTATED         2       47       45        0        13
  DEL PEAK 21(10Q26.3) WILD-TYPE       3       88       95        1        38
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 21(10Q26.3) MUTATED          24         18          2        5
  DEL PEAK 21(10Q26.3) WILD-TYPE        49         54          9       21
D42V3, multiclass
            clus
vv           DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             47                             88
  STAGE IB                             45                             95
  STAGE II                              0                              1
  STAGE IIA                            13                             38
  STAGE IIB                            24                             49
  STAGE IIIA                           18                             54
  STAGE IIIB                            2                              9
  STAGE IV                              5                             21
[1] 9 2
[1] 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(10Q26.3) MUTATED    57  86  11   2
  DEL PEAK 21(10Q26.3) WILD-TYPE 113 192  35  17
D42V4, multiclass
    clus
vv   DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  T1                           57                            113
  T2                           86                            192
  T3                           11                             35
  T4                            2                             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 21(10Q26.3) MUTATED   102  29    21
  DEL PEAK 21(10Q26.3) WILD-TYPE 230  67    55
D42V5, multiclass
       clus
vv      DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  N0                             102                            230
  N1                              29                             67
  N2+N3                           21                             55
[1] 3 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 21(10Q26.3) MUTATED   113   5
  DEL PEAK 21(10Q26.3) WILD-TYPE 235  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q26.3) MUTATED    113    5
  DEL PEAK 21(10Q26.3) WILD-TYPE  235   20
   clus
vv  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  0                          113                            235
  1                            5                             20
[1] 2 2
[1] FALSE
D42V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q26.3) MUTATED    92  64
  DEL PEAK 21(10Q26.3) WILD-TYPE 183 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q26.3) MUTATED     92   64
  DEL PEAK 21(10Q26.3) WILD-TYPE  183  176
        clus
vv       DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  FEMALE                           92                            183
  MALE                             64                            176
[1] 2 2
[1] FALSE
D42V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                            4
  DEL PEAK 21(10Q26.3) WILD-TYPE                         15
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 21(10Q26.3) MUTATED                                  27
  DEL PEAK 21(10Q26.3) WILD-TYPE                                80
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 21(10Q26.3) MUTATED                                                  107
  DEL PEAK 21(10Q26.3) WILD-TYPE                                                212
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 21(10Q26.3) MUTATED                                            1
  DEL PEAK 21(10Q26.3) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 21(10Q26.3) MUTATED                                               6
  DEL PEAK 21(10Q26.3) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                                0
  DEL PEAK 21(10Q26.3) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                                    2
  DEL PEAK 21(10Q26.3) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                              1
  DEL PEAK 21(10Q26.3) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                               3
  DEL PEAK 21(10Q26.3) WILD-TYPE                            20
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                                 1
  DEL PEAK 21(10Q26.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                                               2
  DEL PEAK 21(10Q26.3) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                              2
  DEL PEAK 21(10Q26.3) WILD-TYPE                            8
D42V9, multiclass
                                                    clus
vv                                                   DEL PEAK 21(10Q26.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          107
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 6
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                 3
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 21(10Q26.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              80
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            212
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                                  20
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   3
  MUCINOUS (COLLOID) CARCINOMA                                                    8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q26.3) MUTATED     3 153
  DEL PEAK 21(10Q26.3) WILD-TYPE  18 341
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q26.3) MUTATED      3  153
  DEL PEAK 21(10Q26.3) WILD-TYPE   18  341
     clus
vv    DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  NO                             3                             18
  YES                          153                            341
[1] 2 2
[1] FALSE
D42V11, continuous
D42V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 21(10Q26.3) MUTATED   114   1   1   9
  DEL PEAK 21(10Q26.3) WILD-TYPE 229  11   3  17
D42V13, multiclass
    clus
vv   DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  R0                          114                            229
  R1                            1                             11
  R2                            1                              3
  RX                            9                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(10Q26.3) MUTATED                                  1     1
  DEL PEAK 21(10Q26.3) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(10Q26.3) MUTATED                          11   120
  DEL PEAK 21(10Q26.3) WILD-TYPE                        40   269
D42V14, multiclass
                                  clus
vv                                 DEL PEAK 21(10Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                     120
                                  clus
vv                                 DEL PEAK 21(10Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    40
  WHITE                                                       269
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V15, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q26.3) MUTATED     4 111
  DEL PEAK 21(10Q26.3) WILD-TYPE   3 271
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q26.3) MUTATED      4  111
  DEL PEAK 21(10Q26.3) WILD-TYPE    3  271
                        clus
vv                       DEL PEAK 21(10Q26.3) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          111
                        clus
vv                       DEL PEAK 21(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            271
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 22(11P15.5) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(11P15.5) MUTATED    94  46
  DEL PEAK 22(11P15.5) WILD-TYPE 243 108
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                           140                            351 
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                            46                            108 
$`DEL PEAK 22(11P15.5) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4427 TCGA-05-4434 TCGA-05-5425 
       19.96        45.01        37.02        26.01        15.02        29.00 
TCGA-05-5428 TCGA-35-5375 TCGA-38-4632 TCGA-44-2668 TCGA-44-3917 TCGA-44-5644 
       22.03         8.68        44.61        25.02        38.89        28.37 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7671 TCGA-44-8117 TCGA-44-A47F 
       19.46         7.17        36.07        17.59        12.66        11.08 
TCGA-44-A4SS TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       13.64        12.66        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR9 
       29.46        12.13        22.26        22.26        62.24         8.55 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
        8.22         9.27        14.27        78.67         8.45        15.12 
TCGA-50-5946 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 TCGA-50-8460 
       22.55        25.55        11.05        12.16         0.72        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
       34.29        30.54         9.21        48.62        45.21         2.86 
TCGA-55-6642 TCGA-55-6968 TCGA-55-6972 TCGA-55-6975 TCGA-55-7570 TCGA-55-7573 
       32.65        42.51        48.49         3.88         0.20         0.13 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7994 TCGA-55-7995 
        1.32         1.12         1.78        18.64        19.82         0.16 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8302 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 
        3.29         5.06         0.76         0.26        17.72         0.30 
TCGA-55-8614 TCGA-55-A490 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8397 TCGA-62-8398 
       17.62         1.58        19.99        17.95        42.38        14.60 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A46S TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       88.64        47.80        54.35        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 
       20.65        55.43        87.98        42.90        51.25        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-69-7763 TCGA-69-7974 TCGA-69-7979 TCGA-69-A59K 
        1.02        20.05        22.68         6.05         2.93         7.04 
TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7145 
       23.38         4.31         1.32        23.51        11.18        27.16 
TCGA-78-7147 TCGA-78-7154 TCGA-78-7160 TCGA-78-7535 TCGA-78-8640 TCGA-86-7701 
       19.27        19.50        22.29        31.20       214.62        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8280 TCGA-86-8358 
       34.39        13.87        19.43        16.70        23.05        21.47 
TCGA-86-8669 TCGA-86-8673 TCGA-86-A4JF TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       30.84        14.96        17.62        13.71        12.23        27.68 
TCGA-95-7039 TCGA-95-7043 TCGA-95-8039 TCGA-95-8494 TCGA-97-7553 TCGA-97-8174 
        1.12         1.22        27.29         2.76        43.79         5.39 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AD 
       19.76        20.84        34.85        36.76         5.59        18.08 
TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4T2 
       19.00        12.59        11.87        27.19        38.63        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK 
       86.04         5.29        41.59        29.46        11.05        19.13 
TCGA-NJ-A4YF TCGA-NJ-A4YQ 
       71.05        29.13 

$`DEL PEAK 22(11P15.5) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
       50.07         3.98        14.01         0.00         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       47.05         8.02        19.00        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 
       25.02        25.02        24.00        15.02         4.96         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 
        2.04         0.46         7.40         5.98        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       37.71        49.05        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       26.30         4.37        43.53        46.98        13.15        44.94 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
       24.36        42.08        42.77         3.19        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 
       34.06         6.25        26.56        33.30        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 
       63.72        32.45        61.28        16.44        14.60        12.03 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       18.87        29.00        23.64         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       15.32         9.44        11.54        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 
       28.57        35.54        29.75        55.89        14.63        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AARE 
       17.16        11.64       153.04        63.95        28.90        40.41 
TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       37.32       123.58       211.82       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       71.47        70.55        15.72        60.16        31.04        49.28 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
       40.60        21.47        18.64        29.03        25.12        42.35 
TCGA-50-6591 TCGA-50-6595 TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        3.91         6.21        41.69        10.13        25.61         7.59 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 
       13.94        23.05        38.73         0.07         0.79        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       15.25         0.82         5.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        60.03        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
        0.59         1.15         7.99         3.12        23.18         1.28 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.28         0.79         0.53         6.48        17.65         6.15 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 
       29.72        15.19        19.66        19.73         0.13        23.64 
TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       15.65        17.98         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 
       15.42         1.45         0.95         0.36         0.49         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        4.80         6.64         0.49         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 
       16.93        22.65        20.71        21.40        20.58        19.59 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8394 TCGA-62-8395 TCGA-62-8402 
        0.92        15.81        20.19         4.57        39.98        49.25 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        67.96        72.30        13.61        39.25 
TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-67-3772 
       39.09        37.02        38.37         2.04        28.41        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 
       14.04        12.66         5.72         4.64        13.87         6.64 
TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 
        6.12        13.61         5.42         7.56         2.30        12.56 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 
       14.01        13.45         4.24        26.73         2.01        52.60 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       29.98        26.30        15.35         5.39         1.25        39.09 
TCGA-78-7143 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
      163.10         5.69        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 
       24.99        38.50        32.09         5.88        64.90         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
      104.19       223.96         8.48        88.14        26.53         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       53.33        10.75        39.35        10.55        32.68        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       20.55        19.89        24.49         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8359 
        0.79        15.75        16.08        15.65        15.85        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
        1.15        13.91        27.58         0.62        13.32        13.32 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
        3.81        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       10.19         2.60         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       14.27         1.18         1.45        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7562 
        6.12        23.61         1.08        19.00        17.29         2.86 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       18.67        12.39        15.68        15.65        21.40        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 
       19.89        31.69        64.60        63.52        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 
        0.59         0.72        18.67        17.92        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 
       16.41        14.30        21.60        20.58        20.19        21.44 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8032 
       20.52        17.75        18.67        20.68        24.56         1.45 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       21.63        24.30        23.80        35.47        16.44        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N5 
        3.81         0.20        14.53         1.91        17.46         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TA 
       86.14        58.45        49.35        58.85         5.49        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 
        2.43        10.09        14.66        14.10        11.15        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       62.60         0.13         1.64         0.26         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        9.70        59.11        16.87 

  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                        214.62                         223.96 
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                         19.79                          17.29 
[1] "0.1 - 214.6 (19.8)" "0.0 - 224.0 (17.3)"
[1] "hr=" "1.1"
D43V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(11P15.5) MUTATED         2       32       37        1        14
  DEL PEAK 22(11P15.5) WILD-TYPE       3      103      103        0        37
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 22(11P15.5) MUTATED          26         21          1        9
  DEL PEAK 22(11P15.5) WILD-TYPE        47         51         10       17
D43V3, multiclass
            clus
vv           DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             32                            103
  STAGE IB                             37                            103
  STAGE II                              1                              0
  STAGE IIA                            14                             37
  STAGE IIB                            26                             47
  STAGE IIIA                           21                             51
  STAGE IIIB                            1                             10
  STAGE IV                              9                             17
[1] 9 2
[1] 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(11P15.5) MUTATED    43  78  17   4
  DEL PEAK 22(11P15.5) WILD-TYPE 127 200  29  15
D43V4, multiclass
    clus
vv   DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  T1                           43                            127
  T2                           78                            200
  T3                           17                             29
  T4                            4                             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 22(11P15.5) MUTATED    91  30    21
  DEL PEAK 22(11P15.5) WILD-TYPE 241  66    55
D43V5, multiclass
       clus
vv      DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  N0                              91                            241
  N1                              30                             66
  N2+N3                           21                             55
[1] 3 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 22(11P15.5) MUTATED    95   9
  DEL PEAK 22(11P15.5) WILD-TYPE 253  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11P15.5) MUTATED     95    9
  DEL PEAK 22(11P15.5) WILD-TYPE  253   16
   clus
vv  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  0                           95                            253
  1                            9                             16
[1] 2 2
[1] FALSE
D43V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(11P15.5) MUTATED    64  79
  DEL PEAK 22(11P15.5) WILD-TYPE 211 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11P15.5) MUTATED     64   79
  DEL PEAK 22(11P15.5) WILD-TYPE  211  161
        clus
vv       DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  FEMALE                           64                            211
  MALE                             79                            161
[1] 2 2
[1] FALSE
D43V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                            3
  DEL PEAK 22(11P15.5) WILD-TYPE                         16
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 22(11P15.5) MUTATED                                  30
  DEL PEAK 22(11P15.5) WILD-TYPE                                77
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(11P15.5) MUTATED                                                   98
  DEL PEAK 22(11P15.5) WILD-TYPE                                                221
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 22(11P15.5) MUTATED                                            0
  DEL PEAK 22(11P15.5) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 22(11P15.5) MUTATED                                               4
  DEL PEAK 22(11P15.5) WILD-TYPE                                            15
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                                2
  DEL PEAK 22(11P15.5) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                                    0
  DEL PEAK 22(11P15.5) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                              0
  DEL PEAK 22(11P15.5) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                               5
  DEL PEAK 22(11P15.5) WILD-TYPE                            18
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                                 0
  DEL PEAK 22(11P15.5) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                                               0
  DEL PEAK 22(11P15.5) WILD-TYPE                                             5
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                              1
  DEL PEAK 22(11P15.5) WILD-TYPE                            9
D43V9, multiclass
                                                    clus
vv                                                   DEL PEAK 22(11P15.5) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           98
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 4
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            0
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 5
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 0
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   DEL PEAK 22(11P15.5) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            221
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  15
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              3
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  18
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   5
  MUCINOUS (COLLOID) CARCINOMA                                                    9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, binary
                                cls
clus                               0   1
  DEL PEAK 22(11P15.5) MUTATED     5 138
  DEL PEAK 22(11P15.5) WILD-TYPE  16 356
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11P15.5) MUTATED      5  138
  DEL PEAK 22(11P15.5) WILD-TYPE   16  356
     clus
vv    DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  NO                             5                             16
  YES                          138                            356
[1] 2 2
[1] FALSE
D43V11, continuous
D43V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 22(11P15.5) MUTATED    94   2   1  10
  DEL PEAK 22(11P15.5) WILD-TYPE 249  10   3  16
D43V13, multiclass
    clus
vv   DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  R0                           94                            249
  R1                            2                             10
  R2                            1                              3
  RX                           10                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(11P15.5) MUTATED                                  0     2
  DEL PEAK 22(11P15.5) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(11P15.5) MUTATED                          19   108
  DEL PEAK 22(11P15.5) WILD-TYPE                        32   281
D43V14, multiclass
                                  clus
vv                                 DEL PEAK 22(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                     108
                                  clus
vv                                 DEL PEAK 22(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    32
  WHITE                                                       281
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V15, binary
                                cls
clus                               0   1
  DEL PEAK 22(11P15.5) MUTATED     3 114
  DEL PEAK 22(11P15.5) WILD-TYPE   4 268
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11P15.5) MUTATED      3  114
  DEL PEAK 22(11P15.5) WILD-TYPE    4  268
                        clus
vv                       DEL PEAK 22(11P15.5) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          114
                        clus
vv                       DEL PEAK 22(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            268
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 23(11Q23.2) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(11Q23.2) MUTATED    81  33
  DEL PEAK 23(11Q23.2) WILD-TYPE 256 121
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                           114                            377 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                            33                            121 
$`DEL PEAK 23(11Q23.2) MUTATED`
TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 
       45.01        37.02        24.03        47.05         2.99        14.96 
TCGA-05-4422 TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-35-4122 
       12.00        26.01        24.00        15.02        29.00         7.40 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-44-4112 
        8.68        97.74        49.05        11.64        44.61        26.56 
TCGA-44-5643 TCGA-44-7667 TCGA-44-7671 TCGA-44-A47F TCGA-44-A4SS TCGA-49-4487 
       33.30        36.07        17.59        11.08        13.64        28.11 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6761 
       35.54        32.84        29.46        55.89        29.26        11.64 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AARE TCGA-4B-A93V TCGA-50-5044 TCGA-50-5066 
       22.26        63.95        40.41         9.86        20.52        31.04 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5936 TCGA-50-6673 TCGA-53-7626 TCGA-53-A4EZ 
        8.22        14.27         8.45         0.72        30.54         9.21 
TCGA-55-1595 TCGA-55-5899 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-7283 
       48.62         2.86         0.82        48.49         3.88         1.15 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7995 TCGA-55-8085 
        1.12         0.79         1.78        18.64         0.16        29.72 
TCGA-55-8094 TCGA-55-8203 TCGA-55-8302 TCGA-55-8615 TCGA-55-A490 TCGA-55-A4DF 
        0.13        17.98         0.76         0.49         1.58        20.19 
TCGA-62-8395 TCGA-62-8397 TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 TCGA-62-A472 
       39.98        42.38        54.35        67.96        39.25        29.92 
TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5815 TCGA-69-7763 
       39.09        38.37        87.98        42.90        28.47        22.68 
TCGA-69-7764 TCGA-69-8453 TCGA-73-4662 TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS 
       13.61        26.73        29.98         1.32        23.51        11.18 
TCGA-78-7145 TCGA-78-7148 TCGA-78-7159 TCGA-78-7160 TCGA-78-7220 TCGA-78-8640 
       27.16        20.58        64.90        22.29        26.53       214.62 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8074 TCGA-86-8358 
       31.13        13.87        19.43        24.49         0.79        21.47 
TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6835 TCGA-91-6836 
       30.84        14.96         3.81        17.62         2.60        13.71 
TCGA-91-6849 TCGA-93-8067 TCGA-95-7043 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN 
        1.15         6.12         1.22        27.29         2.76        18.18 
TCGA-97-8174 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-8033 TCGA-L4-A4E5 TCGA-L9-A443 
        5.39        17.75        20.84         5.59        19.00         3.81 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-NJ-A4YF 
       27.19         2.76        37.35        29.46        11.05        71.05 

$`DEL PEAK 23(11Q23.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 
       50.07         3.98        19.96        14.01         0.00         9.96 
TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 
        8.02        19.00        20.05         9.01        29.98        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4434 TCGA-05-5423 
       21.99        26.01        25.02        25.02        15.02         4.96 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4626 
       22.03         9.04         2.04         0.46         5.98       120.79 
TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F 
       37.71        28.41        35.28        14.73        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 
       43.53        46.98        13.15        44.94        24.36        42.08 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
       42.77         3.19        25.02        37.15        38.24        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       34.06         6.25        28.37        12.59        23.77        10.78 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
        9.93        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       32.45        61.28        16.44        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
        7.17        18.87        29.00        23.64        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU 
        8.55        15.98        15.32         9.44        11.54        13.45 
TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 
       76.21        28.57        12.66        46.72        14.07         8.81 
TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6767 TCGA-49-AAR0 
       29.75        14.63        12.13        17.16        22.26       153.04 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ 
       62.24        28.90         8.55        37.32       123.58       211.82 
TCGA-49-AARR TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 
      164.12        71.47        70.55        15.72        60.16        49.28 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 
        9.27        40.60        78.67        21.47        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       29.03        25.12        22.55        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21        41.69        10.13        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
        7.59        27.25        34.29        13.94        23.05        38.73 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       45.21         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       15.25         5.49         7.79         2.20        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       60.03        24.99        40.54       107.21        70.26         0.59 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        1.28         1.28         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       19.82        15.19         3.29        19.66        19.73         5.06 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       23.64        15.65         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42         1.45         0.95         0.36         0.26         0.49 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       17.72         0.30         0.10         4.80         6.64        17.62 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        1.58         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       21.40        20.58        19.59         0.92        15.81        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       17.95         4.57        14.60        88.64        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-64-1676 
       19.53        56.71        72.30        13.61        40.96        56.81 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 
       20.65        55.43        37.02         2.04        28.41        51.25 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
        1.02        20.05        18.84        14.04        12.66         5.72 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7973 
        4.64        13.87         6.64         6.12         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        6.05         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
        4.24         7.04         2.01        52.60        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-78-7143 
       15.35         4.31         5.39         1.25        39.09       163.10 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        35.93        21.90        39.52        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 
       19.50        38.50        32.09         5.88         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      223.96         8.48        88.14        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 
       10.75        39.35        10.55        32.68        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 
       10.55       110.50        27.09        12.36         5.88        34.39 
TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       20.55        19.89        16.70         4.08         4.57        24.33 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
       15.75        16.08        15.65        15.85        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
        1.15        13.91        27.58         0.62        13.32        13.32 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36        16.18        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
        1.18         1.45        19.82         9.76         4.18        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
        1.08        19.00        17.29         1.12         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 
       12.39        15.68        15.65        21.40        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.72        18.67        17.92        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.52        18.67        20.68        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        1.45        21.63        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       16.44        14.30         0.20        14.53         1.91        17.46 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       12.59        11.87        38.63        86.14        58.45        49.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
       86.04        58.85         5.49         5.29        41.59        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
        2.43        10.09        14.66        14.10        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        62.60         0.13         1.64        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.43        19.82         9.70        59.11        16.87 

  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                        214.62                         223.96 
  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE 
                         20.71                          17.65 
[1] "0.1 - 214.6 (20.7)" "0.0 - 224.0 (17.6)"
[1] "hr=" "1.1"
D44V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(11Q23.2) MUTATED         2       30       28        1        15
  DEL PEAK 23(11Q23.2) WILD-TYPE       3      105      112        0        36
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 23(11Q23.2) MUTATED          19         14          3        7
  DEL PEAK 23(11Q23.2) WILD-TYPE        54         58          8       19
D44V3, multiclass
            clus
vv           DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             30                            105
  STAGE IB                             28                            112
  STAGE II                              1                              0
  STAGE IIA                            15                             36
  STAGE IIB                            19                             54
  STAGE IIIA                           14                             58
  STAGE IIIB                            3                              8
  STAGE IV                              7                             19
[1] 9 2
[1] 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(11Q23.2) MUTATED    39  63  11   5
  DEL PEAK 23(11Q23.2) WILD-TYPE 131 215  35  14
D44V4, multiclass
    clus
vv   DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  T1                           39                            131
  T2                           63                            215
  T3                           11                             35
  T4                            5                             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 23(11Q23.2) MUTATED    74  26    17
  DEL PEAK 23(11Q23.2) WILD-TYPE 258  70    59
D44V5, multiclass
       clus
vv      DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  N0                              74                            258
  N1                              26                             70
  N2+N3                           17                             59
[1] 3 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 23(11Q23.2) MUTATED    85   7
  DEL PEAK 23(11Q23.2) WILD-TYPE 263  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.2) MUTATED     85    7
  DEL PEAK 23(11Q23.2) WILD-TYPE  263   18
   clus
vv  DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  0                           85                            263
  1                            7                             18
[1] 2 2
[1] FALSE
D44V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.2) MUTATED    54  65
  DEL PEAK 23(11Q23.2) WILD-TYPE 221 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.2) MUTATED     54   65
  DEL PEAK 23(11Q23.2) WILD-TYPE  221  175
        clus
vv       DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  FEMALE                           54                            221
  MALE                             65                            175
[1] 2 2
[1] FALSE
D44V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                            5
  DEL PEAK 23(11Q23.2) WILD-TYPE                         14
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 23(11Q23.2) MUTATED                                  31
  DEL PEAK 23(11Q23.2) WILD-TYPE                                76
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(11Q23.2) MUTATED                                                   70
  DEL PEAK 23(11Q23.2) WILD-TYPE                                                249
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 23(11Q23.2) MUTATED                                            0
  DEL PEAK 23(11Q23.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 23(11Q23.2) MUTATED                                               3
  DEL PEAK 23(11Q23.2) WILD-TYPE                                            16
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                                1
  DEL PEAK 23(11Q23.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                                    0
  DEL PEAK 23(11Q23.2) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                              0
  DEL PEAK 23(11Q23.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                               5
  DEL PEAK 23(11Q23.2) WILD-TYPE                            18
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                                 0
  DEL PEAK 23(11Q23.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                                               1
  DEL PEAK 23(11Q23.2) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 23(11Q23.2) MUTATED                              3
  DEL PEAK 23(11Q23.2) WILD-TYPE                            7
D44V9, multiclass
                                                    clus
vv                                                   DEL PEAK 23(11Q23.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            31
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           70
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 3
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            0
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 5
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   DEL PEAK 23(11Q23.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            249
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  16
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              3
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  18
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   4
  MUCINOUS (COLLOID) CARCINOMA                                                    7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.2) MUTATED     3 116
  DEL PEAK 23(11Q23.2) WILD-TYPE  18 378
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.2) MUTATED      3  116
  DEL PEAK 23(11Q23.2) WILD-TYPE   18  378
     clus
vv    DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  NO                             3                             18
  YES                          116                            378
[1] 2 2
[1] FALSE
D44V11, continuous
D44V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(11Q23.2) MUTATED    88   2   0   7
  DEL PEAK 23(11Q23.2) WILD-TYPE 255  10   4  19
D44V13, multiclass
    clus
vv   DEL PEAK 23(11Q23.2) MUTATED DEL PEAK 23(11Q23.2) WILD-TYPE
  R0                           88                            255
  R1                            2                             10
  R2                            0                              4
  RX                            7                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(11Q23.2) MUTATED                                  0     2
  DEL PEAK 23(11Q23.2) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(11Q23.2) MUTATED                          13    86
  DEL PEAK 23(11Q23.2) WILD-TYPE                        38   303
D44V14, multiclass
                                  clus
vv                                 DEL PEAK 23(11Q23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      86
                                  clus
vv                                 DEL PEAK 23(11Q23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    38
  WHITE                                                       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"
D44V15, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.2) MUTATED     1  90
  DEL PEAK 23(11Q23.2) WILD-TYPE   6 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.2) MUTATED      1   90
  DEL PEAK 23(11Q23.2) WILD-TYPE    6  292
                        clus
vv                       DEL PEAK 23(11Q23.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           90
                        clus
vv                       DEL PEAK 23(11Q23.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            292
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 24(11Q25) MUTATION ANALYSIS
D45V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 24(11Q25) MUTATED    76  35
  DEL PEAK 24(11Q25) WILD-TYPE 261 119
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                         111                          380 
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                          35                          119 
$`DEL PEAK 24(11Q25) MUTATED`
TCGA-05-4390 TCGA-05-4397 TCGA-05-4415 TCGA-05-4422 TCGA-05-4427 TCGA-05-4433 
       37.02        24.03         2.99        12.00        26.01        24.00 
TCGA-05-5420 TCGA-05-5425 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 
       15.02        29.00         7.40         8.68        97.74        49.05 
TCGA-38-4631 TCGA-38-4632 TCGA-44-3918 TCGA-44-5643 TCGA-44-6779 TCGA-44-7667 
       11.64        44.61        34.06        33.30        16.44        36.07 
TCGA-44-7671 TCGA-44-7672 TCGA-44-A47F TCGA-49-4487 TCGA-49-4506 TCGA-49-4510 
       17.59        23.64        11.08        28.11        32.84        29.46 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AARE TCGA-4B-A93V 
       55.89        29.26        11.64        22.26        40.41         9.86 
TCGA-50-5044 TCGA-50-5066 TCGA-50-5072 TCGA-50-5931 TCGA-50-5936 TCGA-50-6594 
       20.52        31.04         8.22        14.27         8.45        12.16 
TCGA-50-6673 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-5899 TCGA-55-6971 
        0.72        30.54         9.21        48.62         2.86         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-7283 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       48.49         3.88         1.15         1.32         1.12         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-8085 TCGA-55-8094 TCGA-55-8203 TCGA-55-8302 
        1.78        18.64        29.72         0.13        17.98         0.76 
TCGA-55-8615 TCGA-62-8395 TCGA-62-8397 TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 
        0.49        39.98        42.38        54.35        67.96        39.25 
TCGA-62-A472 TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5815 
       29.92        39.09        38.37        87.98        42.90        28.47 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7978 TCGA-69-8453 TCGA-73-4662 TCGA-73-4675 
       22.68        13.61         2.30        26.73        29.98         1.32 
TCGA-73-7499 TCGA-78-7145 TCGA-78-7148 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 
       23.51        27.16        20.58        19.50        64.90        22.29 
TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-78-8662 TCGA-86-7701 
       26.53        10.75        10.55       214.62       110.50        31.13 
TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8074 TCGA-86-8358 TCGA-86-8669 
       13.87        19.43        24.49         0.79        21.47        30.84 
TCGA-86-A4JF TCGA-91-6849 TCGA-93-8067 TCGA-95-7043 TCGA-95-8039 TCGA-95-8494 
       17.62         1.15         6.12         1.22        27.29         2.76 
TCGA-95-A4VN TCGA-97-8174 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-L4-A4E5 TCGA-L9-A443 
       18.18         5.39        17.75        20.84        19.00         3.81 
TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TE 
       12.59        27.19         2.76        37.35         5.29        29.46 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-NJ-A4YF 
       11.05        14.10        71.05 

$`DEL PEAK 24(11Q25) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 
       50.07         3.98        19.96        14.01        45.01         0.00 
TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 
        9.96        47.05         8.02        19.00        20.05        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
        9.01        29.98        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4434 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       25.02        15.02         4.96        22.03         9.04         2.04 
TCGA-35-3615 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 
        0.46         5.98       120.79        37.71        28.41        35.28 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        13.15 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.94        24.36        42.08        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       37.15        38.24        38.89         6.25        26.56        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
       21.63        23.18        63.72        32.45        61.28        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7669 TCGA-44-7670 TCGA-44-8117 
       19.46        12.03         7.17        18.87        29.00        12.66 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
        3.25         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.64        13.45        76.21        28.57        12.66        35.54 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 
       46.72        14.07         8.81        29.75        14.63        12.13 
TCGA-49-6745 TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       17.16        22.26       153.04        63.95        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-50-5045 
        8.55        37.32       123.58       211.82       164.12        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 
       70.55        15.72        60.16        49.28         9.27        40.60 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67        21.47        15.12        18.64        29.03        25.12 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 
       22.55        42.35         3.91        25.55        11.05         6.21 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
       41.69        10.13        25.61         7.59        27.25        34.29 
TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 
       13.94        23.05        38.73        45.21         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6978 TCGA-55-6979 
        0.79        42.51        40.73        15.25         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        2.20        45.34        32.71        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 
      107.21        70.26         0.59         7.99         0.20         0.13 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7907 TCGA-55-7910 
        3.12        23.18         1.28         1.28         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 
       17.65         6.15        19.82         0.16        15.19         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
       19.66        19.73         5.06        23.64        15.65         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
        1.51         2.17        22.16        15.42         1.45         0.95 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 
        0.36         0.26         0.49        17.72         0.30         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        4.80         6.64        17.62         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
       16.93        22.65        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B 
       19.59         0.92        15.81        20.19        19.99        17.95 
TCGA-62-8394 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
        4.57        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 
       56.71        72.30        13.61        40.96        56.81        20.65 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 
       55.43        37.02         2.04        28.41        51.25         1.02 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        12.66         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
       13.87         6.64         6.12         5.42         7.56         6.05 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
        2.93        12.56        14.01        13.45         4.24         7.04 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        2.01        52.60        23.38        26.30        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7146 
        5.39         1.25        39.09        11.18       163.10         5.69 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
       19.27        35.93        21.90        39.52        24.99        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       32.09         5.88         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 
       88.14        31.20         8.02        53.33        39.35        32.68 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59        10.55        27.09        12.36         5.88 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
       34.39        20.55        19.89        16.70         4.08         4.57 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
       24.33        15.75        16.08        15.65        15.85        23.05 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       14.60         1.15        13.91        27.58         0.62        14.96 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32         3.81        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       27.68         7.36        16.18        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.45        19.82         9.76         4.18        23.61         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 
       19.00        17.29         1.12         2.86        18.67        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       15.68        15.65        21.40        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       18.67        20.68        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
        5.59        21.63        24.30        23.80        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 
       16.44        14.30         0.20        14.53         1.91        17.46 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 
       11.87        38.63        86.14        58.45        49.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       58.85         5.49        41.59        31.23         2.43        10.09 
TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.66        11.15        19.13        73.91        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        29.13         0.26         0.43        19.82         9.70 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                        0.13                         0.00 
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                      214.62                       223.96 
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                      20.580                       17.685 
[1] "0.1 - 214.6 (20.6)" "0.0 - 224.0 (17.7)"
[1] "hr=" "1"  
D45V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(11Q25) MUTATED         2       26       27        1        16
  DEL PEAK 24(11Q25) WILD-TYPE       3      109      113        0        35
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 24(11Q25) MUTATED          20         16          2        6
  DEL PEAK 24(11Q25) WILD-TYPE        53         56          9       20
D45V3, multiclass
            clus
vv           DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  STAGE I                             2                            3
  STAGE IA                           26                          109
  STAGE IB                           27                          113
  STAGE II                            1                            0
  STAGE IIA                          16                           35
  STAGE IIB                          20                           53
  STAGE IIIA                         16                           56
  STAGE IIIB                          2                            9
  STAGE IV                            6                           20
[1] 9 2
[1] 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(11Q25) MUTATED    35  66  11   4
  DEL PEAK 24(11Q25) WILD-TYPE 135 212  35  15
D45V4, multiclass
    clus
vv   DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  T1                         35                          135
  T2                         66                          212
  T3                         11                           35
  T4                          4                           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 24(11Q25) MUTATED    67  30    18
  DEL PEAK 24(11Q25) WILD-TYPE 265  66    58
D45V5, multiclass
       clus
vv      DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  N0                            67                          265
  N1                            30                           66
  N2+N3                         18                           58
[1] 3 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 24(11Q25) MUTATED    85   6
  DEL PEAK 24(11Q25) WILD-TYPE 263  19
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(11Q25) MUTATED     85    6
  DEL PEAK 24(11Q25) WILD-TYPE  263   19
   clus
vv  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  0                         85                          263
  1                          6                           19
[1] 2 2
[1] FALSE
D45V7, binary
                              cls
clus                             0   1
  DEL PEAK 24(11Q25) MUTATED    52  64
  DEL PEAK 24(11Q25) WILD-TYPE 223 176
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(11Q25) MUTATED     52   64
  DEL PEAK 24(11Q25) WILD-TYPE  223  176
        clus
vv       DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  FEMALE                         52                          223
  MALE                           64                          176
[1] 2 2
[1] FALSE
D45V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                            4
  DEL PEAK 24(11Q25) WILD-TYPE                         15
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 24(11Q25) MUTATED                                  30
  DEL PEAK 24(11Q25) WILD-TYPE                                77
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(11Q25) MUTATED                                                   69
  DEL PEAK 24(11Q25) WILD-TYPE                                                250
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 24(11Q25) MUTATED                                            0
  DEL PEAK 24(11Q25) WILD-TYPE                                          5
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 24(11Q25) MUTATED                                               2
  DEL PEAK 24(11Q25) WILD-TYPE                                            17
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                                1
  DEL PEAK 24(11Q25) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                                    0
  DEL PEAK 24(11Q25) WILD-TYPE                                  3
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                              0
  DEL PEAK 24(11Q25) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                               5
  DEL PEAK 24(11Q25) WILD-TYPE                            18
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                                 0
  DEL PEAK 24(11Q25) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                                               2
  DEL PEAK 24(11Q25) WILD-TYPE                                             3
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 24(11Q25) MUTATED                              3
  DEL PEAK 24(11Q25) WILD-TYPE                            7
D45V9, multiclass
                                                    clus
vv                                                   DEL PEAK 24(11Q25) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         69
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               2
  LUNG CLEAR CELL ADENOCARCINOMA                                              1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          0
  LUNG MUCINOUS ADENOCARCINOMA                                                0
  LUNG PAPILLARY ADENOCARCINOMA                                               5
  LUNG SIGNET RING ADENOCARCINOMA                                             0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               2
  MUCINOUS (COLLOID) CARCINOMA                                                3
                                                    clus
vv                                                   DEL PEAK 24(11Q25) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          250
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                17
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  2
  LUNG PAPILLARY ADENOCARCINOMA                                                18
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, binary
                              cls
clus                             0   1
  DEL PEAK 24(11Q25) MUTATED     3 113
  DEL PEAK 24(11Q25) WILD-TYPE  18 381
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(11Q25) MUTATED      3  113
  DEL PEAK 24(11Q25) WILD-TYPE   18  381
     clus
vv    DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  NO                           3                           18
  YES                        113                          381
[1] 2 2
[1] FALSE
D45V11, continuous
D45V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 24(11Q25) MUTATED    83   2   0   7
  DEL PEAK 24(11Q25) WILD-TYPE 260  10   4  19
D45V13, multiclass
    clus
vv   DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  R0                         83                          260
  R1                          2                           10
  R2                          0                            4
  RX                          7                           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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(11Q25) MUTATED                                  0     2
  DEL PEAK 24(11Q25) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(11Q25) MUTATED                          14    83
  DEL PEAK 24(11Q25) WILD-TYPE                        37   306
D45V14, multiclass
                                  clus
vv                                 DEL PEAK 24(11Q25) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                14
  WHITE                                                    83
                                  clus
vv                                 DEL PEAK 24(11Q25) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  37
  WHITE                                                     306
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V15, binary
                              cls
clus                             0   1
  DEL PEAK 24(11Q25) MUTATED     1  84
  DEL PEAK 24(11Q25) WILD-TYPE   6 298
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(11Q25) MUTATED      1   84
  DEL PEAK 24(11Q25) WILD-TYPE    6  298
                        clus
vv                       DEL PEAK 24(11Q25) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         84
                        clus
vv                       DEL PEAK 24(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          298
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 25(12P13.2) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(12P13.2) MUTATED    97  39
  DEL PEAK 25(12P13.2) WILD-TYPE 240 115
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                           136                            355 
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                            39                            115 
$`DEL PEAK 25(12P13.2) MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4397 TCGA-05-4405 TCGA-05-4425 
       50.07         3.98        37.02        24.03        20.05        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4432 TCGA-05-4434 TCGA-38-6178 TCGA-44-2657 
       26.01        26.01        25.02        15.02        14.73        13.15 
TCGA-44-2661 TCGA-44-2666 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 TCGA-44-6778 
       24.36         3.19        37.15        38.89        34.06        61.28 
TCGA-44-7662 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47B TCGA-44-A47F 
        7.17        17.59        12.66         8.55         9.44        11.08 
TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-6743 TCGA-49-6745 
       13.45        28.57        12.66        46.72        12.13        17.16 
TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN 
       11.64        22.26       153.04         8.55        40.41        37.32 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 TCGA-50-5935 TCGA-50-5939 TCGA-50-5942 
       70.55        15.72        49.28        21.47        15.12        29.03 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 TCGA-55-1592 
       22.55         3.91        11.05        12.16        25.61        23.05 
TCGA-55-5899 TCGA-55-6968 TCGA-55-6975 TCGA-55-6979 TCGA-55-6986 TCGA-55-7283 
        2.86        42.51         3.88         7.79       107.21         1.15 
TCGA-55-7573 TCGA-55-7727 TCGA-55-7728 TCGA-55-7910 TCGA-55-7914 TCGA-55-8087 
        0.13         1.12         0.79         6.48         6.15        15.19 
TCGA-55-8092 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 
        5.06         0.26        17.72         0.30         6.64        17.62 
TCGA-55-8616 TCGA-55-8619 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A491 TCGA-55-A4DG 
        1.58         1.61        22.65        21.40        20.58        19.99 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-64-1676 TCGA-64-1681 
       56.71        54.35        72.30        13.61        56.81        38.37 
TCGA-64-5778 TCGA-67-3770 TCGA-67-3771 TCGA-67-3774 TCGA-67-6217 TCGA-69-7763 
       42.90         1.02        20.05        12.66        13.87        22.68 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-71-6725 TCGA-73-4662 
        5.42         6.05         2.93        14.01         2.01        29.98 
TCGA-73-4668 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7145 TCGA-78-7147 
       15.35         1.25        39.09        23.51        27.16        19.27 
TCGA-78-7153 TCGA-78-7161 TCGA-78-7535 TCGA-83-5908 TCGA-86-7955 TCGA-86-8073 
       24.99         7.07        31.20        27.09        16.70        24.33 
TCGA-86-8074 TCGA-86-8279 TCGA-86-8358 TCGA-86-8672 TCGA-91-6828 TCGA-91-6835 
        0.79        15.85        21.47         0.62        10.62         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-95-7567 TCGA-95-7947 
       13.71        12.23        27.68         1.15        18.67        15.68 
TCGA-95-7948 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-7938 
       15.65         2.76        31.69        64.60        25.48         0.59 
TCGA-97-8177 TCGA-97-A4M1 TCGA-97-A4M3 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       16.41        19.76        17.75        18.67        24.56        34.85 
TCGA-J2-A4AD TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4TC TCGA-MP-A4TH 
       18.08        12.59        11.87         2.76         2.43        14.66 
TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-O1-A52J 
       71.05         0.13        29.13        59.11 

$`DEL PEAK 25(12P13.2) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 
       19.96        14.01        45.01         0.00         9.96        47.05 
TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 
        8.02        19.00         2.99        14.96         9.01        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 
       12.00        30.02        25.02        24.00        15.02         4.96 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
       29.00        22.03         9.04         2.04         0.46         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F 
       28.41        35.28        11.64        44.61        26.30         4.37 
TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 
       43.53        46.98        44.94        42.08        42.77        25.02 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       38.24         6.25        26.56        33.30        28.37        12.59 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       23.77        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.18        63.72        32.45        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 
       12.03        36.07        18.87        29.00        23.64         3.25 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 
       15.98        15.32        11.54        13.64        76.21        28.11 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       35.54        14.07        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 
       55.89        14.63        29.26        22.26        63.95        62.24 
TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       28.90       123.58       211.82       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       71.47        60.16        31.04         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 TCGA-50-6590 
       40.60        78.67         8.45        18.64        25.12        42.35 
TCGA-50-6592 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 
       25.55         6.21        41.69         0.72        10.13         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       27.25        34.29        30.54        13.94         9.21        38.73 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       48.62        45.21         0.07        32.65         0.79        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 
       15.25         0.82        48.49         5.49         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 
       32.71        60.03        24.99        40.54        70.26         0.59 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        7.99         0.20         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 
        1.28         1.78        18.64         0.53        17.65        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 
        0.16        29.72         3.29        19.66        19.73         0.13 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 
       23.64        15.65        17.98         1.08         1.51         2.17 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42         1.45         0.76         0.95         0.36 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8620 TCGA-55-8621 
        0.49         0.10         4.80         0.49         2.17        16.93 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
       20.71         1.58        19.59         0.92        15.81        20.19 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       17.95         4.57        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 
       49.25        47.80        19.53        67.96        39.25        40.96 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
       29.92        20.65        39.09        55.43        37.02        87.98 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 
        2.04        28.41        51.25        28.47        18.84        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7973 
        5.72         4.64         6.64         6.12        13.61         7.56 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K 
        2.30        12.56        13.45         4.24        26.73         7.04 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       52.60        23.38        26.30         4.31         1.32         5.39 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       11.18       163.10         5.69        20.58        35.93        21.90 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.52        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
       22.29       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 
      214.62        39.75        77.59        10.55       110.50        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8075 TCGA-86-8076 
       19.89        24.49         4.08         4.57        15.75        16.08 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.65        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
       27.58        14.96        13.32        13.32         3.81        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6848 
       13.64        26.47        41.36         1.97        10.19         7.36 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       16.18        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-8039 
       17.29         1.12         1.22         2.86        12.39        27.29 
TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       21.40        18.18        19.89        63.52        43.79         5.95 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 
       14.30        21.60        20.58        20.19        21.44        20.52 
TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R 
       20.84        20.68        36.76         1.45         5.59        21.63 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       24.30        23.80        35.47        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N1 
        3.81         0.20        14.53         1.91        17.46        27.19 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       38.63        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD 
       58.85         5.49         5.29        41.59        31.23        10.09 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       29.46        11.05        14.10        11.15        19.13        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       62.60         1.64         0.26         0.43        19.82         9.70 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                        153.04                         223.96 
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                         16.93                          19.00 
[1] "0.1 - 153.0 (16.9)" "0.0 - 224.0 (19.0)"
[1] "hr=" "1.1"
D46V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(12P13.2) MUTATED         0       43       43        1         9
  DEL PEAK 25(12P13.2) WILD-TYPE       5       92       97        0        42
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 25(12P13.2) MUTATED          15         20          1        6
  DEL PEAK 25(12P13.2) WILD-TYPE        58         52         10       20
D46V3, multiclass
            clus
vv           DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                             43                             92
  STAGE IB                             43                             97
  STAGE II                              1                              0
  STAGE IIA                             9                             42
  STAGE IIB                            15                             58
  STAGE IIIA                           20                             52
  STAGE IIIB                            1                             10
  STAGE IV                              6                             20
[1] 9 2
[1] 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(12P13.2) MUTATED    52  72  10   4
  DEL PEAK 25(12P13.2) WILD-TYPE 118 206  36  15
D46V4, multiclass
    clus
vv   DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  T1                           52                            118
  T2                           72                            206
  T3                           10                             36
  T4                            4                             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 25(12P13.2) MUTATED    95  23    19
  DEL PEAK 25(12P13.2) WILD-TYPE 237  73    57
D46V5, multiclass
       clus
vv      DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  N0                              95                            237
  N1                              23                             73
  N2+N3                           19                             57
[1] 3 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 25(12P13.2) MUTATED    90   5
  DEL PEAK 25(12P13.2) WILD-TYPE 258  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(12P13.2) MUTATED     90    5
  DEL PEAK 25(12P13.2) WILD-TYPE  258   20
   clus
vv  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  0                           90                            258
  1                            5                             20
[1] 2 2
[1] FALSE
D46V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(12P13.2) MUTATED    92  46
  DEL PEAK 25(12P13.2) WILD-TYPE 183 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(12P13.2) MUTATED     92   46
  DEL PEAK 25(12P13.2) WILD-TYPE  183  194
        clus
vv       DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  FEMALE                           92                            183
  MALE                             46                            194
[1] 2 2
[1] FALSE
D46V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                            2
  DEL PEAK 25(12P13.2) WILD-TYPE                         17
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 25(12P13.2) MUTATED                                  34
  DEL PEAK 25(12P13.2) WILD-TYPE                                73
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 25(12P13.2) MUTATED                                                   85
  DEL PEAK 25(12P13.2) WILD-TYPE                                                234
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 25(12P13.2) MUTATED                                            0
  DEL PEAK 25(12P13.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 25(12P13.2) MUTATED                                               7
  DEL PEAK 25(12P13.2) WILD-TYPE                                            12
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                                1
  DEL PEAK 25(12P13.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                                    1
  DEL PEAK 25(12P13.2) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                              0
  DEL PEAK 25(12P13.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                               5
  DEL PEAK 25(12P13.2) WILD-TYPE                            18
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                                 0
  DEL PEAK 25(12P13.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                                               1
  DEL PEAK 25(12P13.2) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                              2
  DEL PEAK 25(12P13.2) WILD-TYPE                            8
D46V9, multiclass
                                                    clus
vv                                                   DEL PEAK 25(12P13.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           85
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 7
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 5
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 25(12P13.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     17
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            234
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  12
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  18
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   4
  MUCINOUS (COLLOID) CARCINOMA                                                    8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, binary
                                cls
clus                               0   1
  DEL PEAK 25(12P13.2) MUTATED     5 133
  DEL PEAK 25(12P13.2) WILD-TYPE  16 361
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(12P13.2) MUTATED      5  133
  DEL PEAK 25(12P13.2) WILD-TYPE   16  361
     clus
vv    DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  NO                             5                             16
  YES                          133                            361
[1] 2 2
[1] FALSE
D46V11, continuous
D46V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(12P13.2) MUTATED    86   4   2   5
  DEL PEAK 25(12P13.2) WILD-TYPE 257   8   2  21
D46V13, multiclass
    clus
vv   DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  R0                           86                            257
  R1                            4                              8
  R2                            2                              2
  RX                            5                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(12P13.2) MUTATED                                  1     1
  DEL PEAK 25(12P13.2) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(12P13.2) MUTATED                          20   103
  DEL PEAK 25(12P13.2) WILD-TYPE                        31   286
D46V14, multiclass
                                  clus
vv                                 DEL PEAK 25(12P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     103
                                  clus
vv                                 DEL PEAK 25(12P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    31
  WHITE                                                       286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V15, binary
                                cls
clus                               0   1
  DEL PEAK 25(12P13.2) MUTATED     1 112
  DEL PEAK 25(12P13.2) WILD-TYPE   6 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(12P13.2) MUTATED      1  112
  DEL PEAK 25(12P13.2) WILD-TYPE    6  270
                        clus
vv                       DEL PEAK 25(12P13.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          112
                        clus
vv                       DEL PEAK 25(12P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            270
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 26(12Q12) MUTATION ANALYSIS
D47V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 26(12Q12) MUTATED    66  30
  DEL PEAK 26(12Q12) WILD-TYPE 271 124
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                          96                          395 
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                          30                          124 
$`DEL PEAK 26(12Q12) MUTATED`
TCGA-05-4250 TCGA-05-4405 TCGA-05-4426 TCGA-35-3615 TCGA-38-4632 TCGA-38-6178 
        3.98        20.05        26.01         0.46        44.61        14.73 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2666 TCGA-44-6775 TCGA-44-6779 TCGA-44-7662 
       13.15        24.36         3.19        23.18        16.44         7.17 
TCGA-44-7671 TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 
       17.59         8.55        11.08        13.45        28.57        12.66 
TCGA-49-6745 TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5049 TCGA-50-5051 
       17.16        22.26       153.04        37.32        70.55        15.72 
TCGA-50-5068 TCGA-50-5939 TCGA-50-6591 TCGA-50-6593 TCGA-50-8457 TCGA-50-8460 
       49.28        15.12         3.91        11.05        25.61        27.25 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6712 TCGA-55-6979 TCGA-55-6981 TCGA-55-7283 
       23.05         2.86         0.79         7.79        45.34         1.15 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7914 TCGA-55-8089 TCGA-55-8092 TCGA-55-8207 
        1.12         0.53         6.15         3.29         5.06         2.17 
TCGA-55-8505 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
        0.95        17.72         6.64        17.62         1.58         1.61 
TCGA-55-A48X TCGA-55-A48Z TCGA-55-A491 TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       22.65        21.40        20.58        56.71        54.35        67.96 
TCGA-62-A46Y TCGA-64-1676 TCGA-64-5778 TCGA-67-6217 TCGA-69-7763 TCGA-69-7765 
       13.61        56.81        42.90        13.87        22.68         5.42 
TCGA-71-6725 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-78-7153 
        2.01         4.31         1.32         1.25        39.09        24.99 
TCGA-78-7535 TCGA-86-6851 TCGA-86-7955 TCGA-86-8074 TCGA-86-8279 TCGA-86-8280 
       31.20         5.88        16.70         0.79        15.85        23.05 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8672 TCGA-91-6847 TCGA-91-6849 TCGA-95-7039 
       14.60        13.91         0.62        27.68         1.15         1.12 
TCGA-95-7043 TCGA-95-7948 TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 
        1.22        15.65        27.29        31.69        64.60        25.48 
TCGA-97-8177 TCGA-97-A4M1 TCGA-99-7458 TCGA-99-8025 TCGA-J2-A4AD TCGA-L9-A8F4 
       16.41        19.76        24.56        34.85        18.08        11.87 
TCGA-MP-A4T6 TCGA-MP-A4TC TCGA-MP-A4TK TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
       58.85         2.43        19.13         0.43         9.70        59.11 

$`DEL PEAK 26(12Q12) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       50.07        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 
        9.96        24.03        47.05         8.02        19.00         2.99 
TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       14.96         9.01        29.98        12.00        30.02        21.99 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       28.41        35.28        11.64        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 
       46.98        44.94        42.08        42.77        25.02        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       38.24        38.89        34.06         6.25        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
       23.15        21.63        63.72        32.45        61.28        14.60 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 
       19.46        12.03        36.07        18.87        29.00        23.64 
TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       12.66         3.25        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 
       13.64        76.21        28.11        35.54        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 
       32.84         8.81        29.46        29.75        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       12.13        29.26        11.64        22.26        63.95        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       28.90         8.55        40.41       123.58       211.82       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
        9.86        20.52        71.47        60.16        31.04         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 
        9.27        14.27        40.60        78.67        21.47         8.45 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 
       18.64        29.03        25.12        22.55        42.35        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 
       12.16         6.21        41.69         0.72        10.13         7.59 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 
       34.29        30.54        13.94         9.21        38.73        48.62 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       45.21         0.07        32.65        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6980 TCGA-55-6982 
        0.82        48.49         3.88         5.49         2.20        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       60.03        24.99        40.54       107.21        70.26         0.59 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
        7.99         0.20         0.13         3.12         1.32        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
        1.28         1.28         0.79         1.78        18.64         6.48 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
       17.65        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
       19.73         0.13        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
        1.51        22.16        15.42         1.45         0.76         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 
        0.26         0.49         0.30         0.10         4.80         0.49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A492 TCGA-55-A493 
        2.17        16.93        20.71         1.58        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
       15.81        20.19        19.99        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
       72.30        39.25        40.96        29.92        20.65        39.09 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
       55.43        37.02        38.37        87.98         2.04        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       51.25        28.47         1.02        20.05        18.84        14.04 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
       12.66         5.72         4.64         6.64         6.12        13.61 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
        7.56         6.05         2.30         2.93        12.56        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 
       13.45         4.24        26.73         7.04        52.60        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS 
       29.98        26.30        15.35         5.39        23.51        11.18 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      163.10        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.52        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       64.90        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        26.53         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       10.55        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
      110.50        27.09        12.36        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       20.55        19.43        19.89        24.49         4.08         4.57 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 TCGA-86-8585 
       24.33        15.75        16.08        15.65        21.47         1.15 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       30.84        27.58        14.96        13.32        13.32         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       17.62        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-7771 
       10.19         2.60        13.71        12.23         7.36        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       16.60        14.27         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8494 TCGA-95-A4VK 
        2.86        18.67        12.39        15.68         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
       18.18        19.89        63.52        43.79         5.95         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.72        18.67        17.92         5.39        18.12        15.39 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 
       14.30        21.60        20.58        20.19        21.44        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 
       17.75        20.84        18.67        20.68        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG 
        5.59        21.63        24.30        23.80        35.47        16.44 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
       19.00        14.30         3.81         0.20        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       17.46        12.59        27.19        38.63         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 
       58.45        49.35        37.35        86.04         5.49         5.29 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       41.59        31.23        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       14.10        11.15        73.91        71.05        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-S2-AA1A 
        1.64        29.13         0.26        19.82        16.87 

  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                        0.43                         0.00 
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                      153.04                       223.96 
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                      15.785                       19.000 
[1] "0.4 - 153.0 (15.8)" "0.0 - 224.0 (19.0)"
[1] "hr=" "1.2"
D47V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(12Q12) MUTATED         0       23       28        0        10
  DEL PEAK 26(12Q12) WILD-TYPE       5      112      112        1        41
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 26(12Q12) MUTATED          11         21          1        4
  DEL PEAK 26(12Q12) WILD-TYPE        62         51         10       22
D47V3, multiclass
            clus
vv           DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  STAGE I                             0                            5
  STAGE IA                           23                          112
  STAGE IB                           28                          112
  STAGE II                            0                            1
  STAGE IIA                          10                           41
  STAGE IIB                          11                           62
  STAGE IIIA                         21                           51
  STAGE IIIB                          1                           10
  STAGE IV                            4                           22
[1] 9 2
[1] 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(12Q12) MUTATED    32  52  11   3
  DEL PEAK 26(12Q12) WILD-TYPE 138 226  35  16
D47V4, multiclass
    clus
vv   DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  T1                         32                          138
  T2                         52                          226
  T3                         11                           35
  T4                          3                           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 26(12Q12) MUTATED    59  20    18
  DEL PEAK 26(12Q12) WILD-TYPE 273  76    58
D47V5, multiclass
       clus
vv      DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  N0                            59                          273
  N1                            20                           76
  N2+N3                         18                           58
[1] 3 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 26(12Q12) MUTATED    57   3
  DEL PEAK 26(12Q12) WILD-TYPE 291  22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(12Q12) MUTATED     57    3
  DEL PEAK 26(12Q12) WILD-TYPE  291   22
   clus
vv  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  0                         57                          291
  1                          3                           22
[1] 2 2
[1] FALSE
D47V7, binary
                              cls
clus                             0   1
  DEL PEAK 26(12Q12) MUTATED    60  38
  DEL PEAK 26(12Q12) WILD-TYPE 215 202
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(12Q12) MUTATED     60   38
  DEL PEAK 26(12Q12) WILD-TYPE  215  202
        clus
vv       DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  FEMALE                         60                          215
  MALE                           38                          202
[1] 2 2
[1] FALSE
D47V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                            3
  DEL PEAK 26(12Q12) WILD-TYPE                         16
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 26(12Q12) MUTATED                                  19
  DEL PEAK 26(12Q12) WILD-TYPE                                88
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(12Q12) MUTATED                                                   63
  DEL PEAK 26(12Q12) WILD-TYPE                                                256
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 26(12Q12) MUTATED                                            1
  DEL PEAK 26(12Q12) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 26(12Q12) MUTATED                                               5
  DEL PEAK 26(12Q12) WILD-TYPE                                            14
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                                0
  DEL PEAK 26(12Q12) WILD-TYPE                              2
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                                    0
  DEL PEAK 26(12Q12) WILD-TYPE                                  3
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                              0
  DEL PEAK 26(12Q12) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                               5
  DEL PEAK 26(12Q12) WILD-TYPE                            18
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                                 0
  DEL PEAK 26(12Q12) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                                               0
  DEL PEAK 26(12Q12) WILD-TYPE                                             5
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 26(12Q12) MUTATED                              2
  DEL PEAK 26(12Q12) WILD-TYPE                            8
D47V9, multiclass
                                                    clus
vv                                                   DEL PEAK 26(12Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          19
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         63
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               5
  LUNG CLEAR CELL ADENOCARCINOMA                                              0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          0
  LUNG MUCINOUS ADENOCARCINOMA                                                0
  LUNG PAPILLARY ADENOCARCINOMA                                               5
  LUNG SIGNET RING ADENOCARCINOMA                                             0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               0
  MUCINOUS (COLLOID) CARCINOMA                                                2
                                                    clus
vv                                                   DEL PEAK 26(12Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            88
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          256
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                14
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  2
  LUNG PAPILLARY ADENOCARCINOMA                                                18
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 5
  MUCINOUS (COLLOID) CARCINOMA                                                  8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, binary
                              cls
clus                             0   1
  DEL PEAK 26(12Q12) MUTATED     2  96
  DEL PEAK 26(12Q12) WILD-TYPE  19 398
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(12Q12) MUTATED      2   96
  DEL PEAK 26(12Q12) WILD-TYPE   19  398
     clus
vv    DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  NO                           2                           19
  YES                         96                          398
[1] 2 2
[1] FALSE
D47V11, continuous
D47V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 26(12Q12) MUTATED    62   1   1   6
  DEL PEAK 26(12Q12) WILD-TYPE 281  11   3  20
D47V13, multiclass
    clus
vv   DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  R0                         62                          281
  R1                          1                           11
  R2                          1                            3
  RX                          6                           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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(12Q12) MUTATED                                  0     1
  DEL PEAK 26(12Q12) WILD-TYPE                                1     6
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(12Q12) MUTATED                          12    80
  DEL PEAK 26(12Q12) WILD-TYPE                        39   309
D47V14, multiclass
                                  clus
vv                                 DEL PEAK 26(12Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                12
  WHITE                                                    80
                                  clus
vv                                 DEL PEAK 26(12Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  39
  WHITE                                                     309
[1] 4 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 26(12Q12) MUTATED     2  84
  DEL PEAK 26(12Q12) WILD-TYPE   5 298
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(12Q12) MUTATED      2   84
  DEL PEAK 26(12Q12) WILD-TYPE    5  298
                        clus
vv                       DEL PEAK 26(12Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         84
                        clus
vv                       DEL PEAK 26(12Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          298
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 27(12Q24.33) MUTATION ANALYSIS
D48V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 27(12Q24.33) MUTATED    82  50
  DEL PEAK 27(12Q24.33) WILD-TYPE 255 104
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                            132                             359 
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                             50                             104 
$`DEL PEAK 27(12Q24.33) MUTATED`
TCGA-05-4424 TCGA-05-4426 TCGA-05-4434 TCGA-35-3615 TCGA-38-4628 TCGA-38-4632 
       30.02        26.01        15.02         0.46        49.05        44.61 
TCGA-38-6178 TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2666 
       14.73        46.98        13.15        24.36        42.08         3.19 
TCGA-44-2668 TCGA-44-5645 TCGA-44-6146 TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 
       25.02        12.59         9.93        23.18        63.72        16.44 
TCGA-44-7662 TCGA-44-7671 TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SU TCGA-49-4488 
        7.17        17.59         8.55        11.08        13.45        28.57 
TCGA-49-4490 TCGA-49-4501 TCGA-49-4510 TCGA-49-6744 TCGA-49-6745 TCGA-49-AAQV 
       12.66        46.72        29.46        29.26        17.16        22.26 
TCGA-49-AAR0 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARQ TCGA-50-5049 
      153.04         8.55        40.41        37.32       211.82        70.55 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5939 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 
       49.28        40.60        15.12        22.55         3.91        11.05 
TCGA-50-6597 TCGA-50-8457 TCGA-50-8460 TCGA-55-1592 TCGA-55-6979 TCGA-55-6980 
       41.69        25.61        27.25        23.05         7.79         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 TCGA-55-6986 TCGA-55-7283 TCGA-55-7727 
       45.34        32.71        24.99       107.21         1.15         1.12 
TCGA-55-7911 TCGA-55-7914 TCGA-55-8087 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
       17.65         6.15        15.19         0.36         0.49        17.72 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-A48X 
        0.30         6.64        17.62         1.58         1.61        22.65 
TCGA-55-A48Z TCGA-55-A4DF TCGA-55-A4DG TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       21.40        20.19        19.99        56.71        54.35        67.96 
TCGA-62-A46Y TCGA-64-5778 TCGA-67-3772 TCGA-67-3774 TCGA-67-6217 TCGA-69-7761 
       13.61        42.90        18.84        12.66        13.87         6.12 
TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-71-6725 
       22.68         5.42         6.05         2.93        14.01         2.01 
TCGA-73-4658 TCGA-73-4670 TCGA-73-4677 TCGA-78-7147 TCGA-78-7150 TCGA-78-7153 
       52.60         4.31         1.25        19.27        21.90        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7167 TCGA-78-7535 TCGA-78-8640 TCGA-86-6562 
       19.50        38.50        88.14        31.20       214.62        12.36 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-A4D0 TCGA-91-6847 
       15.75        15.65        15.85        23.05         3.81        27.68 
TCGA-91-6849 TCGA-91-7771 TCGA-93-7348 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7562 
        1.15        16.18         4.18         1.08         1.12         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 
       15.68        15.65        27.29        31.69        64.60        25.48 
TCGA-97-7937 TCGA-97-8174 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 
        5.95         5.39        20.58        19.76        18.67        24.56 
TCGA-99-8025 TCGA-J2-A4AD TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4T4 
       34.85        18.08        11.87        27.19         2.76        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TK TCGA-NJ-A55O TCGA-NJ-A7XG 
       58.85        41.59         2.43        19.13         0.43         9.70 

$`DEL PEAK 27(12Q24.33) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        0.00         9.96        24.03        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
       20.05         2.99        14.96         9.01        29.98        12.00 
TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 
       21.99        26.01        25.02        25.02        24.00        15.02 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
        4.96        29.00        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
        5.98         8.68        97.74       120.79        37.71        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2659 
       35.28        11.64        26.30         4.37        43.53        44.94 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       42.77        37.15        38.24        38.89        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 
       26.56        33.30        28.37        23.77        10.78        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 
       23.15        21.63        32.45        61.28        14.60        19.46 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 
       12.03        36.07        18.87        29.00        23.64        12.66 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        3.25        15.98        15.32         9.44        11.54        13.64 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       76.21        28.11        35.54        14.07        32.84         8.81 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6761 TCGA-49-6767 
       29.75        55.89        14.63        12.13        11.64        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V 
       63.95        62.24        28.90       123.58       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
       20.52        71.47        15.72        60.16        31.04         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5941 
        9.27        14.27        78.67        21.47         8.45        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 
       29.03        25.12        42.35        25.55        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
        0.72        10.13         7.59        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
        9.21        38.73        48.62        45.21         2.86         0.07 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       32.65         0.79        42.51        40.73        15.25         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 
       48.49         3.88         5.49        60.03        40.54        70.26 
TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 
        0.59         7.99         0.20         0.13         3.12         1.32 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       23.18         1.28         1.28         0.79         1.78        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 
        0.53         6.48        19.82         0.16        29.72         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.66        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8512 TCGA-55-8513 
        1.45         0.76         0.95         0.26         0.10         4.80 
TCGA-55-8615 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 
        0.49         2.17        16.93        20.71         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
       19.59         0.92        15.81        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       42.38        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       72.30        39.25        40.96        29.92        56.81        20.65 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       39.09        55.43        37.02        38.37        87.98         2.04 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 
       28.41        51.25        28.47         1.02        20.05        14.04 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 
        5.72         4.64         6.64        13.61         7.56         2.30 
TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 
       12.56        13.45         4.24        26.73         7.04        23.38 
TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 
       29.98        26.30        15.35         1.32         5.39        39.09 
TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
       23.51        11.18       163.10        27.16         5.69        20.58 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       35.93        39.52        32.09         5.88        64.90        22.29 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 
        7.07       104.19       223.96         8.48        26.53         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       53.33        10.75        39.35        10.55        32.68        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
       77.59        10.55       110.50        27.09         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       34.39        13.87        20.55        19.43        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 
       24.49         4.08         4.57        24.33         0.79        16.08 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       21.47        14.60         1.15        13.91        30.84        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
        0.62        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       26.47        10.62        41.36         1.97        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
       13.71        12.23         7.36        16.60        14.27         1.18 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP 
        1.45        19.82         9.76         6.12        23.61        19.00 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 TCGA-95-A4VK 
       17.29         1.22        18.67        12.39         2.76        21.40 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 
       18.18        19.89        63.52        43.79         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67        17.92        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       21.60        20.19        21.44        20.52        17.75        20.84 
TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       20.68        36.76         1.45         5.59        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
       23.80        35.47        16.44        19.00        14.30         3.81 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N4 
        0.20        14.53         1.91        17.46        12.59        38.63 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T8 
       86.14        58.45        49.35        37.35         5.49         5.29 
TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       31.23        10.09        29.46        11.05        14.66        14.10 
TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       11.15        73.91        71.05        62.60         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       29.13         0.26        19.82        59.11        16.87 

  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                            0.3                             0.0 
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                         214.62                          223.96 
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                         18.375                          18.640 
[1] "0.3 - 214.6 (18.4)" "0.0 - 224.0 (18.6)"
[1] "hr=" "1.2"
D48V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(12Q24.33) MUTATED         2       28       43        1        15
  DEL PEAK 27(12Q24.33) WILD-TYPE       3      107       97        0        36
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 27(12Q24.33) MUTATED          22         19          1        6
  DEL PEAK 27(12Q24.33) WILD-TYPE        51         53         10       20
D48V3, multiclass
            clus
vv           DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  STAGE I                                2                               3
  STAGE IA                              28                             107
  STAGE IB                              43                              97
  STAGE II                               1                               0
  STAGE IIA                             15                              36
  STAGE IIB                             22                              51
  STAGE IIIA                            19                              53
  STAGE IIIB                             1                              10
  STAGE IV                               6                              20
[1] 9 2
[1] 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(12Q24.33) MUTATED    38  84  11   4
  DEL PEAK 27(12Q24.33) WILD-TYPE 132 194  35  15
D48V4, multiclass
    clus
vv   DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  T1                            38                             132
  T2                            84                             194
  T3                            11                              35
  T4                             4                              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(12Q24.33) MUTATED    86  31    18
  DEL PEAK 27(12Q24.33) WILD-TYPE 246  65    58
D48V5, multiclass
       clus
vv      DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  N0                               86                             246
  N1                               31                              65
  N2+N3                            18                              58
[1] 3 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 27(12Q24.33) MUTATED    78   5
  DEL PEAK 27(12Q24.33) WILD-TYPE 270  20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(12Q24.33) MUTATED     78    5
  DEL PEAK 27(12Q24.33) WILD-TYPE  270   20
   clus
vv  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  0                            78                             270
  1                             5                              20
[1] 2 2
[1] FALSE
D48V7, binary
                                 cls
clus                                0   1
  DEL PEAK 27(12Q24.33) MUTATED    81  56
  DEL PEAK 27(12Q24.33) WILD-TYPE 194 184
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(12Q24.33) MUTATED     81   56
  DEL PEAK 27(12Q24.33) WILD-TYPE  194  184
        clus
vv       DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  FEMALE                            81                             194
  MALE                              56                             184
[1] 2 2
[1] FALSE
D48V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                            4
  DEL PEAK 27(12Q24.33) WILD-TYPE                         15
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 27(12Q24.33) MUTATED                                  25
  DEL PEAK 27(12Q24.33) WILD-TYPE                                82
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(12Q24.33) MUTATED                                                   88
  DEL PEAK 27(12Q24.33) WILD-TYPE                                                231
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 27(12Q24.33) MUTATED                                            0
  DEL PEAK 27(12Q24.33) WILD-TYPE                                          5
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 27(12Q24.33) MUTATED                                               7
  DEL PEAK 27(12Q24.33) WILD-TYPE                                            12
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                                0
  DEL PEAK 27(12Q24.33) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                                    1
  DEL PEAK 27(12Q24.33) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                              1
  DEL PEAK 27(12Q24.33) WILD-TYPE                            1
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                               7
  DEL PEAK 27(12Q24.33) WILD-TYPE                            16
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                                 0
  DEL PEAK 27(12Q24.33) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                                               1
  DEL PEAK 27(12Q24.33) WILD-TYPE                                             4
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                              3
  DEL PEAK 27(12Q24.33) WILD-TYPE                            7
D48V9, multiclass
                                                    clus
vv                                                   DEL PEAK 27(12Q24.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            88
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  7
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                  7
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  1
  MUCINOUS (COLLOID) CARCINOMA                                                   3
                                                    clus
vv                                                   DEL PEAK 27(12Q24.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             231
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   12
  LUNG CLEAR CELL ADENOCARCINOMA                                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               2
  LUNG MUCINOUS ADENOCARCINOMA                                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                                   16
  LUNG SIGNET RING ADENOCARCINOMA                                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    4
  MUCINOUS (COLLOID) CARCINOMA                                                     7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, binary
                                 cls
clus                                0   1
  DEL PEAK 27(12Q24.33) MUTATED     2 135
  DEL PEAK 27(12Q24.33) WILD-TYPE  19 359
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(12Q24.33) MUTATED      2  135
  DEL PEAK 27(12Q24.33) WILD-TYPE   19  359
     clus
vv    DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  NO                              2                              19
  YES                           135                             359
[1] 2 2
[1] FALSE
D48V11, continuous
D48V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 27(12Q24.33) MUTATED    84   2   1   8
  DEL PEAK 27(12Q24.33) WILD-TYPE 259  10   3  18
D48V13, multiclass
    clus
vv   DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  R0                            84                             259
  R1                             2                              10
  R2                             1                               3
  RX                             8                              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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(12Q24.33) MUTATED                                  0     1
  DEL PEAK 27(12Q24.33) WILD-TYPE                                1     6
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(12Q24.33) MUTATED                          22   105
  DEL PEAK 27(12Q24.33) WILD-TYPE                        29   284
D48V14, multiclass
                                  clus
vv                                 DEL PEAK 27(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   22
  WHITE                                                      105
                                  clus
vv                                 DEL PEAK 27(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     29
  WHITE                                                        284
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V15, binary
                                 cls
clus                                0   1
  DEL PEAK 27(12Q24.33) MUTATED     2 109
  DEL PEAK 27(12Q24.33) WILD-TYPE   5 273
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(12Q24.33) MUTATED      2  109
  DEL PEAK 27(12Q24.33) WILD-TYPE    5  273
                        clus
vv                       DEL PEAK 27(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           109
                        clus
vv                       DEL PEAK 27(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             273
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 28(13Q12.11) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(13Q12.11) MUTATED   196  85
  DEL PEAK 28(13Q12.11) WILD-TYPE 141  69
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                            281                             210 
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                             85                              69 
$`DEL PEAK 28(13Q12.11) MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
        3.98        19.96        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       47.05         8.02        20.05         2.99        14.96        29.98 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 
       30.02        21.99        26.01        25.02        25.02         4.96 
TCGA-05-5425 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 
       29.00         7.40         5.98         8.68        97.74        49.05 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2662 TCGA-44-2665 TCGA-44-3917 
       44.61        14.73        46.98        42.08        42.77        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6775 TCGA-44-6777 
       34.06         6.25        33.30        28.37        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       61.28        16.44        19.46         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       29.00        12.66         3.25         8.55        15.98         9.44 
TCGA-44-A47F TCGA-44-A4SU TCGA-49-4487 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 
       11.08        13.45        28.11        46.72        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR0 
       29.46        29.75        12.13        11.64        22.26       153.04 
TCGA-49-AAR3 TCGA-49-AARN TCGA-49-AARO TCGA-4B-A93V TCGA-50-5045 TCGA-50-5051 
       62.24        37.32       123.58         9.86        71.47        15.72 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 
       31.04        49.28         9.27        14.27        78.67        21.47 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
        8.45        15.12        18.64        25.12        22.55         3.91 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
       41.69        10.13        27.25        13.94        23.05        38.73 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62        45.21         2.86        32.65         0.79        42.51 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 
        0.82        48.49         3.88         5.49         2.20        45.34 
TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7573 
       32.71        40.54       107.21        70.26         0.20         0.13 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
        1.32        23.18         1.12         1.78        18.64        17.65 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 
       19.82         0.16         3.29        19.66        19.73         5.06 
TCGA-55-8094 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 
        0.13        17.98         1.51         2.17         1.45         0.76 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8614 
        0.36         0.26         0.49        17.72         0.30        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        0.49         1.58         2.17        21.40         1.58        20.58 
TCGA-55-A493 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
        0.92        19.99         4.57        39.98        42.38        88.64 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       47.80        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        20.65        55.43        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       87.98        42.90        28.41        51.25        28.47         1.02 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 
       13.87         6.64         6.12        13.61         5.42         2.30 
TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
       12.56         4.24         7.04         2.01        52.60        23.38 
TCGA-73-4662 TCGA-73-4675 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       29.98         1.32        23.51       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 
       19.27        19.50        38.50        22.29         7.07        88.14 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-8640 TCGA-78-8660 TCGA-83-5908 
       31.20        53.33        10.75       214.62        10.55        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
       12.36         5.88        31.13        34.39        13.87        19.43 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 
       19.89        16.70        24.49         4.08        24.33        15.75 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 
       15.85        23.05        21.47        14.60        13.91        30.84 
TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6828 
       27.58        14.96        13.32         3.81        17.62        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       41.36        10.19         2.60        13.71        12.23        27.68 
TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JQ 
        7.36        16.18         1.18         6.12         1.08        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 
       27.29         2.76        18.18        19.89        31.69        25.48 
TCGA-97-7938 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
        0.59         5.39        16.41        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-99-7458 
       21.44        19.76        20.52        17.75        20.68        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
       34.85        36.76         1.45         5.59        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A743 
       18.08        35.47        16.44        19.00         3.81        17.46 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       12.59        11.87        86.14        37.35        86.04        58.85 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
        5.29        41.59         2.43        10.09        29.46        11.05 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ 
       14.10        11.15        19.13        71.05         0.13        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.26         0.43        19.82         9.70        59.11 

$`DEL PEAK 28(13Q12.11) WILD-TYPE`
TCGA-05-4249 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4418 TCGA-05-4422 
       50.07        14.01         9.96        19.00         9.01        12.00 
TCGA-05-4427 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5428 TCGA-05-5429 
       26.01        24.00        15.02        15.02        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 
        2.04         0.46       120.79        37.71        28.41        35.28 
TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 
       11.64        26.30         4.37        43.53        13.15        44.94 
TCGA-44-2661 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 
       24.36         3.19        25.02        37.15        38.24        26.56 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6776 TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 
       21.63        63.72        14.60        12.03        17.59        23.64 
TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 
       15.32        11.54        13.64        76.21        28.57        12.66 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 
       35.54        14.07        55.89        14.63        29.26        17.16 
TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARQ 
       22.26        63.95        28.90         8.55        40.41       211.82 
TCGA-49-AARR TCGA-50-5044 TCGA-50-5049 TCGA-50-5055 TCGA-50-5072 TCGA-50-5932 
      164.12        20.52        70.55        60.16         8.22        40.60 
TCGA-50-5942 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       29.03        42.35        25.55        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
        0.72        25.61         7.59        34.29        30.54         9.21 
TCGA-55-6543 TCGA-55-6969 TCGA-55-6970 TCGA-55-6979 TCGA-55-6983 TCGA-55-6984 
        0.07        40.73        15.25         7.79        60.03        24.99 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 
        0.59         1.15         7.99         3.12         1.28         1.28 
TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 
        0.79         0.53         6.48         6.15        29.72        15.19 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 
       23.64        15.65         1.08        22.16        15.42         0.95 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
        0.10         4.80         6.64         1.61        16.93        22.65 
TCGA-55-A48Y TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A57B TCGA-62-8398 
       20.71        19.59        15.81        20.19        17.95        14.60 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A470 TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 
       49.25        19.53        39.25        39.09        37.02         2.04 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        12.66         5.72         4.64 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
       22.68         7.56         6.05         2.93        14.01        13.45 
TCGA-69-8453 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
       26.73        26.30        15.35         4.31         5.39         1.25 
TCGA-73-7498 TCGA-73-A9RS TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       39.09        11.18        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 
       24.99        32.09         5.88        64.90       104.19       223.96 
TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.48        26.53         8.02        39.35        10.55        32.68 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-7714 TCGA-86-8056 TCGA-86-8074 
       39.75        77.59       110.50        20.55         4.57         0.79 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8585 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4P7 
       16.08        15.65         1.15         0.62        13.32        13.64 
TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
       26.47         1.97         1.15        16.60        14.27         1.45 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7043 
       19.82         9.76         4.18        23.61        19.00         1.22 
TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 
       21.40        64.60        63.52        43.79         5.95         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-A4M5 
       18.67        17.92        18.12        15.39        14.30        20.84 
TCGA-97-A4M6 TCGA-99-AA5R TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
       18.67        21.63        14.30         0.20        14.53         1.91 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T7 
       27.19        38.63         2.76        58.45        49.35         5.49 
TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-S2-AA1A 
       31.23        14.66        73.91        62.60         1.64        16.87 

  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                           0.00                            0.07 
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                         214.62                          223.96 
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                         19.130                          17.045 
[1] "0.0 - 214.6 (19.1)" "0.1 - 224.0 (17.0)"
[1] "hr=" "1.1"
D49V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(13Q12.11) MUTATED         3       72       84        1        28
  DEL PEAK 28(13Q12.11) WILD-TYPE       2       63       56        0        23
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 28(13Q12.11) MUTATED          43         41          7       14
  DEL PEAK 28(13Q12.11) WILD-TYPE        30         31          4       12
D49V3, multiclass
            clus
vv           DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  STAGE I                                3                               2
  STAGE IA                              72                              63
  STAGE IB                              84                              56
  STAGE II                               1                               0
  STAGE IIA                             28                              23
  STAGE IIB                             43                              30
  STAGE IIIA                            41                              31
  STAGE IIIB                             7                               4
  STAGE IV                              14                              12
[1] 9 2
[1] 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(13Q12.11) MUTATED    90 168  23  11
  DEL PEAK 28(13Q12.11) WILD-TYPE  80 110  23   8
D49V4, multiclass
    clus
vv   DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  T1                            90                              80
  T2                           168                             110
  T3                            23                              23
  T4                            11                               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 28(13Q12.11) MUTATED   190  56    44
  DEL PEAK 28(13Q12.11) WILD-TYPE 142  40    32
D49V5, multiclass
       clus
vv      DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  N0                              190                             142
  N1                               56                              40
  N2+N3                            44                              32
[1] 3 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 28(13Q12.11) MUTATED   195  13
  DEL PEAK 28(13Q12.11) WILD-TYPE 153  12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q12.11) MUTATED    195   13
  DEL PEAK 28(13Q12.11) WILD-TYPE  153   12
   clus
vv  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  0                           195                             153
  1                            13                              12
[1] 2 2
[1] FALSE
D49V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q12.11) MUTATED   146 147
  DEL PEAK 28(13Q12.11) WILD-TYPE 129  93
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q12.11) MUTATED    146  147
  DEL PEAK 28(13Q12.11) WILD-TYPE  129   93
        clus
vv       DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  FEMALE                           146                             129
  MALE                             147                              93
[1] 2 2
[1] FALSE
D49V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                           10
  DEL PEAK 28(13Q12.11) WILD-TYPE                          9
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 28(13Q12.11) MUTATED                                  62
  DEL PEAK 28(13Q12.11) WILD-TYPE                                45
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 28(13Q12.11) MUTATED                                                  186
  DEL PEAK 28(13Q12.11) WILD-TYPE                                                133
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 28(13Q12.11) MUTATED                                            1
  DEL PEAK 28(13Q12.11) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 28(13Q12.11) MUTATED                                              13
  DEL PEAK 28(13Q12.11) WILD-TYPE                                             6
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                                2
  DEL PEAK 28(13Q12.11) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                                    0
  DEL PEAK 28(13Q12.11) WILD-TYPE                                  3
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                              0
  DEL PEAK 28(13Q12.11) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                              12
  DEL PEAK 28(13Q12.11) WILD-TYPE                            11
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                                 1
  DEL PEAK 28(13Q12.11) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                                               3
  DEL PEAK 28(13Q12.11) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                              3
  DEL PEAK 28(13Q12.11) WILD-TYPE                            7
D49V9, multiclass
                                                    clus
vv                                                   DEL PEAK 28(13Q12.11) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           186
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 13
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             0
  LUNG MUCINOUS ADENOCARCINOMA                                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                                 12
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   3
                                                    clus
vv                                                   DEL PEAK 28(13Q12.11) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             133
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    6
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               3
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   11
  LUNG SIGNET RING ADENOCARCINOMA                                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    2
  MUCINOUS (COLLOID) CARCINOMA                                                     7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q12.11) MUTATED     9 284
  DEL PEAK 28(13Q12.11) WILD-TYPE  12 210
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q12.11) MUTATED      9  284
  DEL PEAK 28(13Q12.11) WILD-TYPE   12  210
     clus
vv    DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  NO                              9                              12
  YES                           284                             210
[1] 2 2
[1] FALSE
D49V11, continuous
D49V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(13Q12.11) MUTATED   194   7   2  17
  DEL PEAK 28(13Q12.11) WILD-TYPE 149   5   2   9
D49V13, multiclass
    clus
vv   DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  R0                           194                             149
  R1                             7                               5
  R2                             2                               2
  RX                            17                               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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(13Q12.11) MUTATED                                  0     5
  DEL PEAK 28(13Q12.11) WILD-TYPE                                1     2
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(13Q12.11) MUTATED                          28   221
  DEL PEAK 28(13Q12.11) WILD-TYPE                        23   168
D49V14, multiclass
                                  clus
vv                                 DEL PEAK 28(13Q12.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   28
  WHITE                                                      221
                                  clus
vv                                 DEL PEAK 28(13Q12.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          2
  BLACK OR AFRICAN AMERICAN                                     23
  WHITE                                                        168
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V15, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q12.11) MUTATED     4 220
  DEL PEAK 28(13Q12.11) WILD-TYPE   3 162
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q12.11) MUTATED      4  220
  DEL PEAK 28(13Q12.11) WILD-TYPE    3  162
                        clus
vv                       DEL PEAK 28(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           220
                        clus
vv                       DEL PEAK 28(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             162
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 29(13Q12.13) MUTATION ANALYSIS
D50V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 29(13Q12.13) MUTATED   193  85
  DEL PEAK 29(13Q12.13) WILD-TYPE 144  69
  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                            278                             213 
  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                             85                              69 
$`DEL PEAK 29(13Q12.13) MUTATED`
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
        3.98        45.01        37.02         0.00        24.03        47.05 
TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 
        8.02        20.05         2.99        14.96        29.98        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 
       21.99        26.01        25.02        25.02         4.96        29.00 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 
        7.40         5.98         8.68        97.74        49.05        28.41 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2662 TCGA-44-3917 TCGA-44-3919 
       44.61        14.73        46.98        42.08        38.89         6.25 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       33.30        28.37        23.18        32.45        61.28        16.44 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 
        7.17        36.07        18.87        29.00        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SU TCGA-49-4487 
        8.55        15.98         9.44        11.08        13.45        28.11 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 
       46.72        32.84         8.81        29.46        29.75        12.13 
TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARO 
       11.64        22.26       153.04        62.24         8.55       123.58 
TCGA-4B-A93V TCGA-50-5045 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 
        9.86        71.47        15.72        31.04        49.28        14.27 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 
       78.67        21.47         8.45        15.12        18.64        25.12 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 
       22.55         3.91        41.69        10.13        27.25        13.94 
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 
       23.05        38.73        48.62        45.21         2.86        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
        0.79        42.51         0.82        48.49         3.88         5.49 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        2.20        45.34        32.71        40.54       107.21        70.26 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7727 
        1.15         0.20         0.13         1.32        23.18         1.12 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 
        1.78        18.64        17.65        19.82         3.29        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8203 TCGA-55-8206 TCGA-55-8207 
       19.73         5.06         0.13        17.98         1.51         2.17 
TCGA-55-8301 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        1.45         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
       17.62         0.49         1.58         2.17        21.40         1.58 
TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       20.58         0.92        19.99         4.57        39.98        42.38 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       88.64        47.80        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
       13.61        40.96        29.92        56.81        20.65        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       38.37        87.98        42.90        28.41        51.25        28.47 
TCGA-67-3770 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
        1.02        13.87         6.64         6.12        13.61         5.42 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
        2.30        12.56         4.24         7.04         2.01        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4675 TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 
       23.38        29.98         1.32        23.51       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 
        5.69        19.27        19.50        38.50        22.29         7.07 
TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-8640 TCGA-78-8660 
       88.14        31.20        53.33        10.75       214.62        10.55 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 
       19.43        19.89        16.70        24.49         4.08        24.33 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
       15.75        15.85        23.05        21.47        14.60        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
       30.84        27.58        14.96        13.32         3.81        17.62 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-93-8067 TCGA-93-A4JO 
       27.68         7.36        16.18         1.18         6.12         1.08 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
       17.29         1.12         2.86        18.67        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       15.65        27.29         2.76        18.18        19.89        31.69 
TCGA-97-7554 TCGA-97-7938 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 
       25.48         0.59         5.39        16.41        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M6 
       20.19        21.44        19.76        20.52        17.75        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SV 
        3.81         0.20        17.46        12.59        11.87        86.14 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC 
       37.35        86.04        58.85         5.29        41.59         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
       10.09        29.46        11.05        14.10        11.15        19.13 
TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       71.05         0.13        29.13         0.26         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J 
        9.70        59.11 

$`DEL PEAK 29(13Q12.13) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4418 
       50.07        19.96        14.01         9.96        19.00         9.01 
TCGA-05-4422 TCGA-05-4427 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5428 
       12.00        26.01        24.00        15.02        15.02        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 
        9.04         2.04         0.46       120.79        37.71        35.28 
TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 
       11.64        26.30         4.37        43.53        13.15        44.94 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       24.36        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 
       34.06        26.56        12.59        23.77        10.78         9.93 
TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 
       27.78        23.15        21.63        63.72        14.60        19.46 
TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS 
       12.03        17.59        23.64        15.32        11.54        13.64 
TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4514 
       76.21        28.57        12.66        35.54        14.07        55.89 
TCGA-49-6742 TCGA-49-6744 TCGA-49-6745 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR4 
       14.63        29.26        17.16        22.26        63.95        28.90 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5049 
       40.41        37.32       211.82       164.12        20.52        70.55 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5932 TCGA-50-5942 TCGA-50-6590 
       60.16         8.22         9.27        40.60        29.03        42.35 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 
       25.55        11.05        12.16         6.21         0.72        25.61 
TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6969 
        7.59        34.29        30.54         9.21         0.07        40.73 
TCGA-55-6970 TCGA-55-6979 TCGA-55-6983 TCGA-55-6984 TCGA-55-7281 TCGA-55-7284 
       15.25         7.79        60.03        24.99         0.59         7.99 
TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 
        3.12         1.28         1.28         0.79         0.53         6.48 
TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8097 
        6.15         0.16        29.72        15.19        23.64        15.65 
TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8512 
        1.08        22.16        15.42         0.76         0.95         0.10 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        4.80         6.64         1.61        16.93        22.65        20.71 
TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A57B TCGA-62-8398 TCGA-62-8402 
       19.59        15.81        20.19        17.95        14.60        49.25 
TCGA-62-A46P TCGA-62-A470 TCGA-64-1678 TCGA-64-1680 TCGA-64-5775 TCGA-67-3771 
       19.53        39.25        39.09        37.02         2.04        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 
       18.84        14.04        12.66         5.72         4.64        22.68 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        7.56         6.05         2.93        14.01        13.45        26.73 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       26.30        15.35         4.31         5.39         1.25        39.09 
TCGA-73-A9RS TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       11.18        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       32.09         5.88        64.90       104.19       223.96         8.48 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       26.53         8.02        39.35        10.55        32.68        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-86-7714 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 
       77.59       110.50        20.55         4.57         0.79        16.08 
TCGA-86-8278 TCGA-86-8585 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 
       15.65         1.15         0.62        13.32        13.64        26.47 
TCGA-91-6830 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD 
        1.97         1.15        16.60        14.27         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7043 TCGA-95-A4VK 
        9.76         4.18        23.61        19.00         1.22        21.40 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
       64.60        63.52        43.79         5.95         0.72        18.67 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-A4M5 TCGA-99-AA5R 
       17.92        18.12        15.39        14.30        20.84        21.63 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30        14.53         1.91        27.19        38.63         2.76 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A5C7 
       58.45        49.35         5.49        31.23        14.66        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-S2-AA1A 
       62.60         1.64        16.87 

  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                           0.00                            0.07 
  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                         214.62                          223.96 
  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE 
                          18.77                           17.59 
[1] "0.0 - 214.6 (18.8)" "0.1 - 224.0 (17.6)"
[1] "hr=" "1.1"
D50V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(13Q12.13) MUTATED         3       71       83        1        28
  DEL PEAK 29(13Q12.13) WILD-TYPE       2       64       57        0        23
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 29(13Q12.13) MUTATED          44         41          7       14
  DEL PEAK 29(13Q12.13) WILD-TYPE        29         31          4       12
D50V3, multiclass
            clus
vv           DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  STAGE I                                3                               2
  STAGE IA                              71                              64
  STAGE IB                              83                              57
  STAGE II                               1                               0
  STAGE IIA                             28                              23
  STAGE IIB                             44                              29
  STAGE IIIA                            41                              31
  STAGE IIIB                             7                               4
  STAGE IV                              14                              12
[1] 9 2
[1] 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(13Q12.13) MUTATED    89 165  26  11
  DEL PEAK 29(13Q12.13) WILD-TYPE  81 113  20   8
D50V4, multiclass
    clus
vv   DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  T1                            89                              81
  T2                           165                             113
  T3                            26                              20
  T4                            11                               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 29(13Q12.13) MUTATED   190  55    44
  DEL PEAK 29(13Q12.13) WILD-TYPE 142  41    32
D50V5, multiclass
       clus
vv      DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  N0                              190                             142
  N1                               55                              41
  N2+N3                            44                              32
[1] 3 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 29(13Q12.13) MUTATED   194  13
  DEL PEAK 29(13Q12.13) WILD-TYPE 154  12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(13Q12.13) MUTATED    194   13
  DEL PEAK 29(13Q12.13) WILD-TYPE  154   12
   clus
vv  DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  0                           194                             154
  1                            13                              12
[1] 2 2
[1] FALSE
D50V7, binary
                                 cls
clus                                0   1
  DEL PEAK 29(13Q12.13) MUTATED   147 145
  DEL PEAK 29(13Q12.13) WILD-TYPE 128  95
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(13Q12.13) MUTATED    147  145
  DEL PEAK 29(13Q12.13) WILD-TYPE  128   95
        clus
vv       DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  FEMALE                           147                             128
  MALE                             145                              95
[1] 2 2
[1] FALSE
D50V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                           10
  DEL PEAK 29(13Q12.13) WILD-TYPE                          9
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 29(13Q12.13) MUTATED                                  61
  DEL PEAK 29(13Q12.13) WILD-TYPE                                46
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(13Q12.13) MUTATED                                                  185
  DEL PEAK 29(13Q12.13) WILD-TYPE                                                134
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 29(13Q12.13) MUTATED                                            1
  DEL PEAK 29(13Q12.13) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 29(13Q12.13) MUTATED                                              14
  DEL PEAK 29(13Q12.13) WILD-TYPE                                             5
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                                2
  DEL PEAK 29(13Q12.13) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                                    0
  DEL PEAK 29(13Q12.13) WILD-TYPE                                  3
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                              0
  DEL PEAK 29(13Q12.13) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                              12
  DEL PEAK 29(13Q12.13) WILD-TYPE                            11
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                                 1
  DEL PEAK 29(13Q12.13) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                                               3
  DEL PEAK 29(13Q12.13) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 29(13Q12.13) MUTATED                              3
  DEL PEAK 29(13Q12.13) WILD-TYPE                            7
D50V9, multiclass
                                                    clus
vv                                                   DEL PEAK 29(13Q12.13) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           185
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 14
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             0
  LUNG MUCINOUS ADENOCARCINOMA                                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                                 12
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   3
                                                    clus
vv                                                   DEL PEAK 29(13Q12.13) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             134
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    5
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               3
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   11
  LUNG SIGNET RING ADENOCARCINOMA                                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    2
  MUCINOUS (COLLOID) CARCINOMA                                                     7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, binary
                                 cls
clus                                0   1
  DEL PEAK 29(13Q12.13) MUTATED     8 284
  DEL PEAK 29(13Q12.13) WILD-TYPE  13 210
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(13Q12.13) MUTATED      8  284
  DEL PEAK 29(13Q12.13) WILD-TYPE   13  210
     clus
vv    DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  NO                              8                              13
  YES                           284                             210
[1] 2 2
[1] FALSE
D50V11, continuous
D50V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 29(13Q12.13) MUTATED   193   7   2  17
  DEL PEAK 29(13Q12.13) WILD-TYPE 150   5   2   9
D50V13, multiclass
    clus
vv   DEL PEAK 29(13Q12.13) MUTATED DEL PEAK 29(13Q12.13) WILD-TYPE
  R0                           193                             150
  R1                             7                               5
  R2                             2                               2
  RX                            17                               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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(13Q12.13) MUTATED                                  0     5
  DEL PEAK 29(13Q12.13) WILD-TYPE                                1     2
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(13Q12.13) MUTATED                          28   219
  DEL PEAK 29(13Q12.13) WILD-TYPE                        23   170
D50V14, multiclass
                                  clus
vv                                 DEL PEAK 29(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   28
  WHITE                                                      219
                                  clus
vv                                 DEL PEAK 29(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          2
  BLACK OR AFRICAN AMERICAN                                     23
  WHITE                                                        170
[1] 4 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 29(13Q12.13) MUTATED     4 219
  DEL PEAK 29(13Q12.13) WILD-TYPE   3 163
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(13Q12.13) MUTATED      4  219
  DEL PEAK 29(13Q12.13) WILD-TYPE    3  163
                        clus
vv                       DEL PEAK 29(13Q12.13) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           219
                        clus
vv                       DEL PEAK 29(13Q12.13) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             163
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 30(13Q14.2) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(13Q14.2) MUTATED   188  83
  DEL PEAK 30(13Q14.2) WILD-TYPE 149  71
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                           271                            220 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                            83                             71 
$`DEL PEAK 30(13Q14.2) MUTATED`
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
        3.98        45.01        37.02         0.00        24.03        47.05 
TCGA-05-4402 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 
        8.02        20.05        14.96        29.98        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 TCGA-35-4122 
       26.01        25.02        25.02         4.96        29.00         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 TCGA-38-4632 
        5.98         8.68        97.74        49.05        28.41        44.61 
TCGA-38-6178 TCGA-44-2662 TCGA-44-3917 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 
       14.73        42.08        38.89         6.25        33.30        28.37 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 
       23.18        32.45        61.28        16.44         7.17        18.87 
TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F 
       29.00        12.66         3.25        15.98         9.44        11.08 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       13.45        28.11        46.72        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-AAQV 
       29.46        29.75        12.13        29.26        11.64        22.26 
TCGA-49-AAR0 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-4B-A93V 
      153.04        62.24         8.55        37.32       123.58         9.86 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
       71.47        15.72        31.04        49.28         9.27        14.27 
TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 
       78.67        21.47         8.45        15.12        18.64        25.12 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 
       22.55         3.91        11.05        41.69        10.13        27.25 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 
       13.94         9.21        23.05        48.62        45.21         2.86 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       32.65         0.79        42.51         0.82        48.49         3.88 
TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 
        5.49         2.20        45.34        32.71        40.54       107.21 
TCGA-55-6987 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 TCGA-55-7727 
       70.26         0.20         0.13         1.32        23.18         1.12 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 
        1.78        18.64        17.65        19.82         0.16         3.29 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8094 TCGA-55-8203 TCGA-55-8207 TCGA-55-8301 
       19.66        19.73         0.13        17.98         2.17         1.45 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.76         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        6.64        17.62         0.49        21.40         1.58        20.58 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        19.99         4.57        39.98        42.38 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       88.64        47.80        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
       13.61        40.96        29.92        56.81        20.65        39.09 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       55.43        38.37        87.98        42.90        28.41        51.25 
TCGA-67-3770 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
        1.02        13.87         6.64         6.12        13.61         5.42 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 
        2.30         2.93         4.24         7.04         2.01        52.60 
TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 
       23.38        29.98        26.30        15.35         1.32        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7154 TCGA-78-7155 
      163.10        27.16         5.69        19.27        19.50        38.50 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 TCGA-78-8660 
       22.29         7.07         8.02        10.75       214.62        10.55 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       27.09        12.36         5.88        31.13        34.39        13.87 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 
       19.43        19.89        16.70        24.49         4.08        15.75 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       15.85        23.05        21.47        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
       30.84        27.58        14.96        13.32         3.81        17.62 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       10.62        41.36        10.19         2.60        13.71        12.23 
TCGA-91-8499 TCGA-93-8067 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
        1.18         6.12         1.08         1.12         2.86        18.67 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN 
       12.39        15.68        15.65        27.29         2.76        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 
       19.89        31.69        25.48         5.39        16.41        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 
       20.58        20.19        21.44        19.76        20.52        17.75 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.67        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       24.30        23.80        18.08        35.47        16.44        19.00 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SV 
        3.81         0.20        17.46        12.59        11.87        86.14 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TC 
       37.35        86.04        58.85         5.29        41.59         2.43 
TCGA-MP-A4TD TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF 
       10.09        11.05        14.10        11.15        19.13        71.05 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.13        29.13         0.26         0.43        19.82         9.70 
TCGA-O1-A52J 
       59.11 

$`DEL PEAK 30(13Q14.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4415 
       50.07        19.96        14.01         9.96        19.00         2.99 
TCGA-05-4418 TCGA-05-4422 TCGA-05-4427 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
        9.01        12.00        26.01        24.00        15.02        15.02 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 
       22.03         9.04         2.04         0.46       120.79        37.71 
TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       35.28        11.64        26.30         4.37        43.53        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       13.15        44.94        24.36        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 
       37.15        38.24        34.06        26.56        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
       10.78         9.93        27.78        23.15        21.63        63.72 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7667 TCGA-44-7671 TCGA-44-7672 
       14.60        19.46        12.03        36.07        17.59        23.64 
TCGA-44-8120 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4488 
        8.55        15.32        11.54        13.64        76.21        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-49-6767 
       12.66        35.54        55.89        14.63        17.16        22.26 
TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 
       63.95        28.90        40.41       211.82       164.12        20.52 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5072 TCGA-50-5932 TCGA-50-5942 TCGA-50-6590 
       70.55        60.16         8.22        40.60        29.03        42.35 
TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 
       25.55        12.16         6.21         0.72        25.61         7.59 
TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-6543 TCGA-55-6969 TCGA-55-6970 
       34.29        30.54        38.73         0.07        40.73        15.25 
TCGA-55-6979 TCGA-55-6983 TCGA-55-6984 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        7.79        60.03        24.99         0.59         1.15         7.99 
TCGA-55-7574 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 
        3.12         1.28         1.28         0.79         0.53         6.48 
TCGA-55-7914 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
        6.15        29.72        15.19         5.06        23.64        15.65 
TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8512 
        1.08         1.51        22.16        15.42         0.95         0.10 
TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
        4.80         1.58         1.61         2.17        16.93        22.65 
TCGA-55-A48Y TCGA-55-A492 TCGA-55-A4DF TCGA-55-A57B TCGA-62-8398 TCGA-62-8402 
       20.71        19.59        20.19        17.95        14.60        49.25 
TCGA-62-A46P TCGA-62-A470 TCGA-64-1680 TCGA-64-5775 TCGA-64-5815 TCGA-67-3771 
       19.53        39.25        37.02         2.04        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 
       18.84        14.04        12.66         5.72         4.64        22.68 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        7.56         6.05        12.56        14.01        13.45        26.73 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7148 
        4.31         5.39         1.25        39.09        11.18        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 
       35.93        21.90        39.52        24.99        32.09         5.88 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
       64.90       104.19       223.96         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 
       31.20        53.33        39.35        10.55        32.68        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-86-7714 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       77.59       110.50        20.55         4.57        24.33         0.79 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 
       16.08        15.65         0.62        13.32        13.64        26.47 
TCGA-91-6830 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
        1.97        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.45        19.82         9.76         4.18        23.61 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 
       19.00        17.29         1.22        21.40        64.60        63.52 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
       43.79         5.95         0.59         0.72        18.67        17.92 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-AA5R 
       18.12        15.39        14.30        20.84        20.68        21.63 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30        14.53         1.91        27.19        38.63         2.76 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TH 
       58.45        49.35         5.49        31.23        29.46        14.66 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-S2-AA1A 
       73.91        62.60         1.64        16.87 

  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                          0.00                           0.07 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                        214.62                         223.96 
  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE 
                        18.640                         18.395 
[1] "0.0 - 214.6 (18.6)" "0.1 - 224.0 (18.4)"
[1] "hr=" "1"  
D51V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(13Q14.2) MUTATED         2       69       78        1        30
  DEL PEAK 30(13Q14.2) WILD-TYPE       3       66       62        0        21
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 30(13Q14.2) MUTATED          42         40          6       13
  DEL PEAK 30(13Q14.2) WILD-TYPE        31         32          5       13
D51V3, multiclass
            clus
vv           DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             69                             66
  STAGE IB                             78                             62
  STAGE II                              1                              0
  STAGE IIA                            30                             21
  STAGE IIB                            42                             31
  STAGE IIIA                           40                             32
  STAGE IIIB                            6                              5
  STAGE IV                             13                             13
[1] 9 2
[1] 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(13Q14.2) MUTATED    87 161  22  10
  DEL PEAK 30(13Q14.2) WILD-TYPE  83 117  24   9
D51V4, multiclass
    clus
vv   DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  T1                           87                             83
  T2                          161                            117
  T3                           22                             24
  T4                           10                              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 30(13Q14.2) MUTATED   179  57    42
  DEL PEAK 30(13Q14.2) WILD-TYPE 153  39    34
D51V5, multiclass
       clus
vv      DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  N0                             179                            153
  N1                              57                             39
  N2+N3                           42                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED   186  12
  DEL PEAK 30(13Q14.2) WILD-TYPE 162  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED    186   12
  DEL PEAK 30(13Q14.2) WILD-TYPE  162   13
   clus
vv  DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  0                          186                            162
  1                           12                             13
[1] 2 2
[1] FALSE
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED   151 130
  DEL PEAK 30(13Q14.2) WILD-TYPE 124 110
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED    151  130
  DEL PEAK 30(13Q14.2) WILD-TYPE  124  110
        clus
vv       DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  FEMALE                          151                            124
  MALE                            130                            110
[1] 2 2
[1] FALSE
D51V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                           11
  DEL PEAK 30(13Q14.2) WILD-TYPE                          8
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 30(13Q14.2) MUTATED                                  59
  DEL PEAK 30(13Q14.2) WILD-TYPE                                48
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(13Q14.2) MUTATED                                                  178
  DEL PEAK 30(13Q14.2) WILD-TYPE                                                141
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 30(13Q14.2) MUTATED                                            1
  DEL PEAK 30(13Q14.2) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 30(13Q14.2) MUTATED                                              11
  DEL PEAK 30(13Q14.2) WILD-TYPE                                             8
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                                2
  DEL PEAK 30(13Q14.2) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                                    1
  DEL PEAK 30(13Q14.2) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                              0
  DEL PEAK 30(13Q14.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                              11
  DEL PEAK 30(13Q14.2) WILD-TYPE                            12
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                                 1
  DEL PEAK 30(13Q14.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                                               3
  DEL PEAK 30(13Q14.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 30(13Q14.2) MUTATED                              3
  DEL PEAK 30(13Q14.2) WILD-TYPE                            7
D51V9, multiclass
                                                    clus
vv                                                   DEL PEAK 30(13Q14.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            59
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          178
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                11
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                11
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   DEL PEAK 30(13Q14.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            141
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   8
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  12
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  MUCINOUS (COLLOID) CARCINOMA                                                    7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED    11 270
  DEL PEAK 30(13Q14.2) WILD-TYPE  10 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED     11  270
  DEL PEAK 30(13Q14.2) WILD-TYPE   10  224
     clus
vv    DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  NO                            11                             10
  YES                          270                            224
[1] 2 2
[1] FALSE
D51V11, continuous
D51V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(13Q14.2) MUTATED   190   7   2  15
  DEL PEAK 30(13Q14.2) WILD-TYPE 153   5   2  11
D51V13, multiclass
    clus
vv   DEL PEAK 30(13Q14.2) MUTATED DEL PEAK 30(13Q14.2) WILD-TYPE
  R0                          190                            153
  R1                            7                              5
  R2                            2                              2
  RX                           15                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(13Q14.2) MUTATED                                  1     5
  DEL PEAK 30(13Q14.2) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(13Q14.2) MUTATED                          29   212
  DEL PEAK 30(13Q14.2) WILD-TYPE                        22   177
D51V14, multiclass
                                  clus
vv                                 DEL PEAK 30(13Q14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  29
  WHITE                                                     212
                                  clus
vv                                 DEL PEAK 30(13Q14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    22
  WHITE                                                       177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                                cls
clus                               0   1
  DEL PEAK 30(13Q14.2) MUTATED     5 212
  DEL PEAK 30(13Q14.2) WILD-TYPE   2 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(13Q14.2) MUTATED      5  212
  DEL PEAK 30(13Q14.2) WILD-TYPE    2  170
                        clus
vv                       DEL PEAK 30(13Q14.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          212
                        clus
vv                       DEL PEAK 30(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            170
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 31(13Q34) MUTATION ANALYSIS
D52V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 31(13Q34) MUTATED   160  72
  DEL PEAK 31(13Q34) WILD-TYPE 177  82
  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                         232                          259 
  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                          72                           82 
$`DEL PEAK 31(13Q34) MUTATED`
TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4402 
        3.98        45.01        37.02         0.00        47.05         8.02 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4430 
       20.05        14.96        29.98        30.02        21.99        25.02 
TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       25.02         4.96        29.00         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2662 
       97.74        49.05        44.61        14.73        46.98        42.08 
TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       38.89        33.30        28.37        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8119 
       16.44         7.17        36.07        18.87        12.66         3.25 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-49-4487 TCGA-49-4488 
        8.55        15.98         9.44        11.08        28.11        28.57 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 
       14.07        32.84         8.81        29.46        29.75        29.26 
TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARO TCGA-4B-A93V 
       11.64        22.26        62.24         8.55       123.58         9.86 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5935 
       15.72        49.28         9.27        14.27        78.67        21.47 
TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 
        8.45        18.64        25.12        22.55         3.91        11.05 
TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       41.69        10.13        27.25        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 
       48.62        45.21         2.86        32.65         0.79         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       48.49         3.88         5.49         2.20        45.34        32.71 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7573 TCGA-55-7576 
       40.54       107.21        70.26         0.20         0.13         1.32 
TCGA-55-7724 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-8090 TCGA-55-8091 
       23.18         1.78        18.64        17.65        19.66        19.73 
TCGA-55-8203 TCGA-55-8207 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 
       17.98         2.17         1.45         0.76         0.36        17.72 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A491 TCGA-55-A493 
        6.64        17.62         0.49         1.58        20.58         0.92 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46R 
       19.99        39.98        42.38        88.64        47.80        56.71 
TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       54.35        72.30        13.61        40.96        29.92        56.81 
TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 
       20.65        39.09        55.43        38.37         2.04        28.41 
TCGA-64-5781 TCGA-67-3770 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
       51.25         1.02        13.87         6.64         6.12        13.61 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
        5.42         2.30         2.93         4.24         7.04         2.01 
TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 
       52.60        23.38        29.98        26.30        15.35         1.32 
TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 TCGA-78-7154 TCGA-78-7160 TCGA-78-7161 
       23.51        27.16         5.69        19.50        22.29         7.07 
TCGA-78-7162 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-7701 
      104.19       214.62        10.55       110.50        27.09        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        13.87        19.43        19.89        16.70        24.49 
TCGA-86-8055 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
        4.08        15.85        23.05        14.60         1.15        13.91 
TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6828 
       30.84         0.62        13.32         3.81        17.62        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-8499 
       41.36        10.19         2.60        13.71        12.23         1.18 
TCGA-93-8067 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7562 TCGA-95-7948 TCGA-95-8039 
        6.12         1.08         1.12         2.86        15.65        27.29 
TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7554 TCGA-97-8171 TCGA-97-8174 
        2.76        18.18        19.89        25.48        18.67         5.39 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M2 
       21.60        20.58        20.19        21.44        19.76        20.52 
TCGA-97-A4M3 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       17.75        24.56        34.85        36.76         1.45         5.59 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A443 
       24.30        23.80        18.08        16.44        19.00         3.81 
TCGA-L9-A444 TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4T2 
        0.20        17.46        12.59        11.87        86.14        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF 
       86.04        58.85        41.59         2.43        10.09        11.05 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A 
       14.10        19.13        71.05         0.13        29.13         0.26 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.43        19.82         9.70        59.11 

$`DEL PEAK 31(13Q34) WILD-TYPE`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4397 TCGA-05-4403 
       50.07        19.96        14.01         9.96        24.03        19.00 
TCGA-05-4415 TCGA-05-4418 TCGA-05-4422 TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 
        2.99         9.01        12.00        26.01        26.01        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       15.02        15.02        22.03         9.04         2.04         0.46 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 
      120.79        37.71        28.41        35.28        11.64        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 
        4.37        43.53        13.15        44.94        24.36        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
        3.19        25.02        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       26.56        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       23.15        21.63        63.72        14.60        19.46        12.03 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS 
       29.00        17.59        23.64        15.32        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4514 
       13.45        76.21        12.66        35.54        46.72        55.89 
TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR2 
       14.63        12.13        17.16        22.26       153.04        63.95 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 
       28.90        40.41        37.32       211.82       164.12        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5932 
       71.47        70.55        60.16        31.04         8.22        40.60 
TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 
       15.12        29.03        42.35        25.55        12.16         6.21 
TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 
        0.72        25.61         7.59        34.29        30.54        38.73 
TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6979 TCGA-55-6983 
        0.07        42.51        40.73        15.25         7.79        60.03 
TCGA-55-6984 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 TCGA-55-7725 
       24.99         0.59         1.15         7.99         3.12         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 
        1.28         1.12         0.79         0.53         6.48         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       19.82         0.16        29.72        15.19         3.29         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 
        0.13        23.64        15.65         1.08         1.51        22.16 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8512 
       15.42         0.95         0.26         0.49         0.30         0.10 
TCGA-55-8513 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        4.80         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A57B 
       21.40         1.58        19.59        15.81        20.19        17.95 
TCGA-62-8394 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46U TCGA-62-A470 
        4.57        14.60        49.25        19.53        67.96        39.25 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       37.02        87.98        42.90        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-7973 
       14.04        12.66         5.72         4.64        22.68         7.56 
TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4670 
        6.05        12.56        14.01        13.45        26.73         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7147 
        5.39         1.25        39.09        11.18       163.10        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
       20.58        35.93        21.90        39.52        24.99        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       32.09         5.88        64.90       223.96         8.48        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       26.53        31.20         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-86-6562 TCGA-86-6851 
       10.55        32.68        39.75        77.59        12.36         5.88 
TCGA-86-7714 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       20.55         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8278 TCGA-86-8358 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 
       15.65        21.47        27.58        14.96        13.32        13.64 
TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       26.47         1.97        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.45        19.82         9.76         4.18 
TCGA-93-A4JN TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
       23.61        19.00        17.29         1.22        18.67        12.39 
TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       15.68        21.40        31.69        64.60        63.52        43.79 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8172 TCGA-97-8175 TCGA-97-8176 
        5.95         0.59         0.72        17.92        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-AA5R 
       16.41        14.30        20.84        18.67        20.68        21.63 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N1 TCGA-MN-A4N4 
       35.47        14.30        14.53         1.91        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA 
        2.76        58.45        49.35         5.49         5.29        31.23 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP 
       29.46        14.66        11.15        73.91        62.60         1.64 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                        0.00                         0.07 
  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                      214.62                       223.96 
  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE 
                      18.655                       17.950 
[1] "0.0 - 214.6 (18.7)" "0.1 - 224.0 (17.9)"
[1] "hr=" "1"  
D52V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(13Q34) MUTATED         2       58       68        1        24
  DEL PEAK 31(13Q34) WILD-TYPE       3       77       72        0        27
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 31(13Q34) MUTATED          37         36          4       12
  DEL PEAK 31(13Q34) WILD-TYPE        36         36          7       14
D52V3, multiclass
            clus
vv           DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  STAGE I                             2                            3
  STAGE IA                           58                           77
  STAGE IB                           68                           72
  STAGE II                            1                            0
  STAGE IIA                          24                           27
  STAGE IIB                          37                           36
  STAGE IIIA                         36                           36
  STAGE IIIB                          4                            7
  STAGE IV                           12                           14
[1] 9 2
[1] 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(13Q34) MUTATED    71 138  22  10
  DEL PEAK 31(13Q34) WILD-TYPE  99 140  24   9
D52V4, multiclass
    clus
vv   DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  T1                         71                           99
  T2                        138                          140
  T3                         22                           24
  T4                         10                            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 31(13Q34) MUTATED   155  47    36
  DEL PEAK 31(13Q34) WILD-TYPE 177  49    40
D52V5, multiclass
       clus
vv      DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  N0                           155                          177
  N1                            47                           49
  N2+N3                         36                           40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                              cls
clus                             0   1
  DEL PEAK 31(13Q34) MUTATED   160  11
  DEL PEAK 31(13Q34) WILD-TYPE 188  14
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(13Q34) MUTATED    160   11
  DEL PEAK 31(13Q34) WILD-TYPE  188   14
   clus
vv  DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  0                        160                          188
  1                         11                           14
[1] 2 2
[1] FALSE
D52V7, binary
                              cls
clus                             0   1
  DEL PEAK 31(13Q34) MUTATED   129 113
  DEL PEAK 31(13Q34) WILD-TYPE 146 127
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(13Q34) MUTATED    129  113
  DEL PEAK 31(13Q34) WILD-TYPE  146  127
        clus
vv       DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  FEMALE                        129                          146
  MALE                          113                          127
[1] 2 2
[1] FALSE
D52V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                           10
  DEL PEAK 31(13Q34) WILD-TYPE                          9
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 31(13Q34) MUTATED                                  47
  DEL PEAK 31(13Q34) WILD-TYPE                                60
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(13Q34) MUTATED                                                  157
  DEL PEAK 31(13Q34) WILD-TYPE                                                162
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 31(13Q34) MUTATED                                            1
  DEL PEAK 31(13Q34) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 31(13Q34) MUTATED                                               8
  DEL PEAK 31(13Q34) WILD-TYPE                                            11
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                                1
  DEL PEAK 31(13Q34) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                                    1
  DEL PEAK 31(13Q34) WILD-TYPE                                  2
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                              0
  DEL PEAK 31(13Q34) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                              11
  DEL PEAK 31(13Q34) WILD-TYPE                            12
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                                 0
  DEL PEAK 31(13Q34) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 31(13Q34) MUTATED                                               4
  DEL PEAK 31(13Q34) WILD-TYPE                                             1
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 31(13Q34) MUTATED                              2
  DEL PEAK 31(13Q34) WILD-TYPE                            8
D52V9, multiclass
                                                    clus
vv                                                   DEL PEAK 31(13Q34) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          47
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        157
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               8
  LUNG CLEAR CELL ADENOCARCINOMA                                              1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          1
  LUNG MUCINOUS ADENOCARCINOMA                                                0
  LUNG PAPILLARY ADENOCARCINOMA                                              11
  LUNG SIGNET RING ADENOCARCINOMA                                             0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               4
  MUCINOUS (COLLOID) CARCINOMA                                                2
                                                    clus
vv                                                   DEL PEAK 31(13Q34) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          162
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                11
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  2
  LUNG PAPILLARY ADENOCARCINOMA                                                12
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, binary
                              cls
clus                             0   1
  DEL PEAK 31(13Q34) MUTATED     9 233
  DEL PEAK 31(13Q34) WILD-TYPE  12 261
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(13Q34) MUTATED      9  233
  DEL PEAK 31(13Q34) WILD-TYPE   12  261
     clus
vv    DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  NO                           9                           12
  YES                        233                          261
[1] 2 2
[1] FALSE
D52V11, continuous
D52V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 31(13Q34) MUTATED   155   7   2  15
  DEL PEAK 31(13Q34) WILD-TYPE 188   5   2  11
D52V13, multiclass
    clus
vv   DEL PEAK 31(13Q34) MUTATED DEL PEAK 31(13Q34) WILD-TYPE
  R0                        155                          188
  R1                          7                            5
  R2                          2                            2
  RX                         15                           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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(13Q34) MUTATED                                  1     6
  DEL PEAK 31(13Q34) WILD-TYPE                                0     1
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(13Q34) MUTATED                          25   180
  DEL PEAK 31(13Q34) WILD-TYPE                        26   209
D52V14, multiclass
                                  clus
vv                                 DEL PEAK 31(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     6
  BLACK OR AFRICAN AMERICAN                                25
  WHITE                                                   180
                                  clus
vv                                 DEL PEAK 31(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     209
[1] 4 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 31(13Q34) MUTATED     4 183
  DEL PEAK 31(13Q34) WILD-TYPE   3 199
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(13Q34) MUTATED      4  183
  DEL PEAK 31(13Q34) WILD-TYPE    3  199
                        clus
vv                       DEL PEAK 31(13Q34) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        183
                        clus
vv                       DEL PEAK 31(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          199
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 32(14Q32.12) MUTATION ANALYSIS
D53V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(14Q32.12) MUTATED    91  47
  DEL PEAK 32(14Q32.12) WILD-TYPE 246 107
  DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE 
                            138                             353 
  DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE 
                             47                             107 
$`DEL PEAK 32(14Q32.12) MUTATED`
TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4405 TCGA-05-4418 TCGA-05-4420 
        0.00         9.96        47.05        20.05         9.01        29.98 
TCGA-05-4427 TCGA-05-5425 TCGA-35-4122 TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 
       26.01        29.00         7.40        49.05        11.64        44.61 
TCGA-44-2659 TCGA-44-2662 TCGA-44-3398 TCGA-44-5643 TCGA-44-5644 TCGA-44-6145 
       44.94        42.08        38.24        33.30        28.37        10.78 
TCGA-44-6146 TCGA-44-7659 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 
        9.93        14.60        36.07        18.87        29.00        17.59 
TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SS TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 
        8.55        11.08        13.64         8.81        29.46        55.89 
TCGA-49-6742 TCGA-49-6744 TCGA-49-AAR9 TCGA-49-AARE TCGA-50-5068 TCGA-50-5930 
       14.63        29.26         8.55        40.41        49.28         9.27 
TCGA-50-5931 TCGA-50-5935 TCGA-50-5936 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       14.27        21.47         8.45        25.55        11.05        12.16 
TCGA-50-6597 TCGA-50-8457 TCGA-53-7626 TCGA-55-1592 TCGA-55-1595 TCGA-55-1596 
       41.69        25.61        30.54        23.05        48.62        45.21 
TCGA-55-6712 TCGA-55-6982 TCGA-55-7281 TCGA-55-7283 TCGA-55-7727 TCGA-55-7910 
        0.79        32.71         0.59         1.15         1.12         6.48 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8505 TCGA-55-8508 TCGA-55-8514 
        5.06         0.13        15.65         0.95         0.49         6.64 
TCGA-55-8619 TCGA-55-A491 TCGA-55-A492 TCGA-62-8398 TCGA-62-A46S TCGA-62-A46U 
        1.61        20.58        19.59        14.60        54.35        67.96 
TCGA-62-A471 TCGA-64-1680 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 
       40.96        37.02        42.90        28.41        51.25        20.05 
TCGA-67-3774 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 
       12.66        13.87         6.64         6.12         5.42         6.05 
TCGA-69-7980 TCGA-69-A59K TCGA-73-4662 TCGA-73-4675 TCGA-73-A9RS TCGA-78-7146 
       12.56         7.04        29.98         1.32        11.18         5.69 
TCGA-78-7147 TCGA-78-7220 TCGA-78-7535 TCGA-78-8640 TCGA-78-8660 TCGA-86-7711 
       19.27        26.53        31.20       214.62        10.55        34.39 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 
       13.87        19.43        19.89        16.70        24.49         4.57 
TCGA-86-8279 TCGA-86-8359 TCGA-86-8669 TCGA-86-8672 TCGA-86-A4D0 TCGA-91-6829 
       15.85        14.60        30.84         0.62         3.81        41.36 
TCGA-91-6830 TCGA-91-6848 TCGA-91-7771 TCGA-91-8497 TCGA-93-7347 TCGA-93-A4JO 
        1.97         7.36        16.18        14.27         9.76         1.08 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VN TCGA-95-A4VP 
        1.12        18.67        12.39        15.65        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-A4M0 
       31.69        64.60         5.39        15.39        16.41        21.44 
TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 
       34.85         1.45         5.59        18.08        16.44        19.00 
TCGA-L9-A443 TCGA-L9-A743 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4T7 
        3.81        17.46        12.59        27.19        58.45         5.49 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A7XG 
        5.29         2.43        19.13        71.05        29.13         9.70 

$`DEL PEAK 32(14Q32.12) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
       24.03         8.02        19.00         2.99        14.96        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       30.02        21.99        26.01        25.02        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       15.02        15.02         4.96        22.03         9.04         2.04 
TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        0.46         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       28.41        35.28        14.73        26.30         4.37        43.53 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       46.98        13.15        24.36        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       37.15        38.89        34.06         6.25        26.56        12.59 
TCGA-44-6144 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
       23.77        27.78        23.15        21.63        23.18        63.72 
TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 
       32.45        61.28        16.44        19.46        12.03         7.17 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         3.25        15.98        15.32         9.44 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-6743 
       35.54        46.72        14.07        32.84        29.75        12.13 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       17.16        11.64        22.26        22.26       153.04        63.95 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       62.24        28.90        37.32       123.58       211.82       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
        9.86        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5932 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 
       31.04         8.22        40.60        78.67        15.12        18.64 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6595 
       29.03        25.12        22.55        42.35         3.91         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 
        0.72        10.13         7.59        27.25        34.29        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
        9.21        38.73         2.86         0.07        32.65        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
        7.79         2.20        45.34        60.03        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
      107.21        70.26         7.99         0.20         0.13         3.12 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
        1.32        23.18         1.28         1.28         0.79         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
       18.64         0.53        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 
       29.72        15.19         3.29        19.66        19.73        23.64 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 
        1.45         0.76         0.36         0.26        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
        0.10         4.80        17.62         0.49         1.58         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
       16.93        22.65        20.71        21.40         1.58         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
       15.81        20.19        19.99        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
       42.38        88.64        49.25        47.80        19.53        56.71 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       72.30        13.61        39.25        29.92        56.81        20.65 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5815 
       39.09        55.43        38.37        87.98         2.04        28.47 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 
        1.02        18.84        14.04         5.72         4.64        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 
       13.61         7.56         2.30         2.93        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4666 
        4.24        26.73         2.01        52.60        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
      163.10        27.16        20.58        35.93        21.90        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       24.99        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
       22.29         7.07       104.19       223.96         8.48        88.14 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 
        8.02        53.33        10.75        39.35        10.55        32.68 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59       110.50        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7714 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       31.13        20.55         4.08        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
       16.08        15.65        23.05        21.47         1.15        13.91 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 
       27.58        14.96        13.32        13.32        17.62        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       26.47        10.62        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       27.68         1.15        16.60         1.18         1.45        19.82 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 
        4.18         6.12        23.61        19.00        17.29         1.22 
TCGA-95-7562 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-97-7552 
        2.86        15.68        27.29         2.76        21.40        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       43.79        25.48         5.95         0.59         0.72        18.67 
TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
       17.92        18.12        14.30        21.60        20.58        20.19 
TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       19.76        20.52        17.75        20.84        18.67        20.68 
TCGA-99-7458 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AE 
       24.56        36.76        21.63        24.30        23.80        35.47 
TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 
       14.30         0.20        14.53         1.91        11.87        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        86.14        49.35        37.35        86.04        58.85 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       41.59        31.23        10.09        29.46        11.05        14.66 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       14.10        11.15        73.91        62.60         0.13         1.64 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
        0.26         0.43        19.82        59.11        16.87 

  DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE 
                           0.00                            0.07 
  DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE 
                         214.62                          223.96 
  DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE 
                         16.295                          19.460 
[1] "0.0 - 214.6 (16.3)" "0.1 - 224.0 (19.5)"
[1] "hr=" "1.4"
D53V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(14Q32.12) MUTATED         2       30       28        0        19
  DEL PEAK 32(14Q32.12) WILD-TYPE       3      105      112        1        32
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 32(14Q32.12) MUTATED          30         26          3        6
  DEL PEAK 32(14Q32.12) WILD-TYPE        43         46          8       20
D53V3, multiclass
            clus
vv           DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE
  STAGE I                                2                               3
  STAGE IA                              30                             105
  STAGE IB                              28                             112
  STAGE II                               0                               1
  STAGE IIA                             19                              32
  STAGE IIB                             30                              43
  STAGE IIIA                            26                              46
  STAGE IIIB                             3                               8
  STAGE IV                               6                              20
[1] 9 2
[1] 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(14Q32.12) MUTATED    41  77  19   6
  DEL PEAK 32(14Q32.12) WILD-TYPE 129 201  27  13
D53V4, multiclass
    clus
vv   DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE
  T1                            41                             129
  T2                            77                             201
  T3                            19                              27
  T4                             6                              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 32(14Q32.12) MUTATED    79  40    24
  DEL PEAK 32(14Q32.12) WILD-TYPE 253  56    52
D53V5, multiclass
       clus
vv      DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE
  N0                               79                             253
  N1                               40                              56
  N2+N3                            24                              52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                                 cls
clus                                0   1
  DEL PEAK 32(14Q32.12) MUTATED   103   5
  DEL PEAK 32(14Q32.12) WILD-TYPE 245  20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.12) MUTATED    103    5
  DEL PEAK 32(14Q32.12) WILD-TYPE  245   20
   clus
vv  DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE
  0                           103                             245
  1                             5                              20
[1] 2 2
[1] FALSE
D53V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(14Q32.12) MUTATED    74  70
  DEL PEAK 32(14Q32.12) WILD-TYPE 201 170
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.12) MUTATED     74   70
  DEL PEAK 32(14Q32.12) WILD-TYPE  201  170
        clus
vv       DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE
  FEMALE                            74                             201
  MALE                              70                             170
[1] 2 2
[1] FALSE
D53V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 32(14Q32.12) MUTATED                            7
  DEL PEAK 32(14Q32.12) WILD-TYPE                         12
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 32(14Q32.12) MUTATED                                  31
  DEL PEAK 32(14Q32.12) WILD-TYPE                                76
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(14Q32.12) MUTATED                                                   91
  DEL PEAK 32(14Q32.12) WILD-TYPE                                                228
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 32(14Q32.12) MUTATED                                            0
  DEL PEAK 32(14Q32.12) WILD-TYPE                                          5
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 32(14Q32.12) MUTATED                                               4
  DEL PEAK 32(14Q32.12) WILD-TYPE                                            15
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 32(14Q32.12) MUTATED                                1
  DEL PEAK 32(14Q32.12) WILD-TYPE                              1
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 32(14Q32.12) MUTATED                                    0
  DEL PEAK 32(14Q32.12) WILD-TYPE                                  3
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(14Q32.12) MUTATED                              1
  DEL PEAK 32(14Q32.12) WILD-TYPE                            1
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 32(14Q32.12) MUTATED                               4
  DEL PEAK 32(14Q32.12) WILD-TYPE                            19
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 32(14Q32.12) MUTATED                                 0
  DEL PEAK 32(14Q32.12) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 32(14Q32.12) MUTATED                                               1
  DEL PEAK 32(14Q32.12) WILD-TYPE                                             4
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 32(14Q32.12) MUTATED                              4
  DEL PEAK 32(14Q32.12) WILD-TYPE                            6
D53V9, multiclass
                                                    clus
vv                                                   DEL PEAK 32(14Q32.12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             31
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            91
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  4
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             0
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                  4
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  1
  MUCINOUS (COLLOID) CARCINOMA                                                   4
                                                    clus
vv                                                   DEL PEAK 32(14Q32.12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             228
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   15
  LUNG CLEAR CELL ADENOCARCINOMA                                                   1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               3
  LUNG MUCINOUS ADENOCARCINOMA                                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                                   19
  LUNG SIGNET RING ADENOCARCINOMA                                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    4
  MUCINOUS (COLLOID) CARCINOMA                                                     6
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, binary
                                 cls
clus                                0   1
  DEL PEAK 32(14Q32.12) MUTATED     8 136
  DEL PEAK 32(14Q32.12) WILD-TYPE  13 358
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.12) MUTATED      8  136
  DEL PEAK 32(14Q32.12) WILD-TYPE   13  358
     clus
vv    DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE
  NO                              8                              13
  YES                           136                             358
[1] 2 2
[1] FALSE
D53V11, continuous
D53V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(14Q32.12) MUTATED    95   0   0   7
  DEL PEAK 32(14Q32.12) WILD-TYPE 248  12   4  19
D53V13, multiclass
    clus
vv   DEL PEAK 32(14Q32.12) MUTATED DEL PEAK 32(14Q32.12) WILD-TYPE
  R0                            95                             248
  R1                             0                              12
  R2                             0                               4
  RX                             7                              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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(14Q32.12) MUTATED                                  0     2
  DEL PEAK 32(14Q32.12) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(14Q32.12) MUTATED                          23   100
  DEL PEAK 32(14Q32.12) WILD-TYPE                        28   289
D53V14, multiclass
                                  clus
vv                                 DEL PEAK 32(14Q32.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                      100
                                  clus
vv                                 DEL PEAK 32(14Q32.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     28
  WHITE                                                        289
[1] 4 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 32(14Q32.12) MUTATED     2 112
  DEL PEAK 32(14Q32.12) WILD-TYPE   5 270
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(14Q32.12) MUTATED      2  112
  DEL PEAK 32(14Q32.12) WILD-TYPE    5  270
                        clus
vv                       DEL PEAK 32(14Q32.12) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           112
                        clus
vv                       DEL PEAK 32(14Q32.12) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             270
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 33(15Q11.2) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(15Q11.2) MUTATED   174  74
  DEL PEAK 33(15Q11.2) WILD-TYPE 163  80
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                           248                            243 
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                            74                             80 
$`DEL PEAK 33(15Q11.2) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07        19.96        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 
       47.05         8.02        20.05        14.96        29.98        30.02 
TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       25.02        29.00        22.03         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       97.74        37.71        49.05        35.28        11.64        44.61 
TCGA-38-6178 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-2668 TCGA-44-3917 
       14.73        13.15        44.94        42.08        25.02        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-6144 TCGA-44-6146 TCGA-44-6774 TCGA-44-6775 
       34.06         6.25        23.77         9.93        21.63        23.18 
TCGA-44-6777 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 
       32.45        19.46        12.03         7.17        36.07        29.00 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU 
       23.64        12.66         8.55        11.08        13.64        13.45 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 
       28.11        28.57        12.66        14.07        29.46        29.75 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR0 
       55.89        29.26        17.16        11.64        22.26       153.04 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 
       40.41        37.32       123.58       211.82        71.47        70.55 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 
       15.72        31.04        78.67        21.47        18.64        22.55 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
        3.91        11.05        12.16        41.69         0.72        10.13 
TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1595 TCGA-55-5899 
       27.25        30.54         9.21        23.05        48.62         2.86 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 
       32.65         0.79        42.51        40.73         0.82        48.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 
        7.79         2.20        45.34        32.71        60.03        40.54 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 
        0.59         1.15         3.12         1.32         1.12         1.78 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7914 TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 
       18.64         6.48         6.15         3.29        19.73         0.13 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8301 TCGA-55-8506 TCGA-55-8507 
       17.98         1.08         2.17         1.45         0.36         0.26 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
        0.49        17.72        17.62         0.49         1.58         2.17 
TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DF 
       22.65        21.40         1.58        20.58         0.92        20.19 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-A46R TCGA-62-A46S TCGA-62-A46Y 
       19.99         4.57        42.38        56.71        54.35        13.61 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
       29.92        56.81        20.65        39.09        55.43        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       87.98        42.90        28.41         1.02        20.05        18.84 
TCGA-67-6217 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.87         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
       12.56         7.04        23.38        29.98        26.30        15.35 
TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.32        23.51        11.18       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7153 TCGA-78-7158 TCGA-78-7159 TCGA-78-7167 TCGA-78-7535 
       19.27        24.99         5.88        64.90        88.14        31.20 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.75        10.55       214.62        12.36         5.88        31.13 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       19.43        19.89        16.70        24.33         0.79        15.75 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 
       15.85        21.47        14.60         1.15        30.84        27.58 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6835 TCGA-91-6840 
       13.32         3.81        17.62        10.62         2.60        12.23 
TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 
       27.68        16.18         1.18         1.45         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
        6.12        23.61         1.08         1.12         2.86        18.67 
TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 
        2.76        18.18        19.89        31.69        25.48         5.95 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M3 
       17.92         5.39        16.41        20.19        21.44        17.75 
TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-J2-8192 TCGA-J2-A4AG 
       18.67        20.68        24.56        36.76        24.30        16.44 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
       19.00         3.81         0.20         1.91        12.59        11.87 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
       27.19        38.63        86.14        58.45        37.35        86.04 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
        5.29         2.43        10.09        29.46        11.05        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A55O TCGA-NJ-A55R 
       11.15        19.13        71.05         0.13         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J 
        9.70        59.11 

$`DEL PEAK 33(15Q11.2) WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4415 TCGA-05-4418 
        3.98        14.01         9.96        19.00         2.99         9.01 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
       12.00        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       15.02        15.02         4.96         9.04         2.04         0.46 
TCGA-38-4626 TCGA-38-4629 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
      120.79        28.41        26.30         4.37        43.53        46.98 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 
       24.36        42.77         3.19        37.15        38.24        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 
       33.30        28.37        12.59        10.78        27.78        23.15 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7669 TCGA-44-7671 
       63.72        61.28        16.44        14.60        18.87        17.59 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 
        3.25        15.98        15.32         9.44        11.54        76.21 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-6742 TCGA-49-6743 
       35.54        46.72        32.84         8.81        14.63        12.13 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARR 
       22.26        63.95        62.24        28.90         8.55       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
        9.86        20.52        60.16        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
       14.27        40.60         8.45        15.12        29.03        25.12 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 
       42.35        25.55         6.21        25.61         7.59        34.29 
TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6970 TCGA-55-6975 
       13.94        38.73        45.21         0.07        15.25         3.88 
TCGA-55-6978 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 
        5.49        24.99       107.21        70.26         7.99         0.20 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 
        0.13        23.18         1.28         1.28         0.79         0.53 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
       17.65        19.82         0.16        29.72        15.19        19.66 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
        5.06        23.64        15.65         1.51        22.16        15.42 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 
        0.76         0.95         0.30         0.10         4.80         6.64 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A492 TCGA-55-A494 TCGA-55-A57B 
        1.61        16.93        20.71        19.59        15.81        17.95 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P 
       39.98        14.60        88.64        49.25        47.80        19.53 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1680 TCGA-64-5775 
       67.96        72.30        39.25        40.96        37.02         2.04 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
       51.25        28.47        14.04        12.66         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-8253 TCGA-69-8254 
        6.64         6.12        22.68        13.61        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4670 TCGA-73-4676 
        4.24        26.73         2.01        52.60         4.31         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1.25        39.09        20.58        35.93        21.90        39.52 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       19.50        38.50        32.09        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 
      223.96         8.48        26.53         8.02        53.33        39.35 
TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
       32.68        39.75        77.59        10.55       110.50        27.09 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 
       34.39        13.87        20.55        24.49         4.08         4.57 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8668 TCGA-86-8672 TCGA-86-8673 
       16.08        15.65        23.05        13.91         0.62        14.96 
TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.32        13.64        26.47        41.36         1.97        10.19 
TCGA-91-6836 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
       13.71         7.36         1.15        16.60        14.27        19.82 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
       19.00        17.29         1.22        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 
       27.29        21.40        64.60        63.52        43.79         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 
        0.72        18.67        18.12        15.39        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-99-8025 TCGA-99-8032 
       20.58        19.76        20.52        20.84        34.85         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 
        5.59        21.63        23.80        18.08        35.47        14.30 
TCGA-L9-A50W TCGA-L9-A743 TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 
       14.53        17.46         2.76        49.35        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP 
       41.59        31.23        14.66        73.91        62.60         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-S2-AA1A 
       29.13         0.26        16.87 

  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                          0.00                           0.07 
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                        214.62                         223.96 
  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE 
                         18.67                          17.95 
[1] "0.0 - 214.6 (18.7)" "0.1 - 224.0 (17.9)"
[1] "hr=" "1.1"
D54V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(15Q11.2) MUTATED         4       64       72        0        34
  DEL PEAK 33(15Q11.2) WILD-TYPE       1       71       68        1        17
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 33(15Q11.2) MUTATED          33         35          6       14
  DEL PEAK 33(15Q11.2) WILD-TYPE        40         37          5       12
D54V3, multiclass
            clus
vv           DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                             64                             71
  STAGE IB                             72                             68
  STAGE II                              0                              1
  STAGE IIA                            34                             17
  STAGE IIB                            33                             40
  STAGE IIIA                           35                             37
  STAGE IIIB                            6                              5
  STAGE IV                             14                             12
[1] 9 2
[1] 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(15Q11.2) MUTATED    87 146  20   9
  DEL PEAK 33(15Q11.2) WILD-TYPE  83 132  26  10
D54V4, multiclass
    clus
vv   DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  T1                           87                             83
  T2                          146                            132
  T3                           20                             26
  T4                            9                             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(15Q11.2) MUTATED   166  52    40
  DEL PEAK 33(15Q11.2) WILD-TYPE 166  44    36
D54V5, multiclass
       clus
vv      DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  N0                             166                            166
  N1                              52                             44
  N2+N3                           40                             36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q11.2) MUTATED   182  13
  DEL PEAK 33(15Q11.2) WILD-TYPE 166  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q11.2) MUTATED    182   13
  DEL PEAK 33(15Q11.2) WILD-TYPE  166   12
   clus
vv  DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  0                          182                            166
  1                           13                             12
[1] 2 2
[1] FALSE
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q11.2) MUTATED   145 117
  DEL PEAK 33(15Q11.2) WILD-TYPE 130 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q11.2) MUTATED    145  117
  DEL PEAK 33(15Q11.2) WILD-TYPE  130  123
        clus
vv       DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  FEMALE                          145                            130
  MALE                            117                            123
[1] 2 2
[1] FALSE
D54V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                            8
  DEL PEAK 33(15Q11.2) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 33(15Q11.2) MUTATED                                  47
  DEL PEAK 33(15Q11.2) WILD-TYPE                                60
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(15Q11.2) MUTATED                                                  175
  DEL PEAK 33(15Q11.2) WILD-TYPE                                                144
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 33(15Q11.2) MUTATED                                            0
  DEL PEAK 33(15Q11.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 33(15Q11.2) MUTATED                                               7
  DEL PEAK 33(15Q11.2) WILD-TYPE                                            12
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                                1
  DEL PEAK 33(15Q11.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                                    3
  DEL PEAK 33(15Q11.2) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                              1
  DEL PEAK 33(15Q11.2) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                              13
  DEL PEAK 33(15Q11.2) WILD-TYPE                            10
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                                 1
  DEL PEAK 33(15Q11.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                                               3
  DEL PEAK 33(15Q11.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 33(15Q11.2) MUTATED                              3
  DEL PEAK 33(15Q11.2) WILD-TYPE                            7
D54V9, multiclass
                                                    clus
vv                                                   DEL PEAK 33(15Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            47
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          175
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 7
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                13
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   DEL PEAK 33(15Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            144
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  12
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              0
  LUNG MUCINOUS ADENOCARCINOMA                                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                                  10
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  MUCINOUS (COLLOID) CARCINOMA                                                    7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q11.2) MUTATED    11 251
  DEL PEAK 33(15Q11.2) WILD-TYPE  10 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q11.2) MUTATED     11  251
  DEL PEAK 33(15Q11.2) WILD-TYPE   10  243
     clus
vv    DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  NO                            11                             10
  YES                          251                            243
[1] 2 2
[1] FALSE
D54V11, continuous
D54V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 33(15Q11.2) MUTATED   175   8   2  14
  DEL PEAK 33(15Q11.2) WILD-TYPE 168   4   2  12
D54V13, multiclass
    clus
vv   DEL PEAK 33(15Q11.2) MUTATED DEL PEAK 33(15Q11.2) WILD-TYPE
  R0                          175                            168
  R1                            8                              4
  R2                            2                              2
  RX                           14                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(15Q11.2) MUTATED                                  1     3
  DEL PEAK 33(15Q11.2) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(15Q11.2) MUTATED                          26   197
  DEL PEAK 33(15Q11.2) WILD-TYPE                        25   192
D54V14, multiclass
                                  clus
vv                                 DEL PEAK 33(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     197
                                  clus
vv                                 DEL PEAK 33(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       192
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V15, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q11.2) MUTATED     3 191
  DEL PEAK 33(15Q11.2) WILD-TYPE   4 191
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q11.2) MUTATED      3  191
  DEL PEAK 33(15Q11.2) WILD-TYPE    4  191
                        clus
vv                       DEL PEAK 33(15Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          191
                        clus
vv                       DEL PEAK 33(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            191
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 34(15Q15.1) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(15Q15.1) MUTATED   178  82
  DEL PEAK 34(15Q15.1) WILD-TYPE 159  72
  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                           260                            231 
  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                            82                             72 
$`DEL PEAK 34(15Q15.1) MUTATED`
TCGA-05-4249 TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07        19.96        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 
       47.05         8.02        20.05        14.96        29.98        30.02 
TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       25.02        29.00        22.03         7.40         5.98         8.68 
TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
       97.74        37.71        49.05        35.28        11.64        44.61 
TCGA-38-6178 TCGA-44-2657 TCGA-44-2659 TCGA-44-2662 TCGA-44-2668 TCGA-44-3917 
       14.73        13.15        44.94        42.08        25.02        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-6144 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 
       34.06         6.25        23.77        21.63        32.45        61.28 
TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 
       19.46        12.03         7.17        36.07        23.64        12.66 
TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 
        8.55        11.08        13.64        13.45        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 
       12.66        35.54        46.72        14.07         8.81        29.46 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR0 
       55.89        29.26        17.16        11.64        22.26       153.04 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 
       40.41        37.32       123.58       211.82        71.47        70.55 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 TCGA-50-5946 
       15.72        31.04        78.67        21.47        18.64        22.55 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 
        3.91        25.55        11.05        12.16        41.69         0.72 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
       10.13        27.25        30.54        13.94         9.21        23.05 
TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       48.62        45.21         2.86        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 
       40.73         0.82        48.49         7.79         2.20        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 
       32.71        60.03        40.54         0.59         1.15         3.12 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7914 
        1.32         1.12         1.78        18.64         6.48         6.15 
TCGA-55-7994 TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 TCGA-55-8203 TCGA-55-8205 
       19.82         3.29        19.73         0.13        17.98         1.08 
TCGA-55-8207 TCGA-55-8301 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        2.17         1.45         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48X 
        0.30        17.62         0.49         1.58         2.17        22.65 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG 
       21.40         1.58        20.58         0.92        20.19        19.99 
TCGA-62-8394 TCGA-62-8397 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46Y 
        4.57        42.38        19.53        56.71        54.35        13.61 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
       29.92        56.81        20.65        39.09        55.43        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       87.98        42.90        28.41         1.02        20.05        18.84 
TCGA-67-6217 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.87         5.42         7.56         6.05         2.30         2.93 
TCGA-69-7980 TCGA-69-A59K TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
       12.56         7.04        23.38        29.98        26.30        15.35 
TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
        1.32        23.51        11.18       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7153 TCGA-78-7158 TCGA-78-7159 TCGA-78-7167 TCGA-78-7535 
       19.27        24.99         5.88        64.90        88.14        31.20 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-86-6562 TCGA-86-6851 
        8.02        10.75        10.55       214.62        12.36         5.88 
TCGA-86-7701 TCGA-86-7953 TCGA-86-7954 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 
       31.13        19.43        19.89         4.08        24.33         0.79 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8359 TCGA-86-8669 TCGA-86-8671 TCGA-86-A456 
       15.75        15.85        14.60        30.84        27.58        13.32 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 
        3.81        17.62        10.62        41.36        10.19         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 
       13.71        12.23        27.68         7.36        16.18         1.18 
TCGA-91-A4BC TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO 
        1.45         9.76         4.18         6.12        23.61         1.08 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VN 
       17.29         1.12         2.86        18.67         2.76        18.18 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 
       19.89        31.69        25.48         5.95        17.92         5.39 
TCGA-97-8177 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M3 TCGA-97-A4M7 
       16.41        20.19        21.44        19.76        17.75        20.68 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-J2-8192 TCGA-J2-A4AD TCGA-J2-A4AG 
       24.56        34.85        36.76        24.30        18.08        16.44 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
       19.00         3.81         0.20        12.59        11.87        27.19 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       38.63        86.14        58.45        49.35        37.35        86.04 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
        5.29         2.43        10.09        29.46        11.05        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A55O TCGA-NJ-A55R 
       11.15        19.13        71.05         0.13         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J 
        9.70        59.11 

$`DEL PEAK 34(15Q15.1) WILD-TYPE`
TCGA-05-4250 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4415 TCGA-05-4418 
        3.98        14.01         9.96        19.00         2.99         9.01 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 
       12.00        21.99        26.01        26.01        25.02        24.00 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       15.02        15.02         4.96         9.04         2.04         0.46 
TCGA-38-4626 TCGA-38-4629 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
      120.79        28.41        26.30         4.37        43.53        46.98 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 
       24.36        42.77         3.19        37.15        38.24        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       33.30        28.37        12.59        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6779 TCGA-44-7659 TCGA-44-7669 
       23.15        23.18        63.72        16.44        14.60        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       29.00        17.59         3.25        15.98        15.32         9.44 
TCGA-44-A47G TCGA-49-4486 TCGA-49-4506 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 
       11.54        76.21        32.84        29.75        14.63        12.13 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARR 
       22.26        63.95        62.24        28.90         8.55       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
        9.86        20.52        60.16        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
       14.27        40.60         8.45        15.12        29.03        25.12 
TCGA-50-6590 TCGA-50-6595 TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 TCGA-55-1594 
       42.35         6.21        25.61         7.59        34.29        38.73 
TCGA-55-6543 TCGA-55-6970 TCGA-55-6975 TCGA-55-6978 TCGA-55-6984 TCGA-55-6986 
        0.07        15.25         3.88         5.49        24.99       107.21 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
       70.26         7.99         0.20         0.13        23.18         1.28 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7907 TCGA-55-7911 TCGA-55-7995 TCGA-55-8085 
        1.28         0.79         0.53        17.65         0.16        29.72 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       15.19        19.66         5.06        23.64        15.65         1.51 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 
       22.16        15.42         0.76         0.95         0.10         4.80 
TCGA-55-8514 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A492 TCGA-55-A494 
        6.64         1.61        16.93        20.71        19.59        15.81 
TCGA-55-A57B TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       17.95        39.98        14.60        88.64        49.25        47.80 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1680 TCGA-64-5775 
       67.96        72.30        39.25        40.96        37.02         2.04 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
       51.25        28.47        14.04        12.66         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-8253 TCGA-69-8254 
        6.64         6.12        22.68        13.61        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4658 TCGA-73-4670 TCGA-73-4676 
        4.24        26.73         2.01        52.60         4.31         5.39 
TCGA-73-4677 TCGA-73-7498 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
        1.25        39.09        20.58        35.93        21.90        39.52 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       19.50        38.50        32.09        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 
      223.96         8.48        26.53        53.33        39.35        32.68 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-7711 
       39.75        77.59        10.55       110.50        27.09        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 
       13.87        20.55        16.70        24.49         4.57        16.08 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8672 
       15.65        23.05        21.47         1.15        13.91         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6849 
       14.96        13.32        13.64        26.47         1.97         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-A4JP TCGA-95-7043 TCGA-95-7944 
       16.60        14.27        19.82        19.00         1.22        12.39 
TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK TCGA-97-7547 TCGA-97-7552 
       15.68        15.65        27.29        21.40        64.60        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 
       43.79         0.59         0.72        18.67        18.12        15.39 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 
       14.30        21.60        20.58        20.52        20.84        18.67 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE TCGA-L4-A4E6 
        1.45         5.59        21.63        23.80        35.47        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N5 TCGA-MP-A4T6 TCGA-MP-A4T7 
       14.53         1.91        17.46         2.76        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP 
       41.59        31.23        14.66        73.91        62.60         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-S2-AA1A 
       29.13         0.26        16.87 

  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                          0.00                           0.07 
  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                        214.62                         223.96 
  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE 
                        18.755                         17.650 
[1] "0.0 - 214.6 (18.8)" "0.1 - 224.0 (17.6)"
[1] "hr=" "1"  
D55V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(15Q15.1) MUTATED         4       67       75        0        34
  DEL PEAK 34(15Q15.1) WILD-TYPE       1       68       65        1        17
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 34(15Q15.1) MUTATED          35         39          7       13
  DEL PEAK 34(15Q15.1) WILD-TYPE        38         33          4       13
D55V3, multiclass
            clus
vv           DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                             67                             68
  STAGE IB                             75                             65
  STAGE II                              0                              1
  STAGE IIA                            34                             17
  STAGE IIB                            35                             38
  STAGE IIIA                           39                             33
  STAGE IIIB                            7                              4
  STAGE IV                             13                             13
[1] 9 2
[1] 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(15Q15.1) MUTATED    89 153  22  10
  DEL PEAK 34(15Q15.1) WILD-TYPE  81 125  24   9
D55V4, multiclass
    clus
vv   DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  T1                           89                             81
  T2                          153                            125
  T3                           22                             24
  T4                           10                              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(15Q15.1) MUTATED   173  55    42
  DEL PEAK 34(15Q15.1) WILD-TYPE 159  41    34
D55V5, multiclass
       clus
vv      DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  N0                             173                            159
  N1                              55                             41
  N2+N3                           42                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                                cls
clus                               0   1
  DEL PEAK 34(15Q15.1) MUTATED   188  12
  DEL PEAK 34(15Q15.1) WILD-TYPE 160  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q15.1) MUTATED    188   12
  DEL PEAK 34(15Q15.1) WILD-TYPE  160   13
   clus
vv  DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  0                          188                            160
  1                           12                             13
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(15Q15.1) MUTATED   149 125
  DEL PEAK 34(15Q15.1) WILD-TYPE 126 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q15.1) MUTATED    149  125
  DEL PEAK 34(15Q15.1) WILD-TYPE  126  115
        clus
vv       DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  FEMALE                          149                            126
  MALE                            125                            115
[1] 2 2
[1] FALSE
D55V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 34(15Q15.1) MUTATED                            9
  DEL PEAK 34(15Q15.1) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 34(15Q15.1) MUTATED                                  48
  DEL PEAK 34(15Q15.1) WILD-TYPE                                59
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(15Q15.1) MUTATED                                                  185
  DEL PEAK 34(15Q15.1) WILD-TYPE                                                134
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 34(15Q15.1) MUTATED                                            0
  DEL PEAK 34(15Q15.1) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 34(15Q15.1) MUTATED                                               9
  DEL PEAK 34(15Q15.1) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 34(15Q15.1) MUTATED                                1
  DEL PEAK 34(15Q15.1) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 34(15Q15.1) MUTATED                                    3
  DEL PEAK 34(15Q15.1) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(15Q15.1) MUTATED                              0
  DEL PEAK 34(15Q15.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 34(15Q15.1) MUTATED                              13
  DEL PEAK 34(15Q15.1) WILD-TYPE                            10
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 34(15Q15.1) MUTATED                                 1
  DEL PEAK 34(15Q15.1) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 34(15Q15.1) MUTATED                                               2
  DEL PEAK 34(15Q15.1) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 34(15Q15.1) MUTATED                              3
  DEL PEAK 34(15Q15.1) WILD-TYPE                            7
D55V9, multiclass
                                                    clus
vv                                                   DEL PEAK 34(15Q15.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          185
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 9
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                13
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   DEL PEAK 34(15Q15.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              59
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            134
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  10
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              0
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  10
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   3
  MUCINOUS (COLLOID) CARCINOMA                                                    7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, binary
                                cls
clus                               0   1
  DEL PEAK 34(15Q15.1) MUTATED    13 261
  DEL PEAK 34(15Q15.1) WILD-TYPE   8 233
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q15.1) MUTATED     13  261
  DEL PEAK 34(15Q15.1) WILD-TYPE    8  233
     clus
vv    DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  NO                            13                              8
  YES                          261                            233
[1] 2 2
[1] FALSE
D55V11, continuous
D55V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(15Q15.1) MUTATED   185   6   2  14
  DEL PEAK 34(15Q15.1) WILD-TYPE 158   6   2  12
D55V13, multiclass
    clus
vv   DEL PEAK 34(15Q15.1) MUTATED DEL PEAK 34(15Q15.1) WILD-TYPE
  R0                          185                            158
  R1                            6                              6
  R2                            2                              2
  RX                           14                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(15Q15.1) MUTATED                                  1     4
  DEL PEAK 34(15Q15.1) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(15Q15.1) MUTATED                          27   207
  DEL PEAK 34(15Q15.1) WILD-TYPE                        24   182
D55V14, multiclass
                                  clus
vv                                 DEL PEAK 34(15Q15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     207
                                  clus
vv                                 DEL PEAK 34(15Q15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    24
  WHITE                                                       182
[1] 4 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 34(15Q15.1) MUTATED     1 203
  DEL PEAK 34(15Q15.1) WILD-TYPE   6 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q15.1) MUTATED      1  203
  DEL PEAK 34(15Q15.1) WILD-TYPE    6  179
                        clus
vv                       DEL PEAK 34(15Q15.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          203
                        clus
vv                       DEL PEAK 34(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            179
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 35(16Q23.1) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(16Q23.1) MUTATED   117  45
  DEL PEAK 35(16Q23.1) WILD-TYPE 220 109
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                           162                            329 
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                            45                            109 
$`DEL PEAK 35(16Q23.1) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4402 TCGA-05-4405 
       19.96        45.01        37.02        47.05         8.02        20.05 
TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 
        2.99         9.01        29.98        30.02        26.01        25.02 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4628 TCGA-38-4629 
       22.03         7.40         5.98        97.74        49.05        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-44-2656 TCGA-44-2661 TCGA-44-3918 TCGA-44-3919 
       35.28        11.64        46.98        24.36        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6775 TCGA-44-6777 TCGA-44-7660 
       26.56        33.30        28.37        23.18        32.45        19.46 
TCGA-44-7661 TCGA-44-7669 TCGA-44-8117 TCGA-44-8119 TCGA-44-A47B TCGA-49-4487 
       12.03        18.87        12.66         3.25         9.44        28.11 
TCGA-49-4494 TCGA-49-4507 TCGA-49-4510 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
       35.54         8.81        29.46        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5933 
       17.16        11.64        70.55        31.04        49.28        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-8457 
        8.45        15.12        22.55         3.91        11.05        25.61 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1595 TCGA-55-6712 TCGA-55-6968 
       34.29        13.94         9.21        48.62         0.79        42.51 
TCGA-55-6971 TCGA-55-6978 TCGA-55-6979 TCGA-55-6986 TCGA-55-7281 TCGA-55-7576 
        0.82         5.49         7.79       107.21         0.59         1.32 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-8091 TCGA-55-8205 
       23.18         1.28         1.12        18.64        19.73         1.08 
TCGA-55-8207 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8514 TCGA-55-8616 
        2.17         0.95         0.36         0.26         6.64         1.58 
TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
        2.17        22.65        21.40         1.58        20.58         0.92 
TCGA-62-8394 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 
        4.57        42.38        47.80        67.96        39.25        40.96 
TCGA-62-A472 TCGA-64-1677 TCGA-64-1679 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
       29.92        20.65        55.43        87.98        42.90        28.41 
TCGA-69-7763 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K 
       22.68         6.05         2.30         2.93         4.24         7.04 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4662 TCGA-73-4675 TCGA-78-7143 TCGA-78-7146 
        2.01        52.60        29.98         1.32       163.10         5.69 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7159 TCGA-78-7167 TCGA-78-7220 
       21.90        39.52        38.50        64.90        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
       31.20         8.02        27.09         5.88        34.39        13.87 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 
       19.43        19.89        24.49        24.33        15.75        15.65 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8672 TCGA-86-A4JF TCGA-91-6836 TCGA-91-6847 
       14.60        13.91         0.62        17.62        13.71        27.68 
TCGA-91-7771 TCGA-91-8499 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JQ 
       16.18         1.18         4.18         6.12         1.08        17.29 
TCGA-95-7562 TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VN TCGA-97-7546 TCGA-97-7554 
        2.86        18.67         2.76        18.18        31.69        25.48 
TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 TCGA-97-A4M0 TCGA-97-A4M3 TCGA-J2-A4AG 
        5.95        18.67        18.12        21.44        17.75        16.44 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N5 
       19.00         3.81         0.20        12.59        27.19         2.76 
TCGA-MP-A4TC TCGA-MP-A4TF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A7XG 
        2.43        11.05        62.60         0.13         1.64         9.70 

$`DEL PEAK 35(16Q23.1) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
       50.07         3.98        14.01         0.00         9.96        24.03 
TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       19.00        14.96        12.00        21.99        26.01        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
       24.00        15.02        15.02         4.96        29.00         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 
        2.04         0.46         8.68       120.79        37.71        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 
       14.73        26.30         4.37        43.53        13.15        44.94 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       42.08        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3917 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       38.89        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       23.15        21.63        63.72        61.28        16.44        14.60 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8120 
        7.17        36.07        29.00        17.59        23.64         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32        11.08        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 
       76.21        28.57        12.66        46.72        14.07        32.84 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 
       29.75        55.89        22.26        22.26       153.04        63.95 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO 
       62.24        28.90         8.55        40.41        37.32       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 
      211.82       164.12         9.86        20.52        71.47        15.72 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 
       60.16         8.22         9.27        14.27        40.60        21.47 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 
       18.64        29.03        25.12        42.35        25.55        12.16 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 
        6.21        41.69         0.72        10.13         7.59        27.25 
TCGA-53-7626 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
       30.54        23.05        38.73        45.21         2.86         0.07 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       32.65        40.73        15.25        48.49         3.88         2.20 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 
       45.34        32.71        60.03        24.99        40.54        70.26 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7725 
        1.15         7.99         0.20         0.13         3.12         1.28 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
        0.79         1.78         0.53         6.48        17.65         6.15 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
       19.82         0.16        29.72        15.19         3.29        19.66 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8206 
        5.06         0.13        23.64        15.65        17.98         1.51 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8510 
       22.16        15.42         1.45         0.76         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 
        0.30         0.10         4.80        17.62         0.49         1.61 
TCGA-55-8621 TCGA-55-A48Y TCGA-55-A492 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       16.93        20.71        19.59        15.81        20.19        19.99 
TCGA-55-A57B TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       17.95        39.98        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-64-1676 TCGA-64-1678 
       56.71        54.35        72.30        13.61        56.81        39.09 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       37.02        38.37         2.04        51.25        28.47         1.02 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        12.66         5.72         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
       13.87         6.64         6.12        13.61         5.42         7.56 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4659 TCGA-73-4666 
       12.56        14.01        13.45        26.73        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
       15.35         4.31         5.39         1.25        39.09        23.51 
TCGA-73-A9RS TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 
       11.18        27.16        19.27        20.58        35.93        24.99 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       19.50        32.09         5.88        22.29         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
      223.96         8.48        53.33        10.75        39.35        10.55 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 
       32.68       214.62        39.75        77.59        10.55       110.50 
TCGA-86-6562 TCGA-86-7701 TCGA-86-7714 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
       12.36        31.13        20.55        16.70         4.08         4.57 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 
        0.79        16.08        15.85        23.05        21.47         1.15 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       30.84        27.58        14.96        13.32        13.32         3.81 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.64        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
        2.60        12.23         7.36         1.15        16.60        14.27 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7039 
        1.45        19.82         9.76        23.61        19.00         1.12 
TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
        1.22        12.39        15.68        15.65        27.29        21.40 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 
       19.89        64.60        63.52        43.79         0.59         0.72 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 
       17.92         5.39        15.39        16.41        14.30        21.60 
TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 
       20.58        20.19        19.76        20.52        20.84        18.67 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.68        24.56        34.85        36.76         1.45         5.59 
TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 
       21.63        24.30        23.80        18.08        35.47        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV 
       14.53         1.91        17.46        11.87        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
       58.45        49.35        37.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TH 
        5.29        41.59        31.23        10.09        29.46        14.66 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ 
       14.10        11.15        19.13        73.91        71.05        29.13 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
        0.26         0.43        19.82        59.11        16.87 

  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                        163.10                         223.96 
  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE 
                         18.41                          18.64 
[1] "0.1 - 163.1 (18.4)" "0.0 - 224.0 (18.6)"
[1] "hr=" "1.1"
D56V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(16Q23.1) MUTATED         1       33       52        0        17
  DEL PEAK 35(16Q23.1) WILD-TYPE       4      102       88        1        34
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 35(16Q23.1) MUTATED          26         26          6        8
  DEL PEAK 35(16Q23.1) WILD-TYPE        47         46          5       18
D56V3, multiclass
            clus
vv           DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             33                            102
  STAGE IB                             52                             88
  STAGE II                              0                              1
  STAGE IIA                            17                             34
  STAGE IIB                            26                             47
  STAGE IIIA                           26                             46
  STAGE IIIB                            6                              5
  STAGE IV                              8                             18
[1] 9 2
[1] 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(16Q23.1) MUTATED    47 101  15   6
  DEL PEAK 35(16Q23.1) WILD-TYPE 123 177  31  13
D56V4, multiclass
    clus
vv   DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  T1                           47                            123
  T2                          101                            177
  T3                           15                             31
  T4                            6                             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 35(16Q23.1) MUTATED   104  32    30
  DEL PEAK 35(16Q23.1) WILD-TYPE 228  64    46
D56V5, multiclass
       clus
vv      DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  N0                             104                            228
  N1                              32                             64
  N2+N3                           30                             46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q23.1) MUTATED   118   8
  DEL PEAK 35(16Q23.1) WILD-TYPE 230  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q23.1) MUTATED    118    8
  DEL PEAK 35(16Q23.1) WILD-TYPE  230   17
   clus
vv  DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  0                          118                            230
  1                            8                             17
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q23.1) MUTATED    87  82
  DEL PEAK 35(16Q23.1) WILD-TYPE 188 158
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q23.1) MUTATED     87   82
  DEL PEAK 35(16Q23.1) WILD-TYPE  188  158
        clus
vv       DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  FEMALE                           87                            188
  MALE                             82                            158
[1] 2 2
[1] FALSE
D56V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 35(16Q23.1) MUTATED                            8
  DEL PEAK 35(16Q23.1) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 35(16Q23.1) MUTATED                                  36
  DEL PEAK 35(16Q23.1) WILD-TYPE                                71
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(16Q23.1) MUTATED                                                  103
  DEL PEAK 35(16Q23.1) WILD-TYPE                                                216
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 35(16Q23.1) MUTATED                                            1
  DEL PEAK 35(16Q23.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 35(16Q23.1) MUTATED                                               6
  DEL PEAK 35(16Q23.1) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 35(16Q23.1) MUTATED                                2
  DEL PEAK 35(16Q23.1) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 35(16Q23.1) MUTATED                                    1
  DEL PEAK 35(16Q23.1) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(16Q23.1) MUTATED                              0
  DEL PEAK 35(16Q23.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 35(16Q23.1) MUTATED                               7
  DEL PEAK 35(16Q23.1) WILD-TYPE                            16
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 35(16Q23.1) MUTATED                                 0
  DEL PEAK 35(16Q23.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 35(16Q23.1) MUTATED                                               3
  DEL PEAK 35(16Q23.1) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 35(16Q23.1) MUTATED                              2
  DEL PEAK 35(16Q23.1) WILD-TYPE                            8
D56V9, multiclass
                                                    clus
vv                                                   DEL PEAK 35(16Q23.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            36
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          103
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 6
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 7
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 35(16Q23.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              71
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            216
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  16
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  MUCINOUS (COLLOID) CARCINOMA                                                    8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q23.1) MUTATED     9 160
  DEL PEAK 35(16Q23.1) WILD-TYPE  12 334
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q23.1) MUTATED      9  160
  DEL PEAK 35(16Q23.1) WILD-TYPE   12  334
     clus
vv    DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  NO                             9                             12
  YES                          160                            334
[1] 2 2
[1] FALSE
D56V11, continuous
D56V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(16Q23.1) MUTATED   108   2   1  10
  DEL PEAK 35(16Q23.1) WILD-TYPE 235  10   3  16
D56V13, multiclass
    clus
vv   DEL PEAK 35(16Q23.1) MUTATED DEL PEAK 35(16Q23.1) WILD-TYPE
  R0                          108                            235
  R1                            2                             10
  R2                            1                              3
  RX                           10                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(16Q23.1) MUTATED                                  0     4
  DEL PEAK 35(16Q23.1) WILD-TYPE                                1     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(16Q23.1) MUTATED                          12   133
  DEL PEAK 35(16Q23.1) WILD-TYPE                        39   256
D56V14, multiclass
                                  clus
vv                                 DEL PEAK 35(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                     133
                                  clus
vv                                 DEL PEAK 35(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       256
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V15, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q23.1) MUTATED     5 122
  DEL PEAK 35(16Q23.1) WILD-TYPE   2 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q23.1) MUTATED      5  122
  DEL PEAK 35(16Q23.1) WILD-TYPE    2  260
                        clus
vv                       DEL PEAK 35(16Q23.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          122
                        clus
vv                       DEL PEAK 35(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            260
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 36(17P13.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(17P13.3) MUTATED   186  81
  DEL PEAK 36(17P13.3) WILD-TYPE 151  73
  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                           267                            224 
  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                            81                             73 
$`DEL PEAK 36(17P13.3) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
       50.07        45.01        37.02         0.00         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 
       47.05         8.02         2.99        14.96        29.98        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 
       26.01        26.01        25.02        24.00        15.02        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4630 
       22.03         9.04         7.40         5.98        97.74        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
       11.64        44.61        14.73        13.15        44.94        24.36 
TCGA-44-2662 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.08        37.15        38.89        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-6144 TCGA-44-6147 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       33.30        23.77        27.78        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7670 
       16.44        19.46        12.03         7.17        36.07        29.00 
TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47B TCGA-49-4490 TCGA-49-4501 
       12.66         3.25         8.55         9.44        12.66        46.72 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 
       14.07         8.81        29.46        29.75        12.13        29.26 
TCGA-49-6745 TCGA-49-6761 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR9 
       17.16        11.64        22.26        22.26       153.04         8.55 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-50-5049 TCGA-50-5051 
       40.41        37.32       123.58       211.82        70.55        15.72 
TCGA-50-5068 TCGA-50-5931 TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 TCGA-50-6591 
       49.28        14.27         8.45        18.64        25.12         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-53-7624 
       11.05        12.16        41.69         0.72        10.13        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 
       30.54        13.94        23.05        38.73        48.62        45.21 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 
        0.79        42.51        48.49         3.88         5.49         7.79 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 TCGA-55-7281 
        2.20        45.34        32.71        24.99        40.54         0.59 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7726 TCGA-55-7727 TCGA-55-7815 
        0.13         3.12         1.32         1.28         1.12         1.78 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 
       18.64         6.48        17.65         6.15        19.82         0.16 
TCGA-55-8085 TCGA-55-8089 TCGA-55-8091 TCGA-55-8094 TCGA-55-8097 TCGA-55-8203 
       29.72         3.29        19.73         0.13        15.65        17.98 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 
        1.08         2.17         0.76         0.36        17.72         0.30 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z 
        6.64        17.62         2.17        22.65        20.71        21.40 
TCGA-55-A491 TCGA-55-A57B TCGA-62-8394 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46R 
       20.58        17.95         4.57        42.38        47.80        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       54.35        67.96        29.92        56.81        39.09        55.43 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 
       38.37        87.98        42.90        28.41        28.47         1.02 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 
       20.05        18.84        14.04         5.72        13.87         6.64 
TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
        6.12        13.61         5.42         6.05         2.30         2.93 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 
        4.24        26.73         7.04         2.01        52.60        23.38 
TCGA-73-4668 TCGA-73-4670 TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
       15.35         4.31        23.51        11.18       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7154 TCGA-78-7159 TCGA-78-7535 
        5.69        19.27        21.90        19.50        64.90        31.20 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 
        8.02        10.75        39.35        10.55       214.62        77.59 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
        5.88        31.13        34.39        13.87        19.43        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
       16.70        24.49         4.08         4.57        24.33        15.75 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-A4JF 
       15.65        15.85        23.05        21.47        13.91        17.62 
TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 
       10.62        10.19         2.60        13.71        12.23        27.68 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-7347 TCGA-93-8067 TCGA-93-A4JO TCGA-93-A4JQ 
       16.18         1.45         9.76         6.12         1.08        17.29 
TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.12         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7554 
       27.29         2.76        21.40        18.18        19.89        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 
        5.95         0.59        18.12        21.60        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 
       20.84        18.67        24.56        34.85         5.59        24.30 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A743 
       18.08        35.47        19.00         3.81        14.53        17.46 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       11.87        27.19        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-MP-A4TE 
       49.35        86.04        58.85         5.29        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-NJ-A4YG 
       11.05        14.66        14.10        11.15        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-O1-A52J 
        0.13        29.13        59.11 

$`DEL PEAK 36(17P13.3) WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4403 TCGA-05-4405 TCGA-05-4418 
        3.98        19.96        14.01        19.00        20.05         9.01 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4432 TCGA-05-4434 TCGA-05-5423 TCGA-05-5715 
       12.00        30.02        25.02        15.02         4.96         2.04 
TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
        0.46         8.68       120.79        37.71        49.05        28.41 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2665 TCGA-44-2666 
       26.30         4.37        43.53        46.98        42.77         3.19 
TCGA-44-2668 TCGA-44-3398 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 
       25.02        38.24        28.37        12.59        10.78         9.93 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 TCGA-44-7659 TCGA-44-7669 TCGA-44-7671 
       23.15        21.63        63.72        14.60        18.87        17.59 
TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       23.64        15.98        15.32        11.08        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 
       13.45        76.21        28.11        28.57        35.54        32.84 
TCGA-49-4514 TCGA-49-6742 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARR 
       55.89        14.63        63.95        62.24        28.90       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
        9.86        20.52        71.47        60.16        31.04         8.22 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 TCGA-50-5942 
        9.27        40.60        78.67        21.47        15.12        29.03 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 TCGA-50-8457 TCGA-50-8459 
       22.55        42.35        25.55         6.21        25.61         7.59 
TCGA-50-8460 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 
       27.25         9.21         2.86         0.07        32.65        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 
       15.25         0.82        60.03       107.21        70.26         1.15 
TCGA-55-7284 TCGA-55-7570 TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 TCGA-55-7907 
        7.99         0.20        23.18         1.28         0.79         0.53 
TCGA-55-8087 TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 
       15.19        19.66         5.06        23.64         1.51        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 
       15.42         1.45         0.95         0.26         0.49         0.10 
TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A490 
        4.80         0.49         1.58         1.61        16.93         1.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 
       19.59         0.92        15.81        20.19        19.99        39.98 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46V TCGA-62-A46Y 
       14.60        88.64        49.25        19.53        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 
       39.25        40.96        20.65        37.02         2.04        51.25 
TCGA-67-3774 TCGA-67-6216 TCGA-69-7763 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 
       12.66         4.64        22.68         7.56        12.56        14.01 
TCGA-69-8254 TCGA-73-4662 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       13.45        29.98        26.30         1.32         5.39         1.25 
TCGA-73-7498 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
       39.09        20.58        35.93        39.52        24.99        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
       32.09         5.88        22.29         7.07       104.19       223.96 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-7633 TCGA-78-8648 
        8.48        88.14        26.53        53.33        32.68        39.75 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7714 TCGA-86-8074 
       10.55       110.50        27.09        12.36        20.55         0.79 
TCGA-86-8076 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       16.08        14.60         1.15        30.84        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32         3.81        13.64        26.47 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       41.36         1.97         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7043 
        1.18        19.82         4.18        23.61        19.00         1.22 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 
       31.69        64.60        63.52        43.79         0.72        18.67 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
       17.92         5.39        15.39        16.41        14.30        20.58 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 
       20.19        20.52        17.75        20.68        36.76         1.45 
TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A5IP 
       21.63        23.80        16.44        14.30         0.20         1.91 
TCGA-L9-A7SV TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       12.59        37.35         5.49        41.59        31.23         2.43 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       19.13        73.91         1.64         0.26         0.43        19.82 
TCGA-NJ-A7XG TCGA-S2-AA1A 
        9.70        16.87 

  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                          0.00                           0.07 
  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                        214.62                         223.96 
  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                        18.640                         18.295 
[1] "0.0 - 214.6 (18.6)" "0.1 - 224.0 (18.3)"
[1] "hr=" "1.1"
D57V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(17P13.3) MUTATED         3       64       79        1        32
  DEL PEAK 36(17P13.3) WILD-TYPE       2       71       61        0        19
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 36(17P13.3) MUTATED          42         39          7       14
  DEL PEAK 36(17P13.3) WILD-TYPE        31         33          4       12
D57V3, multiclass
            clus
vv           DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             64                             71
  STAGE IB                             79                             61
  STAGE II                              1                              0
  STAGE IIA                            32                             19
  STAGE IIB                            42                             31
  STAGE IIIA                           39                             33
  STAGE IIIB                            7                              4
  STAGE IV                             14                             12
[1] 9 2
[1] 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(17P13.3) MUTATED    85 164  21  10
  DEL PEAK 36(17P13.3) WILD-TYPE  85 114  25   9
D57V4, multiclass
    clus
vv   DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  T1                           85                             85
  T2                          164                            114
  T3                           21                             25
  T4                           10                              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 36(17P13.3) MUTATED   179  54    42
  DEL PEAK 36(17P13.3) WILD-TYPE 153  42    34
D57V5, multiclass
       clus
vv      DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  N0                             179                            153
  N1                              54                             42
  N2+N3                           42                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                                cls
clus                               0   1
  DEL PEAK 36(17P13.3) MUTATED   195  13
  DEL PEAK 36(17P13.3) WILD-TYPE 153  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17P13.3) MUTATED    195   13
  DEL PEAK 36(17P13.3) WILD-TYPE  153   12
   clus
vv  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  0                          195                            153
  1                           13                             12
[1] 2 2
[1] FALSE
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(17P13.3) MUTATED   160 121
  DEL PEAK 36(17P13.3) WILD-TYPE 115 119
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17P13.3) MUTATED    160  121
  DEL PEAK 36(17P13.3) WILD-TYPE  115  119
        clus
vv       DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  FEMALE                          160                            115
  MALE                            121                            119
[1] 2 2
[1] FALSE
D57V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 36(17P13.3) MUTATED                           10
  DEL PEAK 36(17P13.3) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 36(17P13.3) MUTATED                                  55
  DEL PEAK 36(17P13.3) WILD-TYPE                                52
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(17P13.3) MUTATED                                                  185
  DEL PEAK 36(17P13.3) WILD-TYPE                                                134
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 36(17P13.3) MUTATED                                            2
  DEL PEAK 36(17P13.3) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 36(17P13.3) MUTATED                                               9
  DEL PEAK 36(17P13.3) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 36(17P13.3) MUTATED                                2
  DEL PEAK 36(17P13.3) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 36(17P13.3) MUTATED                                    3
  DEL PEAK 36(17P13.3) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 36(17P13.3) MUTATED                              0
  DEL PEAK 36(17P13.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 36(17P13.3) MUTATED                               8
  DEL PEAK 36(17P13.3) WILD-TYPE                            15
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 36(17P13.3) MUTATED                                 1
  DEL PEAK 36(17P13.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 36(17P13.3) MUTATED                                               4
  DEL PEAK 36(17P13.3) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 36(17P13.3) MUTATED                              2
  DEL PEAK 36(17P13.3) WILD-TYPE                            8
D57V9, multiclass
                                                    clus
vv                                                   DEL PEAK 36(17P13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          185
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 9
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 8
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 4
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 36(17P13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            134
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  10
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              0
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  15
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   1
  MUCINOUS (COLLOID) CARCINOMA                                                    8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, binary
                                cls
clus                               0   1
  DEL PEAK 36(17P13.3) MUTATED     9 272
  DEL PEAK 36(17P13.3) WILD-TYPE  12 222
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17P13.3) MUTATED      9  272
  DEL PEAK 36(17P13.3) WILD-TYPE   12  222
     clus
vv    DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  NO                             9                             12
  YES                          272                            222
[1] 2 2
[1] FALSE
D57V11, continuous
D57V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(17P13.3) MUTATED   191   6   1  17
  DEL PEAK 36(17P13.3) WILD-TYPE 152   6   3   9
D57V13, multiclass
    clus
vv   DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  R0                          191                            152
  R1                            6                              6
  R2                            1                              3
  RX                           17                              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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(17P13.3) MUTATED                                  1     4
  DEL PEAK 36(17P13.3) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(17P13.3) MUTATED                          28   207
  DEL PEAK 36(17P13.3) WILD-TYPE                        23   182
D57V14, multiclass
                                  clus
vv                                 DEL PEAK 36(17P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  28
  WHITE                                                     207
                                  clus
vv                                 DEL PEAK 36(17P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    23
  WHITE                                                       182
[1] 4 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 36(17P13.3) MUTATED     5 200
  DEL PEAK 36(17P13.3) WILD-TYPE   2 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17P13.3) MUTATED      5  200
  DEL PEAK 36(17P13.3) WILD-TYPE    2  182
                        clus
vv                       DEL PEAK 36(17P13.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          200
                        clus
vv                       DEL PEAK 36(17P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            182
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 37(18Q21.32) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 37(18Q21.32) MUTATED   158  82
  DEL PEAK 37(18Q21.32) WILD-TYPE 179  72
  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                            240                             251 
  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                             82                              72 
$`DEL PEAK 37(18Q21.32) MUTATED`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4395 TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 
       50.07         3.98         0.00         9.96        47.05         8.02 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       20.05        14.96         9.01        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4427 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 TCGA-05-5425 
       26.01        26.01        24.00        15.02         4.96        29.00 
TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4627 
        9.04         2.04         7.40         5.98         8.68        37.71 
TCGA-38-4628 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2657 TCGA-44-2662 
       49.05        11.64        44.61        14.73        13.15        42.08 
TCGA-44-2665 TCGA-44-2668 TCGA-44-6145 TCGA-44-6146 TCGA-44-6777 TCGA-44-6779 
       42.77        25.02        10.78         9.93        32.45        16.44 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7672 TCGA-44-A47F 
        7.17        36.07        18.87        29.00        23.64        11.08 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 
       13.45        28.11        28.57        12.66        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 TCGA-49-6761 
       32.84         8.81        29.75        14.63        12.13        11.64 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26        22.26       153.04        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 
       40.41        37.32       123.58        15.72        31.04        49.28 
TCGA-50-5072 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5946 
        8.22        78.67         8.45        15.12        18.64        22.55 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 
       11.05        12.16        41.69        25.61         7.59        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6712 
       30.54         9.21        38.73        48.62        45.21         0.79 
TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6979 TCGA-55-6980 
       42.51         0.82        48.49         3.88         7.79         2.20 
TCGA-55-6982 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7574 
       32.71        40.54         0.59         1.15         0.13         3.12 
TCGA-55-7576 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7910 
        1.32         1.28         1.28         1.12         0.79         6.48 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
       19.82         0.16        15.19         3.29        19.66        19.73 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8207 TCGA-55-8301 TCGA-55-8505 
        0.13        23.64        15.65         2.17         1.45         0.95 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8511 TCGA-55-8616 TCGA-55-A48Z TCGA-55-A490 
        0.26        17.72         0.30         1.58        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
       20.58        19.59         0.92        19.99        17.95         4.57 
TCGA-62-8397 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 
       42.38        47.80        56.71        54.35        67.96        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
       40.96        29.92        55.43        38.37         2.04        42.90 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6216 
       51.25        28.47         1.02        20.05        18.84         4.64 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 
       13.87         6.64         5.42         2.30         2.93        13.45 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 TCGA-73-7498 
       26.73         7.04        29.98        26.30         4.31        39.09 
TCGA-73-7499 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       23.51        11.18       163.10        27.16         5.69        19.27 
TCGA-78-7150 TCGA-78-7155 TCGA-78-7161 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
       21.90        38.50         7.07        31.20         8.02        10.75 
TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       10.55        27.09         5.88        31.13        34.39        13.87 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       20.55        19.89         4.08        24.33         0.79        15.75 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       15.65        15.85        23.05        21.47        14.60         1.15 
TCGA-86-8672 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 
        0.62        41.36         1.97        10.19        13.71        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-7771 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 
       27.68         7.36        16.18         1.45        19.82         4.18 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7567 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 
       17.29         1.22        18.67        15.68        27.29         2.76 
TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 
       18.18        31.69        64.60        63.52         5.95         0.72 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX 
        5.39        15.39        16.41        21.60        20.58        20.19 
TCGA-97-A4M0 TCGA-97-A4M6 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
       21.44        18.67         5.59        24.30        23.80        18.08 
TCGA-J2-A4AE TCGA-L9-A50W TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
       35.47        14.53        17.46        11.87        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
        2.76        58.45        37.35        86.04        58.85         5.49 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A55O 
       11.05        14.10        11.15        19.13        71.05         0.43 

$`DEL PEAK 37(18Q21.32) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4403 
       19.96        14.01        45.01        37.02        24.03        19.00 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5428 
        2.99        29.98        25.02        25.02        15.02        22.03 
TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 
        0.46        97.74       120.79        28.41        35.28        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 
        4.37        43.53        46.98        44.94        24.36         3.19 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       37.15        38.24        38.89        34.06         6.25        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6147 TCGA-44-6148 
       33.30        28.37        12.59        23.77        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 
       21.63        23.18        63.72        61.28        14.60        19.46 
TCGA-44-7661 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       12.03        17.59        12.66         3.25         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 
       15.32         9.44        11.54        13.64        76.21        35.54 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-49-AAR2 TCGA-49-AARQ 
       29.46        55.89        29.26        17.16        63.95       211.82 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
      164.12         9.86        20.52        71.47        70.55        60.16 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 
        9.27        14.27        40.60        21.47        29.03        25.12 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       42.35         3.91        25.55         6.21         0.72        10.13 
TCGA-50-8460 TCGA-53-7813 TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       27.25        13.94        23.05         2.86         0.07        32.65 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6978 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 
       40.73        15.25         5.49        45.34        60.03        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7724 TCGA-55-7815 
      107.21        70.26         7.99         0.20        23.18         1.78 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-8085 TCGA-55-8092 
       18.64         0.53        17.65         6.15        29.72         5.06 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 
       17.98         1.08         1.51        22.16        15.42         0.76 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
        0.36         0.49         0.10         4.80         6.64        17.62 
TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
        0.49         1.61         2.17        16.93        22.65        20.71 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       15.81        20.19        39.98        14.60        88.64        49.25 
TCGA-62-A46P TCGA-62-A46V TCGA-62-A46Y TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
       19.53        72.30        13.61        56.81        20.65        39.09 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 
       37.02        87.98        28.41        14.04        12.66         5.72 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 
        6.12        22.68        13.61         7.56         6.05        12.56 
TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4668 
       14.01         4.24         2.01        52.60        23.38        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
        1.32         5.39         1.25        20.58        35.93        39.52 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       24.99        19.50        32.09         5.88        64.90        22.29 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 
      104.19       223.96         8.48        88.14        26.53        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8662 TCGA-86-6562 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 
      110.50        12.36        19.43        16.70        24.49         4.57 
TCGA-86-8076 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
       16.08        13.91        30.84        27.58        14.96        13.32 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       13.32         3.81        17.62        13.64        26.47        10.62 
TCGA-91-6835 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-93-7347 
        2.60         1.15        16.60        14.27         1.18         9.76 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7562 
        6.12        23.61         1.08        19.00         1.12         2.86 
TCGA-95-7944 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7553 TCGA-97-7554 
       12.39        15.65        21.40        19.89        43.79        25.48 
TCGA-97-7938 TCGA-97-8171 TCGA-97-8172 TCGA-97-8175 TCGA-97-8179 TCGA-97-A4M1 
        0.59        18.67        17.92        18.12        14.30        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8025 
       20.52        17.75        20.84        20.68        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       36.76         1.45        21.63        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MP-A4SV TCGA-MP-A4SY 
        3.81         0.20         1.91        12.59        86.14        49.35 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE 
        5.29        41.59        31.23         2.43        10.09        29.46 
TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       14.66        73.91        62.60         0.13         1.64        29.13 
TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.26        19.82         9.70        59.11        16.87 

  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                           0.00                            0.07 
  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                         163.10                          223.96 
  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                         17.375                          19.430 
[1] "0.0 - 163.1 (17.4)" "0.1 - 224.0 (19.4)"
[1] "hr=" "1.5"
D58V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(18Q21.32) MUTATED         1       51       67        1        31
  DEL PEAK 37(18Q21.32) WILD-TYPE       4       84       73        0        20
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 37(18Q21.32) MUTATED          46         33          6       14
  DEL PEAK 37(18Q21.32) WILD-TYPE        27         39          5       12
D58V3, multiclass
            clus
vv           DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                              51                              84
  STAGE IB                              67                              73
  STAGE II                               1                               0
  STAGE IIA                             31                              20
  STAGE IIB                             46                              27
  STAGE IIIA                            33                              39
  STAGE IIIB                             6                               5
  STAGE IV                              14                              12
[1] 9 2
[1] 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(18Q21.32) MUTATED    74 141  26   9
  DEL PEAK 37(18Q21.32) WILD-TYPE  96 137  20  10
D58V4, multiclass
    clus
vv   DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  T1                            74                              96
  T2                           141                             137
  T3                            26                              20
  T4                             9                              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 37(18Q21.32) MUTATED   152  60    34
  DEL PEAK 37(18Q21.32) WILD-TYPE 180  36    42
D58V5, multiclass
       clus
vv      DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  N0                              152                             180
  N1                               60                              36
  N2+N3                            34                              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18Q21.32) MUTATED   157  13
  DEL PEAK 37(18Q21.32) WILD-TYPE 191  12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18Q21.32) MUTATED    157   13
  DEL PEAK 37(18Q21.32) WILD-TYPE  191   12
   clus
vv  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  0                           157                             191
  1                            13                              12
[1] 2 2
[1] FALSE
D58V7, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18Q21.32) MUTATED   139 112
  DEL PEAK 37(18Q21.32) WILD-TYPE 136 128
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18Q21.32) MUTATED    139  112
  DEL PEAK 37(18Q21.32) WILD-TYPE  136  128
        clus
vv       DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  FEMALE                           139                             136
  MALE                             112                             128
[1] 2 2
[1] FALSE
D58V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 37(18Q21.32) MUTATED                           10
  DEL PEAK 37(18Q21.32) WILD-TYPE                          9
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 37(18Q21.32) MUTATED                                  54
  DEL PEAK 37(18Q21.32) WILD-TYPE                                53
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(18Q21.32) MUTATED                                                  156
  DEL PEAK 37(18Q21.32) WILD-TYPE                                                163
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 37(18Q21.32) MUTATED                                            1
  DEL PEAK 37(18Q21.32) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 37(18Q21.32) MUTATED                                              10
  DEL PEAK 37(18Q21.32) WILD-TYPE                                             9
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 37(18Q21.32) MUTATED                                2
  DEL PEAK 37(18Q21.32) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 37(18Q21.32) MUTATED                                    2
  DEL PEAK 37(18Q21.32) WILD-TYPE                                  1
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 37(18Q21.32) MUTATED                              1
  DEL PEAK 37(18Q21.32) WILD-TYPE                            1
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 37(18Q21.32) MUTATED                               5
  DEL PEAK 37(18Q21.32) WILD-TYPE                            18
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 37(18Q21.32) MUTATED                                 1
  DEL PEAK 37(18Q21.32) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 37(18Q21.32) MUTATED                                               3
  DEL PEAK 37(18Q21.32) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 37(18Q21.32) MUTATED                              6
  DEL PEAK 37(18Q21.32) WILD-TYPE                            4
D58V9, multiclass
                                                    clus
vv                                                   DEL PEAK 37(18Q21.32) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           156
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 10
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                  5
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   6
                                                    clus
vv                                                   DEL PEAK 37(18Q21.32) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             163
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    9
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               1
  LUNG MUCINOUS ADENOCARCINOMA                                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                                   18
  LUNG SIGNET RING ADENOCARCINOMA                                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    2
  MUCINOUS (COLLOID) CARCINOMA                                                     4
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18Q21.32) MUTATED     8 243
  DEL PEAK 37(18Q21.32) WILD-TYPE  13 251
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18Q21.32) MUTATED      8  243
  DEL PEAK 37(18Q21.32) WILD-TYPE   13  251
     clus
vv    DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  NO                              8                              13
  YES                           243                             251
[1] 2 2
[1] FALSE
D58V11, continuous
D58V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 37(18Q21.32) MUTATED   170   8   3   6
  DEL PEAK 37(18Q21.32) WILD-TYPE 173   4   1  20
D58V13, multiclass
    clus
vv   DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  R0                           170                             173
  R1                             8                               4
  R2                             3                               1
  RX                             6                              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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(18Q21.32) MUTATED                                  0     2
  DEL PEAK 37(18Q21.32) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(18Q21.32) MUTATED                          26   186
  DEL PEAK 37(18Q21.32) WILD-TYPE                        25   203
D58V14, multiclass
                                  clus
vv                                 DEL PEAK 37(18Q21.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      186
                                  clus
vv                                 DEL PEAK 37(18Q21.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     25
  WHITE                                                        203
[1] 4 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 37(18Q21.32) MUTATED     4 185
  DEL PEAK 37(18Q21.32) WILD-TYPE   3 197
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18Q21.32) MUTATED      4  185
  DEL PEAK 37(18Q21.32) WILD-TYPE    3  197
                        clus
vv                       DEL PEAK 37(18Q21.32) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           185
                        clus
vv                       DEL PEAK 37(18Q21.32) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             197
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 38(19P13.3) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(19P13.3) MUTATED   173  94
  DEL PEAK 38(19P13.3) WILD-TYPE 164  60
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                           267                            224 
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                            94                             60 
$`DEL PEAK 38(19P13.3) MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4415 TCGA-05-4418 
        9.96        24.03        47.05         8.02         2.99         9.01 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 
       12.00        30.02        26.01        24.00        15.02        29.00 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4628 TCGA-38-4630 
       22.03         7.40         5.98         8.68        49.05        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       11.64        44.61        14.73        43.53        46.98        13.15 
TCGA-44-2662 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-4112 
       42.08         3.19        25.02        38.89        34.06        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6146 TCGA-44-6774 
       33.30        28.37        12.59        23.77         9.93        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 
       23.18        63.72        61.28        16.44        19.46        36.07 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 
       18.87        29.00        17.59         3.25         8.55        15.98 
TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4490 TCGA-49-4501 
       11.08        13.64        13.45        76.21        12.66        46.72 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 
       14.07         8.81        29.46        55.89        14.63        12.13 
TCGA-49-6744 TCGA-49-6745 TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR9 
       29.26        17.16        22.26       153.04        63.95         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
       40.41       123.58       211.82        70.55        15.72        31.04 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 
       49.28         8.22         9.27        14.27        40.60        78.67 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-6591 
       21.47         8.45        15.12        18.64        25.12         3.91 
TCGA-50-6592 TCGA-50-6594 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 
       25.55        12.16        41.69        10.13        34.29        13.94 
TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6971 
        9.21        23.05        38.73        45.21         2.86         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6981 TCGA-55-6982 TCGA-55-7570 
       48.49         3.88         5.49        45.34        32.71         0.20 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7914 TCGA-55-7994 
        1.32         1.12         0.53         6.48         6.15        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8203 
        0.16        29.72         3.29         5.06         0.13        17.98 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8614 TCGA-55-8616 
        0.76         0.95         0.49         0.10        17.62         1.58 
TCGA-55-A48X TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
       22.65         1.58        20.58        19.59         0.92        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       20.19        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       88.64        49.25        47.80        56.71        54.35        67.96 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 
       39.25        40.96        56.81        38.37        87.98        42.90 
TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6217 
       28.41         1.02        20.05        18.84        12.66        13.87 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 
        6.12        22.68        13.61         7.56         2.30        12.56 
TCGA-69-8253 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
       14.01         4.24        26.73         7.04         2.01        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 
       26.30        15.35         4.31         1.32         1.25        39.09 
TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
       23.51        27.16         5.69        19.27        20.58        35.93 
TCGA-78-7150 TCGA-78-7153 TCGA-78-7156 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 
       21.90        24.99        32.09        22.29       104.19         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 
       88.14        26.53        31.20         8.02        10.75        32.68 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
       27.09        31.13        34.39        13.87        19.43        19.89 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
       16.70         4.08        24.33         0.79        15.75        15.85 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8669 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       23.05        21.47        30.84         0.62        13.32        13.32 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 
        3.81        10.62        41.36         1.97        10.19        13.71 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-93-8067 
       12.23         7.36         1.15        16.18        14.27         6.12 
TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7948 
       17.29         1.12         1.22         2.86        12.39        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7937 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       21.40        18.18         5.95        18.67        17.92         5.39 
TCGA-97-8176 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8033 
       15.39        20.19        19.76        18.67        24.56         5.59 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A7SV 
       24.30        18.08        19.00         3.81        14.53        12.59 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 
       11.87        38.63        86.14        49.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.49         5.29        31.23        11.05        14.66        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55O 
       11.15        19.13        73.91        71.05        29.13         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       19.82         9.70        59.11 

$`DEL PEAK 38(19P13.3) WILD-TYPE`
TCGA-05-4249 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 
       50.07        19.00        20.05        14.96        29.98        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4434 TCGA-05-5423 TCGA-05-5429 
       26.01        25.02        25.02        15.02         4.96         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
        2.04         0.46        97.74       120.79        37.71        28.41 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 TCGA-44-3396 
       26.30         4.37        44.94        24.36        42.77        37.15 
TCGA-44-3398 TCGA-44-3919 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6777 
       38.24         6.25        10.78        27.78        23.15        32.45 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7672 TCGA-44-8117 TCGA-44-A47A 
       14.60        12.03         7.17        23.64        12.66        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 
        9.44        11.54        28.11        28.57        35.54        32.84 
TCGA-49-4512 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARN 
       29.75        11.64        22.26        62.24        28.90        37.32 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5942 
      164.12         9.86        20.52        71.47        60.16        29.03 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 
       22.55        42.35        11.05         6.21         0.72        25.61 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 
        7.59        27.25        30.54        48.62         0.07        32.65 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6979 TCGA-55-6980 
        0.79        42.51        40.73        15.25         7.79         2.20 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       60.03        24.99        40.54       107.21        70.26         0.59 
TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 
        1.15         7.99         0.13         3.12        23.18         1.28 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-8087 
        1.28         0.79         1.78        18.64        17.65        15.19 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
       19.66        19.73        23.64        15.65         1.08         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8507 
        2.17        22.16        15.42         1.45         0.36         0.26 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8619 
       17.72         0.30         4.80         6.64         0.49         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A57B TCGA-62-A46P 
        2.17        16.93        20.71        21.40        17.95        19.53 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
       72.30        13.61        29.92        20.65        39.09        55.43 
TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-6215 
       37.02         2.04        51.25        28.47        14.04         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-8254 
        4.64         6.64         5.42         6.05         2.93        13.45 
TCGA-73-4658 TCGA-73-4662 TCGA-73-4676 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7152 
       52.60        29.98         5.39        11.18       163.10        39.52 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7163 
       19.50        38.50         5.88        64.90         7.07       223.96 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       53.33        39.35        10.55       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7714 TCGA-86-8054 
       10.55       110.50        12.36         5.88        20.55        24.49 
TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
        4.57        16.08        15.65        14.60         1.15        13.91 
TCGA-86-8671 TCGA-86-8673 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 
       27.58        14.96        17.62        13.64        26.47         2.60 
TCGA-91-6847 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 
       27.68        16.60         1.18         1.45        19.82         9.76 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7947 
        4.18        23.61         1.08        19.00        18.67        15.68 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        31.69        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 
       43.79        25.48         0.59         0.72        18.12        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 
       14.30        21.60        20.58        21.44        20.52        17.75 
TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R 
       20.84        20.68        34.85        36.76         1.45        21.63 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A5IP 
       23.80        35.47        16.44        14.30         0.20         1.91 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 
       17.46        27.19         2.76        58.45        37.35        41.59 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
        2.43        10.09        29.46        62.60         0.13         1.64 
TCGA-NJ-A55A TCGA-S2-AA1A 
        0.26        16.87 

  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                          0.00                           0.07 
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                        211.82                         223.96 
  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE 
                        18.080                         18.835 
[1] "0.0 - 211.8 (18.1)" "0.1 - 224.0 (18.8)"
[1] "hr=" "1.3"
D59V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 38(19P13.3) MUTATED         3       65       74        0        34
  DEL PEAK 38(19P13.3) WILD-TYPE       2       70       66        1        17
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 38(19P13.3) MUTATED          41         41          8       16
  DEL PEAK 38(19P13.3) WILD-TYPE        32         31          3       10
D59V3, multiclass
            clus
vv           DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             65                             70
  STAGE IB                             74                             66
  STAGE II                              0                              1
  STAGE IIA                            34                             17
  STAGE IIB                            41                             32
  STAGE IIIA                           41                             31
  STAGE IIIB                            8                              3
  STAGE IV                             16                             10
[1] 9 2
[1] 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(19P13.3) MUTATED    82 164  22  13
  DEL PEAK 38(19P13.3) WILD-TYPE  88 114  24   6
D59V4, multiclass
    clus
vv   DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  T1                           82                             88
  T2                          164                            114
  T3                           22                             24
  T4                           13                              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 38(19P13.3) MUTATED   173  62    42
  DEL PEAK 38(19P13.3) WILD-TYPE 159  34    34
D59V5, multiclass
       clus
vv      DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  N0                             173                            159
  N1                              62                             34
  N2+N3                           42                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                                cls
clus                               0   1
  DEL PEAK 38(19P13.3) MUTATED   198  16
  DEL PEAK 38(19P13.3) WILD-TYPE 150   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(19P13.3) MUTATED    198   16
  DEL PEAK 38(19P13.3) WILD-TYPE  150    9
   clus
vv  DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  0                          198                            150
  1                           16                              9
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(19P13.3) MUTATED   137 145
  DEL PEAK 38(19P13.3) WILD-TYPE 138  95
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(19P13.3) MUTATED    137  145
  DEL PEAK 38(19P13.3) WILD-TYPE  138   95
        clus
vv       DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  FEMALE                          137                            138
  MALE                            145                             95
[1] 2 2
[1] FALSE
D59V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                            9
  DEL PEAK 38(19P13.3) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 38(19P13.3) MUTATED                                  57
  DEL PEAK 38(19P13.3) WILD-TYPE                                50
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(19P13.3) MUTATED                                                  180
  DEL PEAK 38(19P13.3) WILD-TYPE                                                139
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 38(19P13.3) MUTATED                                            0
  DEL PEAK 38(19P13.3) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 38(19P13.3) MUTATED                                               9
  DEL PEAK 38(19P13.3) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                                1
  DEL PEAK 38(19P13.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                                    3
  DEL PEAK 38(19P13.3) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                              1
  DEL PEAK 38(19P13.3) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                              13
  DEL PEAK 38(19P13.3) WILD-TYPE                            10
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                                 1
  DEL PEAK 38(19P13.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                                               3
  DEL PEAK 38(19P13.3) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 38(19P13.3) MUTATED                              5
  DEL PEAK 38(19P13.3) WILD-TYPE                            5
D59V9, multiclass
                                                    clus
vv                                                   DEL PEAK 38(19P13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            57
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          180
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 9
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                13
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  5
                                                    clus
vv                                                   DEL PEAK 38(19P13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            139
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  10
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              0
  LUNG MUCINOUS ADENOCARCINOMA                                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                                  10
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  MUCINOUS (COLLOID) CARCINOMA                                                    5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, binary
                                cls
clus                               0   1
  DEL PEAK 38(19P13.3) MUTATED    14 268
  DEL PEAK 38(19P13.3) WILD-TYPE   7 226
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(19P13.3) MUTATED     14  268
  DEL PEAK 38(19P13.3) WILD-TYPE    7  226
     clus
vv    DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  NO                            14                              7
  YES                          268                            226
[1] 2 2
[1] FALSE
D59V11, continuous
D59V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(19P13.3) MUTATED   187   4   2  16
  DEL PEAK 38(19P13.3) WILD-TYPE 156   8   2  10
D59V13, multiclass
    clus
vv   DEL PEAK 38(19P13.3) MUTATED DEL PEAK 38(19P13.3) WILD-TYPE
  R0                          187                            156
  R1                            4                              8
  R2                            2                              2
  RX                           16                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(19P13.3) MUTATED                                  1     5
  DEL PEAK 38(19P13.3) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(19P13.3) MUTATED                          31   207
  DEL PEAK 38(19P13.3) WILD-TYPE                        20   182
D59V14, multiclass
                                  clus
vv                                 DEL PEAK 38(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  31
  WHITE                                                     207
                                  clus
vv                                 DEL PEAK 38(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                       182
[1] 4 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 38(19P13.3) MUTATED     7 206
  DEL PEAK 38(19P13.3) WILD-TYPE   0 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(19P13.3) MUTATED      7  206
  DEL PEAK 38(19P13.3) WILD-TYPE    0  176
                        clus
vv                       DEL PEAK 38(19P13.3) MUTATED
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          206
                        clus
vv                       DEL PEAK 38(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  0
  NOT HISPANIC OR LATINO                            176
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 39(19P13.2) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(19P13.2) MUTATED   173  91
  DEL PEAK 39(19P13.2) WILD-TYPE 164  63
  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                           264                            227 
  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                            91                             63 
$`DEL PEAK 39(19P13.2) MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4415 TCGA-05-4418 
        9.96        24.03        47.05         8.02         2.99         9.01 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4427 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 
       12.00        30.02        26.01        24.00        15.02        29.00 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4628 TCGA-38-4630 
       22.03         7.40         5.98         8.68        49.05        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       11.64        44.61        14.73        43.53        46.98        13.15 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-5643 
       42.08        42.77         3.19        25.02        38.89        33.30 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6146 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 
       28.37        23.77         9.93        21.63        23.18        63.72 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
       61.28        16.44        19.46        36.07        18.87        29.00 
TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47F TCGA-44-A4SS 
       17.59        12.66         3.25         8.55        11.08        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 
       13.45        76.21        12.66        46.72        14.07         8.81 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
       29.46        55.89        14.63        12.13        29.26        17.16 
TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
       22.26       153.04        63.95         8.55        40.41       123.58 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       70.55        15.72        31.04         8.22         9.27        14.27 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       40.60        78.67        21.47         8.45        15.12        18.64 
TCGA-50-5944 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-7109 
       25.12         3.91        11.05        12.16        41.69        10.13 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
       13.94         9.21        23.05        38.73        45.21         2.86 
TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6981 
       42.51         0.82        48.49         3.88         5.49        45.34 
TCGA-55-6982 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 
       32.71         0.20         1.32         1.12         0.53         6.48 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 
        6.15        19.82         0.16        29.72         3.29         5.06 
TCGA-55-8094 TCGA-55-8203 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
        0.13        17.98         0.76         0.95         0.26         0.49 
TCGA-55-8512 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48X TCGA-55-A490 
        0.10        17.62         0.49         1.58        22.65         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 
       47.80        56.71        54.35        67.96        39.25        40.96 
TCGA-64-1676 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 
       56.81        38.37        87.98        42.90        28.41         1.02 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 
       20.05        18.84        12.66        13.87         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 
       13.61         7.56         2.30        12.56        14.01         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       26.73         7.04         2.01        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 
        4.31         1.25        39.09        23.51        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7156 
       19.27        20.58        35.93        21.90        24.99        32.09 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 
       64.90        22.29       104.19         8.48        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-83-5908 TCGA-86-7701 
       31.20         8.02        10.75        32.68        27.09        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       34.39        13.87        19.43        19.89        16.70         4.08 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8669 
       24.33         0.79        15.75        15.85        23.05        30.84 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 
        0.62        13.32        13.32         3.81        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6849 TCGA-91-7771 
        1.97        10.19        13.71        12.23         1.15        16.18 
TCGA-91-8497 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
       14.27         1.45        17.29         1.12         1.22        18.67 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-7937 TCGA-97-8171 TCGA-97-8172 
       15.65        21.40        18.18         5.95        18.67        17.92 
TCGA-97-8174 TCGA-97-8176 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M3 TCGA-97-A4M6 
        5.39        15.39        20.19        19.76        17.75        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 
       24.56        34.85         5.59        24.30        18.08        19.00 
TCGA-L9-A443 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY 
        3.81        12.59        11.87        38.63        86.14        49.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       86.04        58.85         5.49         5.29        31.23         2.43 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       11.05        14.66        14.10        11.15        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       71.05        29.13         0.43        19.82         9.70        59.11 

$`DEL PEAK 39(19P13.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 
       50.07        19.00        20.05        14.96        29.98        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4434 TCGA-05-5423 TCGA-05-5429 
       26.01        25.02        25.02        15.02         4.96         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
        2.04         0.46        97.74       120.79        37.71        28.41 
TCGA-38-7271 TCGA-38-A44F TCGA-44-2659 TCGA-44-2661 TCGA-44-3396 TCGA-44-3398 
       26.30         4.37        44.94        24.36        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 
       34.06         6.25        26.56        12.59        10.78        27.78 
TCGA-44-6148 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7672 
       23.15        32.45        14.60        12.03         7.17        23.64 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4487 TCGA-49-4488 
       15.98        15.32         9.44        11.54        28.11        28.57 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4512 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR3 
       35.54        32.84        29.75        11.64        22.26        62.24 
TCGA-49-AAR4 TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       28.90        37.32       211.82       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 
       71.47        60.16        49.28        29.03        22.55        42.35 
TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       25.55         6.21         0.72        25.61         7.59        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       34.29        30.54        48.62         0.07        32.65         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6979 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 
       40.73        15.25         7.79         2.20        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
        0.13         3.12        23.18         1.28         1.28         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
        1.78        18.64        17.65        15.19        19.66        19.73 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       23.64        15.65         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 
       15.42         1.45         0.36        17.72         0.30         4.80 
TCGA-55-8514 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
        6.64         1.61         2.17        16.93        20.71        21.40 
TCGA-55-A57B TCGA-62-A46P TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1677 
       17.95        19.53        72.30        13.61        29.92        20.65 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 
       39.09        55.43        37.02         2.04        51.25        28.47 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7765 TCGA-69-7974 
       14.04         5.72         4.64         6.64         5.42         6.05 
TCGA-69-7979 TCGA-69-8254 TCGA-73-4658 TCGA-73-4662 TCGA-73-4675 TCGA-73-4676 
        2.93        13.45        52.60        29.98         1.32         5.39 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 
       11.18       163.10        39.52        19.50        38.50         5.88 
TCGA-78-7161 TCGA-78-7163 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        7.07       223.96        53.33        39.35        10.55       214.62 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59        10.55       110.50        12.36         5.88 
TCGA-86-7714 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 
       20.55        24.49         4.57        16.08        15.65        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-A4JF 
       14.60         1.15        13.91        27.58        14.96        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 
       13.64        26.47         2.60        27.68         7.36        16.60 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN 
        1.18        19.82         9.76         4.18         6.12        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 
        1.08        19.00         2.86        12.39        15.68        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        31.69        64.60        63.52        43.79 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
       25.48         0.59         0.72        18.12        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M7 
       21.60        20.58        21.44        20.52        20.84        20.68 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.63        23.80        35.47        16.44 
TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N1 
       14.30         0.20        14.53         1.91        17.46        27.19 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TD TCGA-MP-A4TE 
        2.76        58.45        37.35        41.59        10.09        29.46 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-S2-AA1A 
       62.60         0.13         1.64         0.26        16.87 

  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                          0.00                           0.07 
  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                        153.04                         223.96 
  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE 
                         18.03                          19.00 
[1] "0.0 - 153.0 (18.0)" "0.1 - 224.0 (19.0)"
[1] "hr=" "1.3"
D60V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(19P13.2) MUTATED         2       65       70        0        33
  DEL PEAK 39(19P13.2) WILD-TYPE       3       70       70        1        18
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 39(19P13.2) MUTATED          42         43          8       16
  DEL PEAK 39(19P13.2) WILD-TYPE        31         29          3       10
D60V3, multiclass
            clus
vv           DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             65                             70
  STAGE IB                             70                             70
  STAGE II                              0                              1
  STAGE IIA                            33                             18
  STAGE IIB                            42                             31
  STAGE IIIA                           43                             29
  STAGE IIIB                            8                              3
  STAGE IV                             16                             10
[1] 9 2
[1] 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(19P13.2) MUTATED    84 158  23  13
  DEL PEAK 39(19P13.2) WILD-TYPE  86 120  23   6
D60V4, multiclass
    clus
vv   DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  T1                           84                             86
  T2                          158                            120
  T3                           23                             23
  T4                           13                              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 39(19P13.2) MUTATED   169  60    45
  DEL PEAK 39(19P13.2) WILD-TYPE 163  36    31
D60V5, multiclass
       clus
vv      DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  N0                             169                            163
  N1                              60                             36
  N2+N3                           45                             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                                cls
clus                               0   1
  DEL PEAK 39(19P13.2) MUTATED   199  16
  DEL PEAK 39(19P13.2) WILD-TYPE 149   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(19P13.2) MUTATED    199   16
  DEL PEAK 39(19P13.2) WILD-TYPE  149    9
   clus
vv  DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  0                          199                            149
  1                           16                              9
[1] 2 2
[1] FALSE
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(19P13.2) MUTATED   135 144
  DEL PEAK 39(19P13.2) WILD-TYPE 140  96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(19P13.2) MUTATED    135  144
  DEL PEAK 39(19P13.2) WILD-TYPE  140   96
        clus
vv       DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  FEMALE                          135                            140
  MALE                            144                             96
[1] 2 2
[1] FALSE
D60V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                            9
  DEL PEAK 39(19P13.2) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 39(19P13.2) MUTATED                                  60
  DEL PEAK 39(19P13.2) WILD-TYPE                                47
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(19P13.2) MUTATED                                                  174
  DEL PEAK 39(19P13.2) WILD-TYPE                                                145
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 39(19P13.2) MUTATED                                            0
  DEL PEAK 39(19P13.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 39(19P13.2) MUTATED                                               9
  DEL PEAK 39(19P13.2) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                                1
  DEL PEAK 39(19P13.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                                    3
  DEL PEAK 39(19P13.2) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                              1
  DEL PEAK 39(19P13.2) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                              13
  DEL PEAK 39(19P13.2) WILD-TYPE                            10
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                                 1
  DEL PEAK 39(19P13.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                                               3
  DEL PEAK 39(19P13.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 39(19P13.2) MUTATED                              5
  DEL PEAK 39(19P13.2) WILD-TYPE                            5
D60V9, multiclass
                                                    clus
vv                                                   DEL PEAK 39(19P13.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          174
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 9
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            3
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                13
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  5
                                                    clus
vv                                                   DEL PEAK 39(19P13.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              47
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            145
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  10
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              0
  LUNG MUCINOUS ADENOCARCINOMA                                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                                  10
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  MUCINOUS (COLLOID) CARCINOMA                                                    5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, binary
                                cls
clus                               0   1
  DEL PEAK 39(19P13.2) MUTATED    14 265
  DEL PEAK 39(19P13.2) WILD-TYPE   7 229
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(19P13.2) MUTATED     14  265
  DEL PEAK 39(19P13.2) WILD-TYPE    7  229
     clus
vv    DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  NO                            14                              7
  YES                          265                            229
[1] 2 2
[1] FALSE
D60V11, continuous
D60V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(19P13.2) MUTATED   186   4   2  13
  DEL PEAK 39(19P13.2) WILD-TYPE 157   8   2  13
D60V13, multiclass
    clus
vv   DEL PEAK 39(19P13.2) MUTATED DEL PEAK 39(19P13.2) WILD-TYPE
  R0                          186                            157
  R1                            4                              8
  R2                            2                              2
  RX                           13                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(19P13.2) MUTATED                                  1     4
  DEL PEAK 39(19P13.2) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(19P13.2) MUTATED                          27   209
  DEL PEAK 39(19P13.2) WILD-TYPE                        24   180
D60V14, multiclass
                                  clus
vv                                 DEL PEAK 39(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     209
                                  clus
vv                                 DEL PEAK 39(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    24
  WHITE                                                       180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V15, binary
                                cls
clus                               0   1
  DEL PEAK 39(19P13.2) MUTATED     6 203
  DEL PEAK 39(19P13.2) WILD-TYPE   1 179
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(19P13.2) MUTATED      6  203
  DEL PEAK 39(19P13.2) WILD-TYPE    1  179
                        clus
vv                       DEL PEAK 39(19P13.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          203
                        clus
vv                       DEL PEAK 39(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            179
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 40(19P13.2) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(19P13.2) MUTATED   169  85
  DEL PEAK 40(19P13.2) WILD-TYPE 168  69
  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                           254                            237 
  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                            85                             69 
$`DEL PEAK 40(19P13.2) MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        3.98        19.96        14.01        45.01        37.02         0.00 
TCGA-05-4396 TCGA-05-4398 TCGA-05-4402 TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 
        9.96        47.05         8.02         9.01        29.98        12.00 
TCGA-05-4424 TCGA-05-4427 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 
       30.02        26.01        25.02        24.00        15.02        29.00 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4628 TCGA-38-4631 
       22.03         7.40         5.98         8.68        49.05        11.64 
TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2662 
       44.61        14.73        43.53        46.98        13.15        42.08 
TCGA-44-3917 TCGA-44-5644 TCGA-44-6144 TCGA-44-6146 TCGA-44-6774 TCGA-44-6775 
       38.89        28.37        23.77         9.93        21.63        23.18 
TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       63.72        61.28        16.44        19.46        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47F 
       29.00        17.59        12.66         3.25         8.55        11.08 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4490 TCGA-49-4501 TCGA-49-4505 
       13.64        13.45        76.21        12.66        46.72        14.07 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 
        8.81        29.46        55.89        14.63        12.13        29.26 
TCGA-49-6745 TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE 
       17.16        22.26       153.04        63.95         8.55        40.41 
TCGA-49-AARO TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 
      123.58        70.55        15.72        31.04         8.22         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       14.27        40.60        78.67         8.45        15.12        18.64 
TCGA-50-5944 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 
       25.12        11.05        12.16        41.69        10.13        34.29 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
       13.94         9.21        23.05        38.73        45.21         2.86 
TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6981 
       42.51         0.82        48.49         3.88         5.49        45.34 
TCGA-55-6982 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 
       32.71         0.20         1.32         1.12         0.53         6.48 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 
        6.15        19.82         0.16        29.72         3.29         5.06 
TCGA-55-8094 TCGA-55-8203 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
        0.13        17.98         0.76         0.95         0.26         0.49 
TCGA-55-8512 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48X TCGA-55-A490 
        0.10        17.62         0.49         1.58        22.65         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
       20.58        19.59         0.92        15.81        20.19        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
        4.57        39.98        42.38        14.60        88.64        49.25 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 
       47.80        19.53        56.71        54.35        67.96        39.25 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
       40.96        56.81        38.37        87.98        42.90        28.41 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3774 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
        1.02        18.84        12.66         6.12        22.68        13.61 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-8453 
        7.56         2.30        12.56        14.01         4.24        26.73 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        7.04         2.01        23.38        26.30        15.35         4.31 
TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
        1.25        39.09        23.51        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7156 TCGA-78-7159 
       20.58        35.93        21.90        24.99        32.09        64.90 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
       22.29       104.19         8.48        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7539 TCGA-78-7633 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
        8.02        10.75        32.68        31.13        34.39        13.87 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 
       19.43        19.89        16.70        24.49         4.08        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8669 TCGA-86-8672 
        0.79        15.75        15.85        23.05        30.84         0.62 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       13.32        13.32         3.81        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6849 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ 
       10.19        13.71         1.15        16.18         1.45        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
        1.12         1.22        18.67        15.65        21.40        18.18 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8176 TCGA-97-A4LX TCGA-97-A4M1 
       18.67        17.92         5.39        15.39        20.19        19.76 
TCGA-97-A4M3 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8192 
       17.75        18.67        24.56        34.85         5.59        24.30 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       18.08        19.00         3.81        12.59        11.87        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 
        2.76        86.14        49.35        86.04        58.85         5.49 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        5.29        31.23         2.43        11.05        14.66        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R 
       11.15        19.13        71.05        29.13         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J 
        9.70        59.11 

$`DEL PEAK 40(19P13.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4397 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       50.07        24.03        19.00        20.05         2.99        14.96 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4434 TCGA-05-5423 TCGA-05-5429 
       21.99        26.01        25.02        15.02         4.96         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 
        2.04         0.46        97.74       120.79        37.71        28.41 
TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2659 TCGA-44-2661 TCGA-44-2665 
       35.28        26.30         4.37        44.94        24.36        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 
        3.19        25.02        37.15        38.24        34.06         6.25 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 
       26.56        33.30        12.59        10.78        27.78        23.15 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 TCGA-44-7662 TCGA-44-7672 TCGA-44-A479 
       32.45        14.60        12.03         7.17        23.64        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 
       15.32         9.44        11.54        28.11        28.57        35.54 
TCGA-49-4506 TCGA-49-4512 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 
       32.84        29.75        11.64        22.26        62.24        28.90 
TCGA-49-AARN TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
       37.32       211.82       164.12         9.86        20.52        71.47 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5935 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 
       60.16        49.28        21.47        29.03        22.55        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 
        3.91        25.55         6.21         0.72        25.61         7.59 
TCGA-50-8460 TCGA-53-7626 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       27.25        30.54        48.62         0.07        32.65         0.79 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6979 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 
       40.73        15.25         7.79         2.20        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
        0.13         3.12        23.18         1.28         1.28         0.79 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-8087 TCGA-55-8090 TCGA-55-8091 
        1.78        18.64        17.65        15.19        19.66        19.73 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 
       23.64        15.65         1.08         1.51         2.17        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 
       15.42         1.45         0.36        17.72         0.30         4.80 
TCGA-55-8514 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z 
        6.64         1.61         2.17        16.93        20.71        21.40 
TCGA-55-A57B TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 
       17.95        72.30        13.61        29.92        20.65        39.09 
TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
       55.43        37.02         2.04        51.25        28.47        20.05 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 
       14.04         5.72         4.64        13.87         6.64         5.42 
TCGA-69-7974 TCGA-69-7979 TCGA-69-8254 TCGA-73-4658 TCGA-73-4662 TCGA-73-4675 
        6.05         2.93        13.45        52.60        29.98         1.32 
TCGA-73-4676 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 
        5.39        11.18       163.10        39.52        19.50        38.50 
TCGA-78-7158 TCGA-78-7161 TCGA-78-7163 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 
        5.88         7.07       223.96        53.33        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 
      214.62        39.75        77.59        10.55       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7714 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 
       12.36         5.88        20.55         4.57        16.08        15.65 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 
       21.47        14.60         1.15        13.91        27.58        14.96 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       17.62        13.64        26.47         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        7.36        16.60        14.27         1.18        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7562 
        4.18         6.12        23.61         1.08        19.00         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       12.39        15.68        27.29         2.76        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        43.79        25.48         5.95         0.59 
TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        0.72        18.12        16.41        14.30        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 
       21.44        20.52        20.84        20.68        36.76         1.45 
TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A444 
       21.63        23.80        35.47        16.44        14.30         0.20 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4SW TCGA-MP-A4T2 
       14.53         1.91        17.46        27.19        58.45        37.35 
TCGA-MP-A4T9 TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       41.59        10.09        29.46        73.91        62.60         0.13 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-S2-AA1A 
        1.64         0.26        16.87 

  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                          0.00                           0.07 
  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                        153.04                         223.96 
  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                         18.13                          19.00 
[1] "0.0 - 153.0 (18.1)" "0.1 - 224.0 (19.0)"
[1] "hr=" "1.2"
D61V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(19P13.2) MUTATED         2       61       67        0        32
  DEL PEAK 40(19P13.2) WILD-TYPE       3       74       73        1        19
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 40(19P13.2) MUTATED          42         42          7       16
  DEL PEAK 40(19P13.2) WILD-TYPE        31         30          4       10
D61V3, multiclass
            clus
vv           DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             61                             74
  STAGE IB                             67                             73
  STAGE II                              0                              1
  STAGE IIA                            32                             19
  STAGE IIB                            42                             31
  STAGE IIIA                           42                             30
  STAGE IIIB                            7                              4
  STAGE IV                             16                             10
[1] 9 2
[1] 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(19P13.2) MUTATED    80 153  23  12
  DEL PEAK 40(19P13.2) WILD-TYPE  90 125  23   7
D61V4, multiclass
    clus
vv   DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  T1                           80                             90
  T2                          153                            125
  T3                           23                             23
  T4                           12                              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
  DEL PEAK 40(19P13.2) MUTATED   162  59    43
  DEL PEAK 40(19P13.2) WILD-TYPE 170  37    33
D61V5, multiclass
       clus
vv      DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  N0                             162                            170
  N1                              59                             37
  N2+N3                           43                             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"
D61V6, binary
                                cls
clus                               0   1
  DEL PEAK 40(19P13.2) MUTATED   191  16
  DEL PEAK 40(19P13.2) WILD-TYPE 157   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.2) MUTATED    191   16
  DEL PEAK 40(19P13.2) WILD-TYPE  157    9
   clus
vv  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  0                          191                            157
  1                           16                              9
[1] 2 2
[1] FALSE
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(19P13.2) MUTATED   126 143
  DEL PEAK 40(19P13.2) WILD-TYPE 149  97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.2) MUTATED    126  143
  DEL PEAK 40(19P13.2) WILD-TYPE  149   97
        clus
vv       DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  FEMALE                          126                            149
  MALE                            143                             97
[1] 2 2
[1] FALSE
D61V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 40(19P13.2) MUTATED                           10
  DEL PEAK 40(19P13.2) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 40(19P13.2) MUTATED                                  61
  DEL PEAK 40(19P13.2) WILD-TYPE                                46
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(19P13.2) MUTATED                                                  164
  DEL PEAK 40(19P13.2) WILD-TYPE                                                155
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 40(19P13.2) MUTATED                                            0
  DEL PEAK 40(19P13.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 40(19P13.2) MUTATED                                               9
  DEL PEAK 40(19P13.2) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 40(19P13.2) MUTATED                                1
  DEL PEAK 40(19P13.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 40(19P13.2) MUTATED                                    2
  DEL PEAK 40(19P13.2) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 40(19P13.2) MUTATED                              1
  DEL PEAK 40(19P13.2) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 40(19P13.2) MUTATED                              12
  DEL PEAK 40(19P13.2) WILD-TYPE                            11
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 40(19P13.2) MUTATED                                 1
  DEL PEAK 40(19P13.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 40(19P13.2) MUTATED                                               3
  DEL PEAK 40(19P13.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 40(19P13.2) MUTATED                              5
  DEL PEAK 40(19P13.2) WILD-TYPE                            5
D61V9, multiclass
                                                    clus
vv                                                   DEL PEAK 40(19P13.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          164
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 9
  LUNG CLEAR CELL ADENOCARCINOMA                                                1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                12
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  5
                                                    clus
vv                                                   DEL PEAK 40(19P13.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            155
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  10
  LUNG CLEAR CELL ADENOCARCINOMA                                                  1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                                  11
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   2
  MUCINOUS (COLLOID) CARCINOMA                                                    5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, binary
                                cls
clus                               0   1
  DEL PEAK 40(19P13.2) MUTATED    12 257
  DEL PEAK 40(19P13.2) WILD-TYPE   9 237
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.2) MUTATED     12  257
  DEL PEAK 40(19P13.2) WILD-TYPE    9  237
     clus
vv    DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  NO                            12                              9
  YES                          257                            237
[1] 2 2
[1] FALSE
D61V11, continuous
D61V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(19P13.2) MUTATED   182   3   2  13
  DEL PEAK 40(19P13.2) WILD-TYPE 161   9   2  13
D61V13, multiclass
    clus
vv   DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  R0                          182                            161
  R1                            3                              9
  R2                            2                              2
  RX                           13                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(19P13.2) MUTATED                                  1     4
  DEL PEAK 40(19P13.2) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(19P13.2) MUTATED                          25   201
  DEL PEAK 40(19P13.2) WILD-TYPE                        26   188
D61V14, multiclass
                                  clus
vv                                 DEL PEAK 40(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     201
                                  clus
vv                                 DEL PEAK 40(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       188
[1] 4 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 40(19P13.2) MUTATED     6 193
  DEL PEAK 40(19P13.2) WILD-TYPE   1 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.2) MUTATED      6  193
  DEL PEAK 40(19P13.2) WILD-TYPE    1  189
                        clus
vv                       DEL PEAK 40(19P13.2) MUTATED
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          193
                        clus
vv                       DEL PEAK 40(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            189
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 41(19Q11) MUTATION ANALYSIS
D62V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 41(19Q11) MUTATED    83  47
  DEL PEAK 41(19Q11) WILD-TYPE 254 107
  DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE 
                         130                          361 
  DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE 
                          47                          107 
$`DEL PEAK 41(19Q11) MUTATED`
TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4420 TCGA-35-4123 
        9.96        24.03        47.05         8.02        29.98         5.98 
TCGA-38-6178 TCGA-44-2655 TCGA-44-2656 TCGA-44-3917 TCGA-44-6146 TCGA-44-6778 
       14.73        43.53        46.98        38.89         9.93        61.28 
TCGA-44-6779 TCGA-44-7670 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4488 
       16.44        29.00        12.66         8.55        13.45        28.57 
TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-6742 TCGA-49-6745 TCGA-49-6767 
       12.66        14.07         8.81        14.63        17.16        22.26 
TCGA-49-AAR0 TCGA-49-AARO TCGA-50-5051 TCGA-50-5066 TCGA-50-5933 TCGA-50-5939 
      153.04       123.58        15.72        31.04        78.67        15.12 
TCGA-50-5941 TCGA-50-5944 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-55-1592 
       18.64        25.12         3.91        11.05        12.16        23.05 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6975 TCGA-55-6978 TCGA-55-6981 TCGA-55-6982 
       45.21         2.86         3.88         5.49        45.34        32.71 
TCGA-55-7570 TCGA-55-7727 TCGA-55-7994 TCGA-55-8089 TCGA-55-8203 TCGA-55-8616 
        0.20         1.12        19.82         3.29        17.98         1.58 
TCGA-55-A48X TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46R 
       22.65        19.99        39.98        42.38        49.25        56.71 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 TCGA-64-5775 TCGA-67-3770 
       39.25        40.96        56.81        38.37         2.04         1.02 
TCGA-67-3772 TCGA-69-7978 TCGA-69-8255 TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 
       18.84         2.30         4.24         2.01        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7145 
       15.35         4.31         1.25        39.09        23.51        27.16 
TCGA-78-7146 TCGA-78-7149 TCGA-78-7153 TCGA-78-7162 TCGA-78-7167 TCGA-78-7535 
        5.69        35.93        24.99       104.19        88.14        31.20 
TCGA-78-7542 TCGA-86-7701 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8279 
       10.55        31.13        19.43        19.89        16.70        15.85 
TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6831 
       30.84         0.62        13.32         3.81        10.62        10.19 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC 
       13.71        12.23         7.36        16.18         1.18         1.45 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VN TCGA-97-8171 
        1.12        18.67        15.65         2.76        18.18        18.67 
TCGA-97-8176 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 
       15.39        21.60        20.19        19.76        18.67        24.56 
TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A7SV 
       24.30        18.08        19.00         3.81         0.20        12.59 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TA 
        2.76        86.14        49.35        58.85         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
        2.43        10.09        14.10        19.13        73.91        71.05 
TCGA-NJ-A4YQ TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       29.13        19.82         9.70        59.11 

$`DEL PEAK 41(19Q11) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
        0.00        19.00        20.05         2.99        14.96         9.01 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 
       12.00        30.02        21.99        26.01        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
       25.02        24.00        15.02        15.02         4.96        29.00 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-5375 
       22.03         9.04         2.04         0.46         7.40         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 
       11.64        44.61        26.30         4.37        13.15        44.94 
TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       24.36        42.08        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        34.06         6.25        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       12.59        23.77        10.78        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       23.18        63.72        32.45        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-7672 TCGA-44-8119 
        7.17        36.07        18.87        17.59        23.64         3.25 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
       15.98        15.32         9.44        11.08        11.54        13.64 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4510 
       76.21        28.11        35.54        46.72        32.84        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6761 TCGA-49-AAQV 
       29.75        55.89        12.13        29.26        11.64        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN 
       63.95        62.24        28.90         8.55        40.41        37.32 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      211.82       164.12         9.86        20.52        71.47        70.55 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 
       60.16        49.28         8.22         9.27        14.27        40.60 
TCGA-50-5935 TCGA-50-5936 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 
       21.47         8.45        29.03        22.55        42.35        25.55 
TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
        6.21        41.69         0.72        10.13        25.61         7.59 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       27.25        34.29        30.54        13.94         9.21        38.73 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       48.62         0.07        32.65         0.79        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6979 TCGA-55-6980 TCGA-55-6983 
       15.25         0.82        48.49         7.79         2.20        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 
       24.99        40.54       107.21        70.26         0.59         1.15 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        7.99         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        1.28         0.79         1.78        18.64         0.53         6.48 
TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8090 
       17.65         6.15         0.16        29.72        15.19        19.66 
TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8205 
       19.73         5.06         0.13        23.64        15.65         1.08 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        1.51         2.17        22.16        15.42         1.45         0.76 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
        0.95         0.36         0.26         0.49        17.72         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 
        0.10         4.80         6.64        17.62         0.49         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
        2.17        16.93        20.71        21.40         1.58        20.58 
TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A57B TCGA-62-8394 
       19.59         0.92        15.81        20.19        17.95         4.57 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U 
       14.60        88.64        47.80        19.53        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 
       72.30        13.61        29.92        20.65        39.09        55.43 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
       37.02        87.98        42.90        28.41        51.25        28.47 
TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
       20.05        14.04        12.66         5.72         4.64        13.87 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        6.64         6.12        22.68        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        6.05         2.93        12.56        14.01        13.45        26.73 
TCGA-69-A59K TCGA-73-4658 TCGA-73-4662 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS 
        7.04        52.60        29.98         1.32         5.39        11.18 
TCGA-78-7143 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
      163.10        19.27        20.58        21.90        39.52        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
      223.96         8.48        26.53         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
       39.35        32.68       214.62        39.75        77.59        10.55 
TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
      110.50        27.09        12.36         5.88        34.39        13.87 
TCGA-86-7714 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       20.55        24.49         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       15.75        16.08        15.65        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF 
        1.15        13.91        27.58        14.96        13.32        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 
       13.64        26.47        41.36         1.97         2.60        27.68 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
        1.15        16.60        14.27        19.82         9.76         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 
        6.12        23.61         1.08        19.00        17.29         1.22 
TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VP 
        2.86        12.39        15.68        27.29        21.40        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
        0.59         0.72        17.92         5.39        18.12        16.41 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 
       14.30        20.58        21.44        20.52        17.75        20.84 
TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R 
       20.68        34.85        36.76         1.45         5.59        21.63 
TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       23.80        35.47        16.44        14.30        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T2 
       17.46        11.87        27.19        38.63        58.45        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       86.04         5.49        41.59        29.46        11.05        14.66 
TCGA-MP-A4TJ TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       11.15        62.60         0.13         1.64         0.26         0.43 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE 
                         0.2                          0.0 
  DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE 
                      153.04                       223.96 
  DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE 
                       18.41                        18.64 
[1] "0.2 - 153.0 (18.4)" "0.0 - 224.0 (18.6)"
[1] "hr=" "1.2"
D62V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(19Q11) MUTATED         1       37       27        0        12
  DEL PEAK 41(19Q11) WILD-TYPE       4       98      113        1        39
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 41(19Q11) MUTATED          21         24          4        8
  DEL PEAK 41(19Q11) WILD-TYPE        52         48          7       18
D62V3, multiclass
            clus
vv           DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE
  STAGE I                             1                            4
  STAGE IA                           37                           98
  STAGE IB                           27                          113
  STAGE II                            0                            1
  STAGE IIA                          12                           39
  STAGE IIB                          21                           52
  STAGE IIIA                         24                           48
  STAGE IIIB                          4                            7
  STAGE IV                            8                           18
[1] 9 2
[1] 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(19Q11) MUTATED    45  69  12   8
  DEL PEAK 41(19Q11) WILD-TYPE 125 209  34  11
D62V4, multiclass
    clus
vv   DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE
  T1                         45                          125
  T2                         69                          209
  T3                         12                           34
  T4                          8                           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 41(19Q11) MUTATED    83  28    22
  DEL PEAK 41(19Q11) WILD-TYPE 249  68    54
D62V5, multiclass
       clus
vv      DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE
  N0                            83                          249
  N1                            28                           68
  N2+N3                         22                           54
[1] 3 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 41(19Q11) MUTATED    95   8
  DEL PEAK 41(19Q11) WILD-TYPE 253  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(19Q11) MUTATED     95    8
  DEL PEAK 41(19Q11) WILD-TYPE  253   17
   clus
vv  DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE
  0                         95                          253
  1                          8                           17
[1] 2 2
[1] FALSE
D62V7, binary
                              cls
clus                             0   1
  DEL PEAK 41(19Q11) MUTATED    69  65
  DEL PEAK 41(19Q11) WILD-TYPE 206 175
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(19Q11) MUTATED     69   65
  DEL PEAK 41(19Q11) WILD-TYPE  206  175
        clus
vv       DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE
  FEMALE                         69                          206
  MALE                           65                          175
[1] 2 2
[1] FALSE
D62V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 41(19Q11) MUTATED                            3
  DEL PEAK 41(19Q11) WILD-TYPE                         16
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 41(19Q11) MUTATED                                  27
  DEL PEAK 41(19Q11) WILD-TYPE                                80
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(19Q11) MUTATED                                                   89
  DEL PEAK 41(19Q11) WILD-TYPE                                                230
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 41(19Q11) MUTATED                                            0
  DEL PEAK 41(19Q11) WILD-TYPE                                          5
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 41(19Q11) MUTATED                                               3
  DEL PEAK 41(19Q11) WILD-TYPE                                            16
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 41(19Q11) MUTATED                                0
  DEL PEAK 41(19Q11) WILD-TYPE                              2
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 41(19Q11) MUTATED                                    2
  DEL PEAK 41(19Q11) WILD-TYPE                                  1
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 41(19Q11) MUTATED                              1
  DEL PEAK 41(19Q11) WILD-TYPE                            1
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 41(19Q11) MUTATED                               5
  DEL PEAK 41(19Q11) WILD-TYPE                            18
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 41(19Q11) MUTATED                                 0
  DEL PEAK 41(19Q11) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 41(19Q11) MUTATED                                               3
  DEL PEAK 41(19Q11) WILD-TYPE                                             2
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 41(19Q11) MUTATED                              1
  DEL PEAK 41(19Q11) WILD-TYPE                            9
D62V9, multiclass
                                                    clus
vv                                                   DEL PEAK 41(19Q11) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         89
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               3
  LUNG CLEAR CELL ADENOCARCINOMA                                              0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          2
  LUNG MUCINOUS ADENOCARCINOMA                                                1
  LUNG PAPILLARY ADENOCARCINOMA                                               5
  LUNG SIGNET RING ADENOCARCINOMA                                             0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               3
  MUCINOUS (COLLOID) CARCINOMA                                                1
                                                    clus
vv                                                   DEL PEAK 41(19Q11) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            80
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          230
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                16
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                18
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, binary
                              cls
clus                             0   1
  DEL PEAK 41(19Q11) MUTATED     4 130
  DEL PEAK 41(19Q11) WILD-TYPE  17 364
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(19Q11) MUTATED      4  130
  DEL PEAK 41(19Q11) WILD-TYPE   17  364
     clus
vv    DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE
  NO                           4                           17
  YES                        130                          364
[1] 2 2
[1] FALSE
D62V11, continuous
D62V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 41(19Q11) MUTATED    86   2   1   6
  DEL PEAK 41(19Q11) WILD-TYPE 257  10   3  20
D62V13, multiclass
    clus
vv   DEL PEAK 41(19Q11) MUTATED DEL PEAK 41(19Q11) WILD-TYPE
  R0                         86                          257
  R1                          2                           10
  R2                          1                            3
  RX                          6                           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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(19Q11) MUTATED                                  1     4
  DEL PEAK 41(19Q11) WILD-TYPE                                0     3
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(19Q11) MUTATED                          10   106
  DEL PEAK 41(19Q11) WILD-TYPE                        41   283
D62V14, multiclass
                                  clus
vv                                 DEL PEAK 41(19Q11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     4
  BLACK OR AFRICAN AMERICAN                                10
  WHITE                                                   106
                                  clus
vv                                 DEL PEAK 41(19Q11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  41
  WHITE                                                     283
[1] 4 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 41(19Q11) MUTATED     2 103
  DEL PEAK 41(19Q11) WILD-TYPE   5 279
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 41(19Q11) MUTATED      2  103
  DEL PEAK 41(19Q11) WILD-TYPE    5  279
                        clus
vv                       DEL PEAK 41(19Q11) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                        103
                        clus
vv                       DEL PEAK 41(19Q11) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          279
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 42(19Q13.33) MUTATION ANALYSIS
D63V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 42(19Q13.33) MUTATED   121  65
  DEL PEAK 42(19Q13.33) WILD-TYPE 216  89
  DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE 
                            186                             305 
  DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE 
                             65                              89 
$`DEL PEAK 42(19Q13.33) MUTATED`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4395 TCGA-05-4396 
        3.98        19.96        14.01        45.01         0.00         9.96 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 TCGA-05-4420 TCGA-05-4422 TCGA-05-4426 
       24.03        47.05         8.02        29.98        12.00        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-05-5425 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       15.02        15.02        29.00         2.04         7.40         5.98 
TCGA-38-4625 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2662 
       97.74        35.28        44.61        14.73        43.53        42.08 
TCGA-44-2665 TCGA-44-3917 TCGA-44-3918 TCGA-44-5644 TCGA-44-6144 TCGA-44-6778 
       42.77        38.89        34.06        28.37        23.77        61.28 
TCGA-44-6779 TCGA-44-7670 TCGA-44-7671 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       16.44        29.00        17.59        12.66         3.25         8.55 
TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       13.45        28.57        12.66        14.07        32.84         8.81 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6745 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 
       55.89        14.63        17.16        22.26        22.26       153.04 
TCGA-49-AAR2 TCGA-49-AARE TCGA-49-AARO TCGA-50-5051 TCGA-50-5072 TCGA-50-5932 
       63.95        40.41       123.58        15.72         8.22        40.60 
TCGA-50-5935 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
       21.47        15.12        18.64        25.12        22.55         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-55-1592 TCGA-55-1596 TCGA-55-5899 
       11.05        12.16        41.69        23.05        45.21         2.86 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6982 TCGA-55-6985 
       48.49         3.88         5.49         7.79        32.71        40.54 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7727 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        1.15         0.20         1.12        19.82         0.16        29.72 
TCGA-55-8091 TCGA-55-8094 TCGA-55-8203 TCGA-55-8507 TCGA-55-8511 TCGA-55-8514 
       19.73         0.13        17.98         0.26         0.30         6.64 
TCGA-55-8615 TCGA-55-8616 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DG 
        0.49         1.58        22.65        20.58        19.59        19.99 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R 
        4.57        39.98        42.38        49.25        47.80        56.71 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       72.30        39.25        40.96        56.81        39.09        55.43 
TCGA-64-1681 TCGA-67-3770 TCGA-67-3772 TCGA-69-7760 TCGA-69-7764 TCGA-69-7978 
       38.37         1.02        18.84         6.64        13.61         2.30 
TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4662 
        2.93         4.24         7.04         2.01        23.38        29.98 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-78-7146 
       26.30         4.31         1.25        39.09        23.51         5.69 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7156 TCGA-78-7161 TCGA-78-7162 
       20.58        35.93        24.99        32.09         7.07       104.19 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 TCGA-86-7701 
       88.14        26.53        31.20         8.02        10.55        31.13 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8074 TCGA-86-8279 TCGA-86-8669 TCGA-86-8672 
       19.89        16.70         0.79        15.85        30.84         0.62 
TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       13.32         3.81        10.62        41.36         1.97        10.19 
TCGA-91-6836 TCGA-91-6848 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC TCGA-95-7039 
       13.71         7.36        16.18         1.18         1.45         1.12 
TCGA-95-7567 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8171 
       18.67        15.65         2.76        21.40        18.18        18.67 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8547 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M6 
        5.39        15.39        21.60        20.19        19.76        18.67 
TCGA-99-7458 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV 
       24.56         5.59        24.30        18.08        19.00        12.59 
TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       27.19         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T6 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TI TCGA-MP-A4TK 
       58.85         5.29        31.23        10.09        14.10        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       73.91        71.05        29.13        19.82         9.70        59.11 

$`DEL PEAK 42(19Q13.33) WILD-TYPE`
TCGA-05-4249 TCGA-05-4390 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 
       50.07        37.02        19.00        20.05         2.99        14.96 
TCGA-05-4418 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
        9.01        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-5375 
       24.00         4.96        22.03         9.04         0.46         8.68 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-7271 
      120.79        37.71        49.05        28.41        11.64        26.30 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 
        4.37        46.98        13.15        44.94        24.36         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       25.02        37.15        38.24         6.25        26.56        33.30 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
       12.59        10.78         9.93        27.78        23.15        21.63 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       23.18        63.72        32.45        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A 
        7.17        36.07        18.87        23.64        15.98        15.32 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 
        9.44        11.08        11.54        13.64        76.21        28.11 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 
       35.54        46.72        29.46        29.75        12.13        29.26 
TCGA-49-6761 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARQ 
       11.64        62.24        28.90         8.55        37.32       211.82 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
      164.12         9.86        20.52        71.47        70.55        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       31.04        49.28         9.27        14.27        78.67         8.45 
TCGA-50-5942 TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       29.03        42.35        25.55         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       25.61         7.59        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
        9.21        38.73        48.62         0.07        32.65         0.79 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6980 TCGA-55-6981 
       42.51        40.73        15.25         0.82         2.20        45.34 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 
       60.03        24.99       107.21        70.26         0.59         7.99 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        0.13         3.12         1.32        23.18         1.28         1.28 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
        0.79         1.78        18.64         0.53         6.48        17.65 
TCGA-55-7914 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8096 
        6.15        15.19         3.29        19.66         5.06        23.64 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
        1.45         0.76         0.95         0.36         0.49        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        0.10         4.80        17.62         1.61         2.17        16.93 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF 
       20.71        21.40         1.58         0.92        15.81        20.19 
TCGA-55-A57B TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U 
       17.95        14.60        88.64        19.53        54.35        67.96 
TCGA-62-A46Y TCGA-62-A472 TCGA-64-1677 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 
       13.61        29.92        20.65        37.02        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 
       42.90        28.41        51.25        28.47        20.05        14.04 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 
       12.66         5.72         4.64        13.87         6.12        22.68 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        5.42         7.56         6.05        12.56        14.01        13.45 
TCGA-69-8453 TCGA-73-4658 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS 
       26.73        52.60        15.35         1.32         5.39        11.18 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 
      163.10        27.16        19.27        21.90        39.52        19.50 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 
       38.50         5.88        64.90        22.29       223.96         8.48 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
       53.33        10.75        39.35        32.68       214.62        39.75 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59        10.55       110.50        27.09        12.36         5.88 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 
       34.39        13.87        20.55        19.43        24.49         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
        4.57        24.33        15.75        16.08        15.65        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 
       21.47        14.60         1.15        13.91        27.58        14.96 
TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6840 
       13.32        17.62        13.64        26.47         2.60        12.23 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 
       27.68         1.15        16.60        14.27        19.82         9.76 
TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ 
        4.18         6.12        23.61         1.08        19.00        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VP 
        1.22         2.86        12.39        15.68        27.29        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       31.69        64.60        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8172 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
        0.59         0.72        17.92        18.12        16.41        14.30 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 
       20.58        21.44        20.52        17.75        20.84        20.68 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE 
       34.85        36.76         1.45        21.63        23.80        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP 
       16.44        14.30         3.81         0.20        14.53         1.91 
TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
       17.46        11.87        38.63        86.04         5.49        41.59 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-NJ-A4YG 
        2.43        29.46        11.05        14.66        11.15        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-S2-AA1A 
        0.13         1.64         0.26         0.43        16.87 

  DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE 
                           0.00                            0.07 
  DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE 
                         153.04                          223.96 
  DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE 
                         19.065                          17.650 
[1] "0.0 - 153.0 (19.1)" "0.1 - 224.0 (17.6)"
[1] "hr=" "1.1"
D63V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(19Q13.33) MUTATED         1       48       48        1        17
  DEL PEAK 42(19Q13.33) WILD-TYPE       4       87       92        0        34
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 42(19Q13.33) MUTATED          30         32          5       12
  DEL PEAK 42(19Q13.33) WILD-TYPE        43         40          6       14
D63V3, multiclass
            clus
vv           DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                              48                              87
  STAGE IB                              48                              92
  STAGE II                               1                               0
  STAGE IIA                             17                              34
  STAGE IIB                             30                              43
  STAGE IIIA                            32                              40
  STAGE IIIB                             5                               6
  STAGE IV                              12                              14
[1] 9 2
[1] 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(19Q13.33) MUTATED    58 108  18   9
  DEL PEAK 42(19Q13.33) WILD-TYPE 112 170  28  10
D63V4, multiclass
    clus
vv   DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE
  T1                            58                             112
  T2                           108                             170
  T3                            18                              28
  T4                             9                              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 42(19Q13.33) MUTATED   120  41    31
  DEL PEAK 42(19Q13.33) WILD-TYPE 212  55    45
D63V5, multiclass
       clus
vv      DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE
  N0                              120                             212
  N1                               41                              55
  N2+N3                            31                              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                                 cls
clus                                0   1
  DEL PEAK 42(19Q13.33) MUTATED   136  12
  DEL PEAK 42(19Q13.33) WILD-TYPE 212  13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(19Q13.33) MUTATED    136   12
  DEL PEAK 42(19Q13.33) WILD-TYPE  212   13
   clus
vv  DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE
  0                           136                             212
  1                            12                              13
[1] 2 2
[1] FALSE
D63V7, binary
                                 cls
clus                                0   1
  DEL PEAK 42(19Q13.33) MUTATED   100  94
  DEL PEAK 42(19Q13.33) WILD-TYPE 175 146
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(19Q13.33) MUTATED    100   94
  DEL PEAK 42(19Q13.33) WILD-TYPE  175  146
        clus
vv       DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE
  FEMALE                           100                             175
  MALE                              94                             146
[1] 2 2
[1] FALSE
D63V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 42(19Q13.33) MUTATED                            6
  DEL PEAK 42(19Q13.33) WILD-TYPE                         13
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 42(19Q13.33) MUTATED                                  48
  DEL PEAK 42(19Q13.33) WILD-TYPE                                59
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(19Q13.33) MUTATED                                                  120
  DEL PEAK 42(19Q13.33) WILD-TYPE                                                199
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 42(19Q13.33) MUTATED                                            0
  DEL PEAK 42(19Q13.33) WILD-TYPE                                          5
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 42(19Q13.33) MUTATED                                               5
  DEL PEAK 42(19Q13.33) WILD-TYPE                                            14
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 42(19Q13.33) MUTATED                                0
  DEL PEAK 42(19Q13.33) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 42(19Q13.33) MUTATED                                    1
  DEL PEAK 42(19Q13.33) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 42(19Q13.33) MUTATED                              0
  DEL PEAK 42(19Q13.33) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 42(19Q13.33) MUTATED                              10
  DEL PEAK 42(19Q13.33) WILD-TYPE                            13
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 42(19Q13.33) MUTATED                                 0
  DEL PEAK 42(19Q13.33) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 42(19Q13.33) MUTATED                                               3
  DEL PEAK 42(19Q13.33) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 42(19Q13.33) MUTATED                              1
  DEL PEAK 42(19Q13.33) WILD-TYPE                            9
D63V9, multiclass
                                                    clus
vv                                                   DEL PEAK 42(19Q13.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           120
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  5
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                                 10
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   1
                                                    clus
vv                                                   DEL PEAK 42(19Q13.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               59
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             199
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   14
  LUNG CLEAR CELL ADENOCARCINOMA                                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               2
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   13
  LUNG SIGNET RING ADENOCARCINOMA                                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    2
  MUCINOUS (COLLOID) CARCINOMA                                                     9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, binary
                                 cls
clus                                0   1
  DEL PEAK 42(19Q13.33) MUTATED     7 187
  DEL PEAK 42(19Q13.33) WILD-TYPE  14 307
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(19Q13.33) MUTATED      7  187
  DEL PEAK 42(19Q13.33) WILD-TYPE   14  307
     clus
vv    DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE
  NO                              7                              14
  YES                           187                             307
[1] 2 2
[1] FALSE
D63V11, continuous
D63V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 42(19Q13.33) MUTATED   127   4   3   9
  DEL PEAK 42(19Q13.33) WILD-TYPE 216   8   1  17
D63V13, multiclass
    clus
vv   DEL PEAK 42(19Q13.33) MUTATED DEL PEAK 42(19Q13.33) WILD-TYPE
  R0                           127                             216
  R1                             4                               8
  R2                             3                               1
  RX                             9                              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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 42(19Q13.33) MUTATED                                  0     4
  DEL PEAK 42(19Q13.33) WILD-TYPE                                1     3
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(19Q13.33) MUTATED                          17   145
  DEL PEAK 42(19Q13.33) WILD-TYPE                        34   244
D63V14, multiclass
                                  clus
vv                                 DEL PEAK 42(19Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      145
                                  clus
vv                                 DEL PEAK 42(19Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          3
  BLACK OR AFRICAN AMERICAN                                     34
  WHITE                                                        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"
D63V15, binary
                                 cls
clus                                0   1
  DEL PEAK 42(19Q13.33) MUTATED     2 139
  DEL PEAK 42(19Q13.33) WILD-TYPE   5 243
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 42(19Q13.33) MUTATED      2  139
  DEL PEAK 42(19Q13.33) WILD-TYPE    5  243
                        clus
vv                       DEL PEAK 42(19Q13.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           139
                        clus
vv                       DEL PEAK 42(19Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             243
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 43(20P13) MUTATION ANALYSIS
D64V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 43(20P13) MUTATED    77  46
  DEL PEAK 43(20P13) WILD-TYPE 260 108
  DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE 
                         123                          368 
  DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE 
                          46                          108 
$`DEL PEAK 43(20P13) MUTATED`
TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 TCGA-05-5423 TCGA-38-4629 TCGA-38-6178 
        0.00        47.05         2.99         4.96        28.41        14.73 
TCGA-44-2656 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3917 TCGA-44-3919 
       46.98        42.08        42.77        25.02        38.89         6.25 
TCGA-44-6779 TCGA-44-8117 TCGA-44-A47A TCGA-44-A47G TCGA-49-4501 TCGA-49-4505 
       16.44        12.66        15.32        11.54        46.72        14.07 
TCGA-49-4512 TCGA-49-6743 TCGA-49-6745 TCGA-49-AAQV TCGA-49-AARO TCGA-49-AARQ 
       29.75        12.13        17.16        22.26       123.58       211.82 
TCGA-50-5051 TCGA-50-5072 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 
       15.72         8.22        78.67         8.45        15.12        25.12 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       11.05        12.16        41.69        27.25        34.29        30.54 
TCGA-55-1594 TCGA-55-1595 TCGA-55-6712 TCGA-55-6975 TCGA-55-6978 TCGA-55-6980 
       38.73        48.62         0.79         3.88         5.49         2.20 
TCGA-55-6984 TCGA-55-7283 TCGA-55-7576 TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 
       24.99         1.15         1.32         1.28         1.12        18.64 
TCGA-55-7907 TCGA-55-7994 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8207 
        0.53        19.82        19.66         5.06         0.13         2.17 
TCGA-55-8506 TCGA-55-8616 TCGA-55-A491 TCGA-55-A493 TCGA-62-8397 TCGA-62-A46O 
        0.36         1.58        20.58         0.92        42.38        47.80 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       67.96        72.30        13.61        40.96        29.92        56.81 
TCGA-64-1678 TCGA-64-1681 TCGA-64-5781 TCGA-67-3773 TCGA-67-6216 TCGA-69-7761 
       39.09        38.37        51.25        14.04         4.64         6.12 
TCGA-69-7974 TCGA-69-8453 TCGA-69-A59K TCGA-73-4662 TCGA-73-4666 TCGA-73-4670 
        6.05        26.73         7.04        29.98        26.30         4.31 
TCGA-73-7499 TCGA-78-7143 TCGA-78-7145 TCGA-78-7148 TCGA-78-7158 TCGA-78-7159 
       23.51       163.10        27.16        20.58         5.88        64.90 
TCGA-78-7535 TCGA-78-8660 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 TCGA-86-7953 
       31.20        10.55       110.50        12.36         5.88        19.43 
TCGA-86-7955 TCGA-86-8278 TCGA-86-8280 TCGA-86-8673 TCGA-91-6828 TCGA-91-6835 
       16.70        15.65        23.05        14.96        10.62         2.60 
TCGA-93-7347 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-A4VN 
        9.76         1.12         1.22         2.86        18.67        18.18 
TCGA-97-7554 TCGA-97-A4M0 TCGA-99-7458 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-A4AD 
       25.48        21.44        24.56         5.59        24.30        18.08 
TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A7SV TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SV 
       19.00         0.20        12.59        27.19        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TJ 
       58.45         5.29        31.23         2.43        14.10        11.15 
TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-O1-A52J 
       19.13        71.05        59.11 

$`DEL PEAK 43(20P13) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4396 TCGA-05-4397 TCGA-05-4402 TCGA-05-4403 TCGA-05-4405 TCGA-05-4417 
        9.96        24.03         8.02        19.00        20.05        14.96 
TCGA-05-4418 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        9.01        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 
       26.01        25.02        25.02        24.00        15.02        15.02 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
       29.00        22.03         9.04         2.04         0.46         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        5.98         8.68        97.74       120.79        37.71        49.05 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       35.28        11.64        44.61        26.30         4.37        43.53 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
       13.15        44.94        24.36         3.19        37.15        38.24 
TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       34.06        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       10.78         9.93        27.78        23.15        21.63        23.18 
TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 
       63.72        32.45        61.28        14.60        19.46        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS 
        3.25         8.55        15.98         9.44        11.08        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       13.45        76.21        28.11        28.57        12.66        35.54 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 
       32.84         8.81        29.46        55.89        14.63        29.26 
TCGA-49-6761 TCGA-49-6767 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       11.64        22.26       153.04        63.95        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
        8.55        40.41        37.32       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
       71.47        70.55        60.16        31.04        49.28         9.27 
TCGA-50-5931 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 
       14.27        40.60        21.47        18.64        29.03        22.55 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       42.35         3.91        25.55         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1596 
       25.61         7.59        13.94         9.21        23.05        45.21 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
        2.86         0.07        32.65        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6979 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        0.82        48.49         7.79        45.34        32.71        60.03 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7570 
       40.54       107.21        70.26         0.59         7.99         0.20 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7724 TCGA-55-7726 TCGA-55-7728 TCGA-55-7815 
        0.13         3.12        23.18         1.28         0.79         1.78 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        6.48        17.65         6.15         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8203 TCGA-55-8205 
        3.29        19.73        23.64        15.65        17.98         1.08 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
        1.51        22.16        15.42         1.45         0.76         0.95 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 
        0.26         0.49        17.72         0.30         0.10         4.80 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 
        6.64        17.62         0.49         1.61         2.17        16.93 
TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A492 TCGA-55-A494 
       22.65        20.71        21.40         1.58        19.59        15.81 
TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 
       20.19        19.99        17.95         4.57        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A470 
       88.64        49.25        19.53        56.71        54.35        39.25 
TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       20.65        55.43        37.02        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 
       28.41        28.47         1.02        20.05        18.84        12.66 
TCGA-67-6215 TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        5.72        13.87         6.64        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         2.30         2.93        12.56        14.01        13.45 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 
        4.24         2.01        52.60        23.38        15.35         1.32 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-78-7146 TCGA-78-7147 
        5.39         1.25        39.09        11.18         5.69        19.27 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       35.93        21.90        39.52        24.99        19.50        38.50 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 
       32.09        22.29         7.07       104.19       223.96         8.48 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
       88.14        26.53         8.02        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 
       10.55        32.68       214.62        39.75        77.59        27.09 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
       31.13        34.39        13.87        20.55        19.89        24.49 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
        4.08         4.57        24.33         0.79        15.75        16.08 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.85        21.47        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
       27.58         0.62        13.32        13.32         3.81        17.62 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 
       13.64        26.47        41.36         1.97        10.19        13.71 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 
       12.23        27.68         7.36         1.15        16.18        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 TCGA-93-8067 
       14.27         1.18         1.45        19.82         4.18         6.12 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7944 TCGA-95-7947 
       23.61         1.08        19.00        17.29        12.39        15.68 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-7546 
       15.65        27.29         2.76        21.40        19.89        31.69 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        43.79         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       18.67        17.92         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 
       14.30        21.60        20.58        20.19        19.76        20.52 
TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 
       17.75        20.84        18.67        20.68        34.85        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
        1.45        21.63        23.80        35.47        16.44        14.30 
TCGA-L9-A443 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N5 
        3.81        14.53         1.91        17.46        11.87         2.76 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       49.35        37.35        86.04        58.85         5.49        41.59 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG 
       10.09        29.46        11.05        14.66        73.91        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-NJ-A7XG TCGA-S2-AA1A 
        9.70        16.87 

  DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE 
                        0.00                         0.07 
  DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE 
                      211.82                       223.96 
  DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE 
                      18.180                       18.655 
[1] "0.0 - 211.8 (18.2)" "0.1 - 224.0 (18.7)"
[1] "hr=" "1.2"
D64V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(20P13) MUTATED         2       29       28        1        15
  DEL PEAK 43(20P13) WILD-TYPE       3      106      112        0        36
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 43(20P13) MUTATED          24         21          5        6
  DEL PEAK 43(20P13) WILD-TYPE        49         51          6       20
D64V3, multiclass
            clus
vv           DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE
  STAGE I                             2                            3
  STAGE IA                           29                          106
  STAGE IB                           28                          112
  STAGE II                            1                            0
  STAGE IIA                          15                           36
  STAGE IIB                          24                           49
  STAGE IIIA                         21                           51
  STAGE IIIB                          5                            6
  STAGE IV                            6                           20
[1] 9 2
[1] 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(20P13) MUTATED    38  73  12   7
  DEL PEAK 43(20P13) WILD-TYPE 132 205  34  12
D64V4, multiclass
    clus
vv   DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE
  T1                         38                          132
  T2                         73                          205
  T3                         12                           34
  T4                          7                           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 43(20P13) MUTATED    75  29    25
  DEL PEAK 43(20P13) WILD-TYPE 257  67    51
D64V5, multiclass
       clus
vv      DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE
  N0                            75                          257
  N1                            29                           67
  N2+N3                         25                           51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                              cls
clus                             0   1
  DEL PEAK 43(20P13) MUTATED    94   6
  DEL PEAK 43(20P13) WILD-TYPE 254  19
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(20P13) MUTATED     94    6
  DEL PEAK 43(20P13) WILD-TYPE  254   19
   clus
vv  DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE
  0                         94                          254
  1                          6                           19
[1] 2 2
[1] FALSE
D64V7, binary
                              cls
clus                             0   1
  DEL PEAK 43(20P13) MUTATED    80  51
  DEL PEAK 43(20P13) WILD-TYPE 195 189
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(20P13) MUTATED     80   51
  DEL PEAK 43(20P13) WILD-TYPE  195  189
        clus
vv       DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE
  FEMALE                         80                          195
  MALE                           51                          189
[1] 2 2
[1] FALSE
D64V8, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 43(20P13) MUTATED                            3
  DEL PEAK 43(20P13) WILD-TYPE                         16
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 43(20P13) MUTATED                                  26
  DEL PEAK 43(20P13) WILD-TYPE                                81
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(20P13) MUTATED                                                   85
  DEL PEAK 43(20P13) WILD-TYPE                                                234
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 43(20P13) MUTATED                                            0
  DEL PEAK 43(20P13) WILD-TYPE                                          5
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 43(20P13) MUTATED                                               6
  DEL PEAK 43(20P13) WILD-TYPE                                            13
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 43(20P13) MUTATED                                2
  DEL PEAK 43(20P13) WILD-TYPE                              0
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 43(20P13) MUTATED                                    1
  DEL PEAK 43(20P13) WILD-TYPE                                  2
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 43(20P13) MUTATED                              0
  DEL PEAK 43(20P13) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 43(20P13) MUTATED                               4
  DEL PEAK 43(20P13) WILD-TYPE                            19
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 43(20P13) MUTATED                                 1
  DEL PEAK 43(20P13) WILD-TYPE                               0
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 43(20P13) MUTATED                                               1
  DEL PEAK 43(20P13) WILD-TYPE                                             4
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 43(20P13) MUTATED                              2
  DEL PEAK 43(20P13) WILD-TYPE                            8
D64V9, multiclass
                                                    clus
vv                                                   DEL PEAK 43(20P13) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          26
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         85
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               6
  LUNG CLEAR CELL ADENOCARCINOMA                                              2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          1
  LUNG MUCINOUS ADENOCARCINOMA                                                0
  LUNG PAPILLARY ADENOCARCINOMA                                               4
  LUNG SIGNET RING ADENOCARCINOMA                                             1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               1
  MUCINOUS (COLLOID) CARCINOMA                                                2
                                                    clus
vv                                                   DEL PEAK 43(20P13) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            81
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          234
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                13
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  2
  LUNG PAPILLARY ADENOCARCINOMA                                                19
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 4
  MUCINOUS (COLLOID) CARCINOMA                                                  8
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, binary
                              cls
clus                             0   1
  DEL PEAK 43(20P13) MUTATED     5 126
  DEL PEAK 43(20P13) WILD-TYPE  16 368
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(20P13) MUTATED      5  126
  DEL PEAK 43(20P13) WILD-TYPE   16  368
     clus
vv    DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE
  NO                           5                           16
  YES                        126                          368
[1] 2 2
[1] FALSE
D64V11, continuous
D64V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 43(20P13) MUTATED    94   4   1   4
  DEL PEAK 43(20P13) WILD-TYPE 249   8   3  22
D64V13, multiclass
    clus
vv   DEL PEAK 43(20P13) MUTATED DEL PEAK 43(20P13) WILD-TYPE
  R0                         94                          249
  R1                          4                            8
  R2                          1                            3
  RX                          4                           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                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 43(20P13) MUTATED                                  0     1
  DEL PEAK 43(20P13) WILD-TYPE                                1     6
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(20P13) MUTATED                          10   102
  DEL PEAK 43(20P13) WILD-TYPE                        41   287
D64V14, multiclass
                                  clus
vv                                 DEL PEAK 43(20P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                10
  WHITE                                                   102
                                  clus
vv                                 DEL PEAK 43(20P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  41
  WHITE                                                     287
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V15, binary
                              cls
clus                             0   1
  DEL PEAK 43(20P13) MUTATED     1  99
  DEL PEAK 43(20P13) WILD-TYPE   6 283
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 43(20P13) MUTATED      1   99
  DEL PEAK 43(20P13) WILD-TYPE    6  283
                        clus
vv                       DEL PEAK 43(20P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         99
                        clus
vv                       DEL PEAK 43(20P13) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          283
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 44(20Q13.12) MUTATION ANALYSIS
D65V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 44(20Q13.12) MUTATED    49  25
  DEL PEAK 44(20Q13.12) WILD-TYPE 288 129
  DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE 
                             74                             417 
  DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE 
                             25                             129 
$`DEL PEAK 44(20Q13.12) MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4422 
        8.02        20.05         2.99        14.96         9.01        12.00 
TCGA-05-5715 TCGA-38-4628 TCGA-44-3919 TCGA-44-6779 TCGA-44-A47B TCGA-44-A47G 
        2.04        49.05         6.25        16.44         9.44        11.54 
TCGA-49-4501 TCGA-49-4506 TCGA-49-6743 TCGA-49-6745 TCGA-49-AARE TCGA-50-5051 
       46.72        32.84        12.13        17.16        40.41        15.72 
TCGA-50-5072 TCGA-50-5936 TCGA-50-6593 TCGA-50-8460 TCGA-53-7624 TCGA-53-A4EZ 
        8.22         8.45        11.05        27.25        34.29         9.21 
TCGA-55-1595 TCGA-55-8087 TCGA-55-8090 TCGA-55-8508 TCGA-55-8512 TCGA-55-8615 
       48.62        15.19        19.66         0.49         0.10         0.49 
TCGA-55-A494 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U TCGA-62-A471 
       15.81        42.38        47.80        54.35        67.96        40.96 
TCGA-62-A472 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 
       29.92         1.02        14.04        12.66         5.72         4.64 
TCGA-69-7763 TCGA-69-8253 TCGA-69-8453 TCGA-69-A59K TCGA-73-4675 TCGA-78-7143 
       22.68        14.01        26.73         7.04         1.32       163.10 
TCGA-78-7146 TCGA-78-7152 TCGA-78-7158 TCGA-78-7160 TCGA-78-7167 TCGA-78-7537 
        5.69        39.52         5.88        22.29        88.14        53.33 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8358 TCGA-91-6828 TCGA-91-6831 TCGA-93-7347 
       19.43        24.49        21.47        10.62        10.19         9.76 
TCGA-95-A4VK TCGA-97-8172 TCGA-97-8174 TCGA-97-8547 TCGA-97-A4M0 TCGA-99-7458 
       21.40        17.92         5.39        21.60        21.44        24.56 
TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-MP-A4SW TCGA-MP-A4TC 
       34.85         5.59        35.47        19.00        58.45         2.43 
TCGA-MP-A4TH TCGA-MP-A4TI 
       14.66        14.10 

$`DEL PEAK 44(20Q13.12) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 TCGA-05-4390 
       50.07         3.98        19.96        14.01        45.01        37.02 
TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4420 
        0.00         9.96        24.03        47.05        19.00        29.98 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 
       30.02        21.99        26.01        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       24.00        15.02        15.02         4.96        29.00        22.03 
TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        9.04         0.46         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 
      120.79        37.71        28.41        35.28        11.64        44.61 
TCGA-38-6178 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 
       14.73        26.30         4.37        43.53        46.98        13.15 
TCGA-44-2659 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.94        24.36        42.08        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 
       37.15        38.24        38.89        34.06        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
       28.37        12.59        23.77        10.78         9.93        27.78 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
       23.15        21.63        23.18        63.72        32.45        61.28 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       14.60        19.46        12.03         7.17        36.07        18.87 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
       29.00        17.59        23.64        12.66         3.25         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47F TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.98        15.32        11.08        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 
       28.11        28.57        12.66        35.54        14.07         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6744 TCGA-49-6761 
       29.46        29.75        55.89        14.63        29.26        11.64 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       22.26        22.26       153.04        63.95        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARN TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
        8.55        37.32       123.58       211.82       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47        70.55        60.16        31.04        49.28 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5939 
        9.27        14.27        40.60        78.67        21.47        15.12 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       18.64        29.03        25.12        22.55        42.35         3.91 
TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
       25.55        12.16         6.21        41.69         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-53-7626 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
       25.61         7.59        30.54        13.94        23.05        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       45.21         2.86         0.07        32.65         0.79        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6978 
       40.73        15.25         0.82        48.49         3.88         5.49 
TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        7.79         2.20        45.34        32.71        60.03        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
       40.54       107.21        70.26         0.59         1.15         7.99 
TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
        0.20         0.13         3.12         1.32        23.18         1.28 
TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
        1.28         1.12         0.79         1.78        18.64         0.53 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        6.48        17.65         6.15        19.82         0.16        29.72 
TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
        3.29        19.73         5.06         0.13        23.64        15.65 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       17.98         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 
        1.45         0.76         0.95         0.36         0.26        17.72 
TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 
        0.30         4.80         6.64        17.62         1.58         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
        2.17        16.93        22.65        20.71        21.40         1.58 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-55-A57B 
       20.58        19.59         0.92        20.19        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
        4.57        39.98        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-64-1676 TCGA-64-1677 
       56.71        72.30        13.61        39.25        56.81        20.65 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       39.09        55.43        37.02        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        51.25        28.47        20.05        18.84 
TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
       13.87         6.64         6.12        13.61         5.42         7.56 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 
        6.05         2.30         2.93        12.56        13.45         4.24 
TCGA-71-6725 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
        2.01        52.60        23.38        29.98        26.30        15.35 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS 
        4.31         5.39         1.25        39.09        23.51        11.18 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 
       27.16        19.27        20.58        35.93        21.90        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 
       19.50        38.50        32.09        64.90         7.07       104.19 
TCGA-78-7163 TCGA-78-7166 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
      223.96         8.48        26.53        31.20         8.02        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 
       39.35        10.55        32.68       214.62        39.75        77.59 
TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        27.09        12.36         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       34.39        13.87        20.55        19.89        16.70         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.57        24.33         0.79        15.75        16.08        15.65 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       15.85        23.05        14.60         1.15        13.91        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       27.58         0.62        14.96        13.32        13.32         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
       17.62        13.64        26.47        41.36         1.97         2.60 
TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 
       13.71        12.23        27.68         7.36         1.15        16.18 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7348 
       16.60        14.27         1.18         1.45        19.82         4.18 
TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7039 
        6.12        23.61         1.08        19.00        17.29         1.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
        1.22         2.86        18.67        12.39        15.68        15.65 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       27.29         2.76        18.18        19.89        31.69        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        43.79        25.48         5.95         0.59         0.72 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 
       18.67        18.12        15.39        16.41        14.30        20.58 
TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M6 
       20.19        19.76        20.52        17.75        20.84        18.67 
TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 
       20.68        36.76         1.45        21.63        24.30        23.80 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W 
       18.08        16.44        14.30         3.81         0.20        14.53 
TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
        1.91        17.46        12.59        11.87        27.19        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        86.14        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-MP-A4TE 
        5.49         5.29        41.59        31.23        10.09        29.46 
TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       11.05        11.15        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        29.13         0.26         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        9.70        59.11        16.87 

  DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE 
                            0.1                             0.0 
  DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE 
                         163.10                          223.96 
  DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE 
                         15.765                          18.670 
[1] "0.1 - 163.1 (15.8)" "0.0 - 224.0 (18.7)"
[1] "hr=" "1.2"
D65V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(20Q13.12) MUTATED         1       14       23        0         6
  DEL PEAK 44(20Q13.12) WILD-TYPE       4      121      117        1        45
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 44(20Q13.12) MUTATED          11         16          2        7
  DEL PEAK 44(20Q13.12) WILD-TYPE        62         56          9       19
D65V3, multiclass
            clus
vv           DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                              14                             121
  STAGE IB                              23                             117
  STAGE II                               0                               1
  STAGE IIA                              6                              45
  STAGE IIB                             11                              62
  STAGE IIIA                            16                              56
  STAGE IIIB                             2                               9
  STAGE IV                               7                              19
[1] 9 2
[1] 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(20Q13.12) MUTATED    20  47   8   4
  DEL PEAK 44(20Q13.12) WILD-TYPE 150 231  38  15
D65V4, multiclass
    clus
vv   DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE
  T1                            20                             150
  T2                            47                             231
  T3                             8                              38
  T4                             4                              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 44(20Q13.12) MUTATED    46  14    18
  DEL PEAK 44(20Q13.12) WILD-TYPE 286  82    58
D65V5, multiclass
       clus
vv      DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE
  N0                               46                             286
  N1                               14                              82
  N2+N3                            18                              58
[1] 3 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 44(20Q13.12) MUTATED    59   7
  DEL PEAK 44(20Q13.12) WILD-TYPE 289  18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(20Q13.12) MUTATED     59    7
  DEL PEAK 44(20Q13.12) WILD-TYPE  289   18
   clus
vv  DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE
  0                            59                             289
  1                             7                              18
[1] 2 2
[1] FALSE
D65V7, binary
                                 cls
clus                                0   1
  DEL PEAK 44(20Q13.12) MUTATED    47  33
  DEL PEAK 44(20Q13.12) WILD-TYPE 228 207
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(20Q13.12) MUTATED     47   33
  DEL PEAK 44(20Q13.12) WILD-TYPE  228  207
        clus
vv       DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE
  FEMALE                            47                             228
  MALE                              33                             207
[1] 2 2
[1] FALSE
D65V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 44(20Q13.12) MUTATED                            3
  DEL PEAK 44(20Q13.12) WILD-TYPE                         16
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 44(20Q13.12) MUTATED                                  22
  DEL PEAK 44(20Q13.12) WILD-TYPE                                85
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(20Q13.12) MUTATED                                                   42
  DEL PEAK 44(20Q13.12) WILD-TYPE                                                277
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 44(20Q13.12) MUTATED                                            0
  DEL PEAK 44(20Q13.12) WILD-TYPE                                          5
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 44(20Q13.12) MUTATED                                               3
  DEL PEAK 44(20Q13.12) WILD-TYPE                                            16
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 44(20Q13.12) MUTATED                                2
  DEL PEAK 44(20Q13.12) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 44(20Q13.12) MUTATED                                    1
  DEL PEAK 44(20Q13.12) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 44(20Q13.12) MUTATED                              0
  DEL PEAK 44(20Q13.12) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 44(20Q13.12) MUTATED                               4
  DEL PEAK 44(20Q13.12) WILD-TYPE                            19
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 44(20Q13.12) MUTATED                                 0
  DEL PEAK 44(20Q13.12) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 44(20Q13.12) MUTATED                                               0
  DEL PEAK 44(20Q13.12) WILD-TYPE                                             5
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 44(20Q13.12) MUTATED                              3
  DEL PEAK 44(20Q13.12) WILD-TYPE                            7
D65V9, multiclass
                                                    clus
vv                                                   DEL PEAK 44(20Q13.12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            42
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  3
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                                  4
  LUNG SIGNET RING ADENOCARCINOMA                                                0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  0
  MUCINOUS (COLLOID) CARCINOMA                                                   3
                                                    clus
vv                                                   DEL PEAK 44(20Q13.12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      16
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             277
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   16
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               2
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   19
  LUNG SIGNET RING ADENOCARCINOMA                                                  1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    5
  MUCINOUS (COLLOID) CARCINOMA                                                     7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, binary
                                 cls
clus                                0   1
  DEL PEAK 44(20Q13.12) MUTATED     2  78
  DEL PEAK 44(20Q13.12) WILD-TYPE  19 416
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(20Q13.12) MUTATED      2   78
  DEL PEAK 44(20Q13.12) WILD-TYPE   19  416
     clus
vv    DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE
  NO                              2                              19
  YES                            78                             416
[1] 2 2
[1] FALSE
D65V11, continuous
D65V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 44(20Q13.12) MUTATED    56   2   1   6
  DEL PEAK 44(20Q13.12) WILD-TYPE 287  10   3  20
D65V13, multiclass
    clus
vv   DEL PEAK 44(20Q13.12) MUTATED DEL PEAK 44(20Q13.12) WILD-TYPE
  R0                            56                             287
  R1                             2                              10
  R2                             1                               3
  RX                             6                              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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 44(20Q13.12) MUTATED                                  0     1
  DEL PEAK 44(20Q13.12) WILD-TYPE                                1     6
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(20Q13.12) MUTATED                           5    59
  DEL PEAK 44(20Q13.12) WILD-TYPE                        46   330
D65V14, multiclass
                                  clus
vv                                 DEL PEAK 44(20Q13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    5
  WHITE                                                       59
                                  clus
vv                                 DEL PEAK 44(20Q13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     46
  WHITE                                                        330
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V15, binary
                                 cls
clus                                0   1
  DEL PEAK 44(20Q13.12) MUTATED     2  53
  DEL PEAK 44(20Q13.12) WILD-TYPE   5 329
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 44(20Q13.12) MUTATED      2   53
  DEL PEAK 44(20Q13.12) WILD-TYPE    5  329
                        clus
vv                       DEL PEAK 44(20Q13.12) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            53
                        clus
vv                       DEL PEAK 44(20Q13.12) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             329
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 45(21Q11.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 45(21Q11.2) MUTATED   123  57
  DEL PEAK 45(21Q11.2) WILD-TYPE 214  97
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                           180                            311 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                            57                             97 
$`DEL PEAK 45(21Q11.2) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
       50.07        45.01        37.02         0.00         9.96        24.03 
TCGA-05-4398 TCGA-05-4402 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       47.05         8.02        14.96        29.98        12.00        30.02 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-05-5420 TCGA-05-5425 TCGA-05-5429 
       26.01        25.02        25.02        15.02        29.00         9.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4627 TCGA-38-4630 TCGA-44-2656 TCGA-44-2659 
        7.40         5.98        37.71        35.28        46.98        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 
       42.77         3.19        25.02        38.89        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6778 TCGA-44-6779 
       12.59        23.77        10.78         9.93        61.28        16.44 
TCGA-44-7661 TCGA-44-7667 TCGA-44-7670 TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 
       12.03        36.07        29.00        23.64        12.66        15.98 
TCGA-44-A47B TCGA-44-A47F TCGA-44-A4SS TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        9.44        11.08        13.64        32.84         8.81        29.46 
TCGA-49-4514 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AAR2 TCGA-49-AAR4 
       55.89        17.16        11.64       153.04        63.95        28.90 
TCGA-49-AARE TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 
       40.41         9.86        71.47        70.55        15.72        49.28 
TCGA-50-5072 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5944 TCGA-50-5946 
        8.22        40.60        78.67        21.47        25.12        22.55 
TCGA-50-6592 TCGA-50-6595 TCGA-50-7109 TCGA-53-7813 TCGA-55-1592 TCGA-55-1594 
       25.55         6.21        10.13        13.94        23.05        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6972 TCGA-55-6978 TCGA-55-6979 
       45.21         2.86        42.51        48.49         5.49         7.79 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7570 TCGA-55-7576 TCGA-55-7724 
       60.03        40.54       107.21         0.20         1.32        23.18 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 
        0.79         1.78         0.53         6.48        17.65        19.82 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8203 TCGA-55-8205 
        3.29        19.66         5.06         0.13        17.98         1.08 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8514 
        0.76         0.36         0.26         0.49        17.72         6.64 
TCGA-55-8615 TCGA-55-A490 TCGA-55-A491 TCGA-55-A4DF TCGA-62-8402 TCGA-62-A46S 
        0.49         1.58        20.58        20.19        49.25        54.35 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       39.25        40.96        20.65        55.43        38.37        87.98 
TCGA-64-5775 TCGA-64-5781 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 
        2.04        51.25         6.64         6.12         5.42         6.05 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8453 TCGA-69-A59K TCGA-73-4658 TCGA-73-4659 
        2.93        12.56        26.73         7.04        52.60        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-A9RS TCGA-78-7146 
       26.30        15.35         4.31         1.32        11.18         5.69 
TCGA-78-7148 TCGA-78-7153 TCGA-78-7154 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
       20.58        24.99        19.50        88.14        26.53         8.02 
TCGA-78-8640 TCGA-78-8660 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 TCGA-86-8054 
      214.62        10.55        31.13        34.39        19.43        24.49 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4JF 
       15.65        23.05        14.60         1.15        30.84        17.62 
TCGA-91-6828 TCGA-91-6836 TCGA-91-6840 TCGA-91-7771 TCGA-93-A4JQ TCGA-95-7043 
       10.62        13.71        12.23        16.18        17.29         1.22 
TCGA-95-7562 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-8172 
        2.86        15.65         2.76        19.89        64.60        17.92 
TCGA-97-8175 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       18.12        18.67        34.85        36.76         1.45         5.59 
TCGA-J2-A4AE TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T8 
       35.47        12.59        11.87        86.14        49.35         5.29 
TCGA-MP-A4TE TCGA-MP-A4TJ TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       29.46        11.15        29.13         0.43        19.82         9.70 

$`DEL PEAK 45(21Q11.2) WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4403 TCGA-05-4405 TCGA-05-4415 
        3.98        19.96        14.01        19.00        20.05         2.99 
TCGA-05-4418 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 TCGA-05-4434 TCGA-05-5423 
        9.01        21.99        26.01        24.00        15.02         4.96 
TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
       22.03         2.04         0.46         8.68        97.74       120.79 
TCGA-38-4628 TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
       49.05        28.41        11.64        44.61        14.73        26.30 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-3396 
        4.37        43.53        13.15        24.36        42.08        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-6147 TCGA-44-6148 
       38.24        34.06         6.25        26.56        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 
       21.63        23.18        63.72        32.45        14.60        19.46 
TCGA-44-7662 TCGA-44-7669 TCGA-44-7671 TCGA-44-8119 TCGA-44-8120 TCGA-44-A47A 
        7.17        18.87        17.59         3.25         8.55        15.32 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       11.54        13.45        76.21        28.11        28.57        12.66 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 TCGA-49-6742 TCGA-49-6743 
       35.54        46.72        14.07        29.75        14.63        12.13 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARN 
       29.26        22.26        22.26        62.24         8.55        37.32 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5055 TCGA-50-5066 
      123.58       211.82       164.12        20.52        60.16        31.04 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        9.27        14.27         8.45        15.12        18.64        29.03 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6597 TCGA-50-6673 
       42.35         3.91        11.05        12.16        41.69         0.72 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ 
       25.61         7.59        27.25        34.29        30.54         9.21 
TCGA-55-1595 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
       48.62         0.07        32.65         0.79        40.73        15.25 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 
        0.82         3.88         2.20        45.34        32.71        24.99 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 
       70.26         0.59         1.15         7.99         0.13         3.12 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7903 TCGA-55-7914 TCGA-55-7995 
        1.28         1.28         1.12        18.64         6.15         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       29.72        15.19        19.73        23.64        15.65         1.51 
TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8511 
        2.17        22.16        15.42         1.45         0.95         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 
        0.10         4.80        17.62         1.58         1.61         2.17 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A492 TCGA-55-A493 
       16.93        22.65        20.71        21.40        19.59         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       15.81        19.99        17.95         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U 
       14.60        88.64        47.80        19.53        56.71        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 
       72.30        13.61        29.92        56.81        39.09        37.02 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
       42.90        28.41        28.47         1.02        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7763 
       14.04        12.66         5.72         4.64        13.87        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
       13.61         7.56         2.30        14.01        13.45         4.24 
TCGA-71-6725 TCGA-73-4662 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
        2.01        29.98         5.39         1.25        39.09        23.51 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
      163.10        27.16        19.27        35.93        21.90        39.52 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       38.50        32.09         5.88        64.90        22.29         7.07 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
      104.19       223.96         8.48        31.20        53.33        10.75 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55        32.68        39.75        77.59       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 
       27.09        12.36         5.88        13.87        20.55        19.89 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       16.70         4.08         4.57        24.33         0.79        15.75 
TCGA-86-8076 TCGA-86-8279 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
       16.08        15.85        21.47        13.91        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
       14.96        13.32        13.32         3.81        13.64        26.47 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 
       41.36         1.97        10.19         2.60        27.68         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
        1.15        16.60        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
        9.76         4.18         6.12        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-8039 TCGA-95-A4VK 
        1.12        18.67        12.39        15.68        27.29        21.40 
TCGA-95-A4VN TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       18.18        31.69        63.52        43.79        25.48         5.95 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 
        0.59         0.72        18.67         5.39        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4LX TCGA-97-A4M0 TCGA-97-A4M1 
       14.30        21.60        20.58        20.19        21.44        19.76 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-97-A4M7 TCGA-99-7458 TCGA-99-AA5R 
       20.52        17.75        20.84        20.68        24.56        21.63 
TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       24.30        23.80        18.08        16.44        19.00        14.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N1 
        3.81         0.20        14.53         1.91        17.46        27.19 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       38.63         2.76        58.45        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TF 
        5.49        41.59        31.23         2.43        10.09        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.66        14.10        19.13        73.91        71.05        62.60 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-O1-A52J TCGA-S2-AA1A 
        0.13         1.64         0.26        59.11        16.87 

  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                          0.00                           0.07 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                        214.62                         223.96 
  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE 
                        18.395                         18.640 
[1] "0.0 - 214.6 (18.4)" "0.1 - 224.0 (18.6)"
[1] "hr=" "1"  
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(21Q11.2) MUTATED         1       43       49        0        15
  DEL PEAK 45(21Q11.2) WILD-TYPE       4       92       91        1        36
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 45(21Q11.2) MUTATED          35         28          5        9
  DEL PEAK 45(21Q11.2) WILD-TYPE        38         44          6       17
D66V3, multiclass
            clus
vv           DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             43                             92
  STAGE IB                             49                             91
  STAGE II                              0                              1
  STAGE IIA                            15                             36
  STAGE IIB                            35                             38
  STAGE IIIA                           28                             44
  STAGE IIIB                            5                              6
  STAGE IV                              9                             17
[1] 9 2
[1] 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(21Q11.2) MUTATED    51 106  19   8
  DEL PEAK 45(21Q11.2) WILD-TYPE 119 172  27  11
D66V4, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  T1                           51                            119
  T2                          106                            172
  T3                           19                             27
  T4                            8                             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 45(21Q11.2) MUTATED   117  38    27
  DEL PEAK 45(21Q11.2) WILD-TYPE 215  58    49
D66V5, multiclass
       clus
vv      DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  N0                             117                            215
  N1                              38                             58
  N2+N3                           27                             49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED   128   8
  DEL PEAK 45(21Q11.2) WILD-TYPE 220  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED    128    8
  DEL PEAK 45(21Q11.2) WILD-TYPE  220   17
   clus
vv  DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  0                          128                            220
  1                            8                             17
[1] 2 2
[1] FALSE
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED    90  95
  DEL PEAK 45(21Q11.2) WILD-TYPE 185 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED     90   95
  DEL PEAK 45(21Q11.2) WILD-TYPE  185  145
        clus
vv       DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  FEMALE                           90                            185
  MALE                             95                            145
[1] 2 2
[1] FALSE
D66V8, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                           10
  DEL PEAK 45(21Q11.2) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 45(21Q11.2) MUTATED                                  29
  DEL PEAK 45(21Q11.2) WILD-TYPE                                78
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(21Q11.2) MUTATED                                                  127
  DEL PEAK 45(21Q11.2) WILD-TYPE                                                192
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 45(21Q11.2) MUTATED                                            0
  DEL PEAK 45(21Q11.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 45(21Q11.2) MUTATED                                               3
  DEL PEAK 45(21Q11.2) WILD-TYPE                                            16
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                                0
  DEL PEAK 45(21Q11.2) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                                    1
  DEL PEAK 45(21Q11.2) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                              1
  DEL PEAK 45(21Q11.2) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                               6
  DEL PEAK 45(21Q11.2) WILD-TYPE                            17
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                                 1
  DEL PEAK 45(21Q11.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                                               2
  DEL PEAK 45(21Q11.2) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 45(21Q11.2) MUTATED                              5
  DEL PEAK 45(21Q11.2) WILD-TYPE                            5
D66V9, multiclass
                                                    clus
vv                                                   DEL PEAK 45(21Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            29
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          127
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 3
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                 6
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  5
                                                    clus
vv                                                   DEL PEAK 45(21Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            192
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  16
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    1
  LUNG PAPILLARY ADENOCARCINOMA                                                  17
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                   3
  MUCINOUS (COLLOID) CARCINOMA                                                    5
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED    12 173
  DEL PEAK 45(21Q11.2) WILD-TYPE   9 321
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED     12  173
  DEL PEAK 45(21Q11.2) WILD-TYPE    9  321
     clus
vv    DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  NO                            12                              9
  YES                          173                            321
[1] 2 2
[1] FALSE
D66V11, continuous
D66V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 45(21Q11.2) MUTATED   122   3   1   7
  DEL PEAK 45(21Q11.2) WILD-TYPE 221   9   3  19
D66V13, multiclass
    clus
vv   DEL PEAK 45(21Q11.2) MUTATED DEL PEAK 45(21Q11.2) WILD-TYPE
  R0                          122                            221
  R1                            3                              9
  R2                            1                              3
  RX                            7                             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                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 45(21Q11.2) MUTATED                                  1     1
  DEL PEAK 45(21Q11.2) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(21Q11.2) MUTATED                          25   129
  DEL PEAK 45(21Q11.2) WILD-TYPE                        26   260
D66V14, multiclass
                                  clus
vv                                 DEL PEAK 45(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     129
                                  clus
vv                                 DEL PEAK 45(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       260
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V15, binary
                                cls
clus                               0   1
  DEL PEAK 45(21Q11.2) MUTATED     3 135
  DEL PEAK 45(21Q11.2) WILD-TYPE   4 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(21Q11.2) MUTATED      3  135
  DEL PEAK 45(21Q11.2) WILD-TYPE    4  247
                        clus
vv                       DEL PEAK 45(21Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          135
                        clus
vv                       DEL PEAK 45(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            247
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 46(22Q13.32) MUTATION ANALYSIS
D67V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 46(22Q13.32) MUTATED   169  75
  DEL PEAK 46(22Q13.32) WILD-TYPE 168  79
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                            244                             247 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                             75                              79 
$`DEL PEAK 46(22Q13.32) MUTATED`
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 
       50.07        45.01        37.02         0.00         9.96        24.03 
TCGA-05-4415 TCGA-05-4418 TCGA-05-4420 TCGA-05-4424 TCGA-05-4426 TCGA-05-4427 
        2.99         9.01        29.98        30.02        26.01        26.01 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 
       25.02        24.00        15.02        29.00        22.03         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4628 TCGA-38-4630 TCGA-38-4632 TCGA-38-6178 
        5.98         8.68        49.05        35.28        44.61        14.73 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 
       46.98        44.94        42.08        25.02        38.89        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
        6.25        26.56        33.30        28.37        12.59        23.77 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 
       10.78         9.93        27.78        21.63        23.18        61.28 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7671 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        17.59        12.66         8.55 
TCGA-44-A479 TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4488 TCGA-49-4501 TCGA-49-4505 
       15.98        13.64        13.45        28.57        46.72        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-6744 TCGA-49-6761 TCGA-49-6767 
       32.84         8.81        29.46        29.26        11.64        22.26 
TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-4B-A93V TCGA-50-5051 
       63.95         8.55        40.41        37.32         9.86        15.72 
TCGA-50-5930 TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 
        9.27        40.60        78.67        21.47         8.45        15.12 
TCGA-50-5941 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6597 
       18.64        42.35         3.91        25.55        11.05        41.69 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
        0.72        10.13        25.61        34.29        13.94         9.21 
TCGA-55-1594 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 
       38.73        32.65         0.79        42.51        40.73         0.82 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 
       48.49         3.88         2.20        40.54         0.59         1.15 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 TCGA-55-7910 
        0.20         3.12         1.32         1.12        18.64         6.48 
TCGA-55-7911 TCGA-55-7994 TCGA-55-8092 TCGA-55-8094 TCGA-55-8203 TCGA-55-8205 
       17.65        19.82         5.06         0.13        17.98         1.08 
TCGA-55-8207 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
        2.17         0.95         0.36         0.26         0.49        17.72 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
        0.30         0.10         0.49         1.58         2.17        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8399 
       21.40         1.58         0.92        20.19        19.99        88.64 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 
       54.35        67.96        13.61        29.92        56.81        20.65 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       39.09        55.43        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
       28.41        51.25        20.05        13.87         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       22.68        13.61         7.56         2.30         2.93        12.56 
TCGA-69-8253 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
       14.01         4.24        26.73         7.04         2.01        23.38 
TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7145 
       29.98        15.35         4.31        11.18       163.10        27.16 
TCGA-78-7146 TCGA-78-7152 TCGA-78-7159 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 
        5.69        39.52        64.90       223.96        88.14        31.20 
TCGA-78-7536 TCGA-78-8640 TCGA-78-8660 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 
        8.02       214.62        10.55       110.50        27.09         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       31.13        34.39        19.43        19.89        16.70        24.49 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
        4.57         0.79        15.85        21.47        14.60         1.15 
TCGA-86-8672 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
        0.62         3.81        17.62        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 
       10.19        13.71        12.23        27.68        16.18         1.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JN TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
        1.45         6.12        23.61         1.12         2.86        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 
       12.39        27.29         2.76        18.18        19.89        31.69 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-A4M0 TCGA-97-A4M3 
       63.52        25.48         5.95         0.59        21.44        17.75 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AG TCGA-L4-A4E5 
       24.56        36.76         1.45         5.59        16.44        19.00 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 
        0.20        14.53        12.59        11.87        27.19         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE 
       86.14        49.35        37.35         5.29        31.23        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI 
       11.05        14.66        11.15        19.13        71.05         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       29.13        19.82         9.70        59.11 

$`DEL PEAK 46(22Q13.32) WILD-TYPE`
TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4398 TCGA-05-4402 TCGA-05-4403 
        3.98        19.96        14.01        47.05         8.02        19.00 
TCGA-05-4405 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4430 TCGA-05-4434 
       20.05        14.96        12.00        21.99        25.02        15.02 
TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 
        4.96         9.04         2.04         0.46        97.74       120.79 
TCGA-38-4627 TCGA-38-4629 TCGA-38-4631 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
       37.71        28.41        11.64        26.30         4.37        43.53 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 
       13.15        24.36        42.77         3.19        37.15        38.24 
TCGA-44-6148 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.15        63.72        32.45        16.44        14.60        19.46 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7672 TCGA-44-8119 TCGA-44-A47A TCGA-44-A47B 
       12.03        29.00        23.64         3.25        15.32         9.44 
TCGA-44-A47F TCGA-44-A47G TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 
       11.08        11.54        76.21        28.11        12.66        35.54 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6745 TCGA-49-AAQV 
       29.75        55.89        14.63        12.13        17.16        22.26 
TCGA-49-AAR0 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
      153.04        62.24        28.90       123.58       211.82       164.12 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47        70.55        60.16        31.04        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6594 
        8.22        14.27        29.03        25.12        22.55        12.16 
TCGA-50-6595 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1592 TCGA-55-1595 
        6.21         7.59        27.25        30.54        23.05        48.62 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6970 TCGA-55-6978 TCGA-55-6979 
       45.21         2.86         0.07        15.25         5.49         7.79 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 
       45.34        32.71        60.03        24.99       107.21        70.26 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
        7.99         0.13        23.18         1.28         1.28         0.79 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7914 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
        1.78         0.53         6.15         0.16        29.72        15.19 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
        3.29        19.66        19.73        23.64        15.65         1.51 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8513 TCGA-55-8514 
       22.16        15.42         1.45         0.76         4.80         6.64 
TCGA-55-8614 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       17.62         1.61        16.93        22.65        20.58        19.59 
TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        17.95         4.57        39.98        42.38        14.60 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46V TCGA-62-A470 
       49.25        47.80        19.53        56.71        72.30        39.25 
TCGA-62-A471 TCGA-64-1680 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
       40.96        37.02        28.47         1.02        18.84        14.04 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7765 TCGA-69-7974 TCGA-69-8254 
       12.66         5.72         4.64         5.42         6.05        13.45 
TCGA-73-4658 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
       52.60        26.30         1.32         5.39         1.25        39.09 
TCGA-73-7499 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 
       23.51        19.27        20.58        35.93        21.90        24.99 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 
       19.50        38.50        32.09         5.88        22.29         7.07 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
      104.19         8.48        26.53        53.33        10.75        39.35 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8648 TCGA-78-8655 TCGA-86-6562 TCGA-86-7713 
       10.55        32.68        39.75        77.59        12.36        13.87 
TCGA-86-7714 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
       20.55         4.08        24.33        15.75        16.08        15.65 
TCGA-86-8280 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
       23.05        13.91        30.84        27.58        14.96        13.32 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 
       13.32        13.64        26.47         2.60         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO 
       16.60        14.27        19.82         9.76         4.18         1.08 
TCGA-93-A4JP TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       19.00        17.29         1.22        15.68        15.65        21.40 
TCGA-97-7547 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 
       64.60        43.79         0.72        18.67        17.92         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.12        15.39        16.41        14.30        21.60        20.58 
TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-97-A4M7 
       20.19        19.76        20.52        20.84        18.67        20.68 
TCGA-99-8025 TCGA-99-AA5R TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        21.63        24.30        23.80        18.08        35.47 
TCGA-L4-A4E6 TCGA-L9-A443 TCGA-L9-A5IP TCGA-L9-A743 TCGA-MN-A4N4 TCGA-MP-A4SW 
       14.30         3.81         1.91        17.46        38.63        58.45 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TD 
       86.04        58.85         5.49        41.59         2.43        10.09 
TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       14.10        73.91        62.60         1.64         0.26         0.43 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                           0.00                            0.07 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                         223.96                          211.82 
  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE 
                         17.735                          19.000 
[1] "0.0 - 224.0 (17.7)" "0.1 - 211.8 (19.0)"
[1] "hr=" "1"  
D67V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(22Q13.32) MUTATED         3       59       69        0        28
  DEL PEAK 46(22Q13.32) WILD-TYPE       2       76       71        1        23
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 46(22Q13.32) MUTATED          37         38          6       14
  DEL PEAK 46(22Q13.32) WILD-TYPE        36         34          5       12
D67V3, multiclass
            clus
vv           DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  STAGE I                                3                               2
  STAGE IA                              59                              76
  STAGE IB                              69                              71
  STAGE II                               0                               1
  STAGE IIA                             28                              23
  STAGE IIB                             37                              36
  STAGE IIIA                            38                              34
  STAGE IIIB                             6                               5
  STAGE IV                              14                              12
[1] 9 2
[1] 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(22Q13.32) MUTATED    82 138  23  10
  DEL PEAK 46(22Q13.32) WILD-TYPE  88 140  23   9
D67V4, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  T1                            82                              88
  T2                           138                             140
  T3                            23                              23
  T4                            10                               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 46(22Q13.32) MUTATED   166  46    38
  DEL PEAK 46(22Q13.32) WILD-TYPE 166  50    38
D67V5, multiclass
       clus
vv      DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  N0                              166                             166
  N1                               46                              50
  N2+N3                            38                              38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED   169  14
  DEL PEAK 46(22Q13.32) WILD-TYPE 179  11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED    169   14
  DEL PEAK 46(22Q13.32) WILD-TYPE  179   11
   clus
vv  DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  0                           169                             179
  1                            14                              11
[1] 2 2
[1] FALSE
D67V7, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED   124 130
  DEL PEAK 46(22Q13.32) WILD-TYPE 151 110
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED    124  130
  DEL PEAK 46(22Q13.32) WILD-TYPE  151  110
        clus
vv       DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  FEMALE                           124                             151
  MALE                             130                             110
[1] 2 2
[1] FALSE
D67V8, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                           12
  DEL PEAK 46(22Q13.32) WILD-TYPE                          7
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 46(22Q13.32) MUTATED                                  44
  DEL PEAK 46(22Q13.32) WILD-TYPE                                63
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(22Q13.32) MUTATED                                                  167
  DEL PEAK 46(22Q13.32) WILD-TYPE                                                152
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 46(22Q13.32) MUTATED                                            1
  DEL PEAK 46(22Q13.32) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 46(22Q13.32) MUTATED                                              10
  DEL PEAK 46(22Q13.32) WILD-TYPE                                             9
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                                0
  DEL PEAK 46(22Q13.32) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                                    2
  DEL PEAK 46(22Q13.32) WILD-TYPE                                  1
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                              1
  DEL PEAK 46(22Q13.32) WILD-TYPE                            1
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                               9
  DEL PEAK 46(22Q13.32) WILD-TYPE                            14
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                                 1
  DEL PEAK 46(22Q13.32) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                                               4
  DEL PEAK 46(22Q13.32) WILD-TYPE                                             1
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 46(22Q13.32) MUTATED                              3
  DEL PEAK 46(22Q13.32) WILD-TYPE                            7
D67V9, multiclass
                                                    clus
vv                                                   DEL PEAK 46(22Q13.32) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             44
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           167
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 10
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   1
  LUNG PAPILLARY ADENOCARCINOMA                                                  9
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  MUCINOUS (COLLOID) CARCINOMA                                                   3
                                                    clus
vv                                                   DEL PEAK 46(22Q13.32) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               63
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             152
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    9
  LUNG CLEAR CELL ADENOCARCINOMA                                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               1
  LUNG MUCINOUS ADENOCARCINOMA                                                     1
  LUNG PAPILLARY ADENOCARCINOMA                                                   14
  LUNG SIGNET RING ADENOCARCINOMA                                                  0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                    1
  MUCINOUS (COLLOID) CARCINOMA                                                     7
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, binary
                                 cls
clus                                0   1
  DEL PEAK 46(22Q13.32) MUTATED    10 244
  DEL PEAK 46(22Q13.32) WILD-TYPE  11 250
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED     10  244
  DEL PEAK 46(22Q13.32) WILD-TYPE   11  250
     clus
vv    DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  NO                             10                              11
  YES                           244                             250
[1] 2 2
[1] FALSE
D67V11, continuous
D67V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 46(22Q13.32) MUTATED   167   6   1  13
  DEL PEAK 46(22Q13.32) WILD-TYPE 176   6   3  13
D67V13, multiclass
    clus
vv   DEL PEAK 46(22Q13.32) MUTATED DEL PEAK 46(22Q13.32) WILD-TYPE
  R0                           167                             176
  R1                             6                               6
  R2                             1                               3
  RX                            13                              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                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 46(22Q13.32) MUTATED                                  1     2
  DEL PEAK 46(22Q13.32) WILD-TYPE                                0     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(22Q13.32) MUTATED                          31   186
  DEL PEAK 46(22Q13.32) WILD-TYPE                        20   203
D67V14, multiclass
                                  clus
vv                                 DEL PEAK 46(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      186
                                  clus
vv                                 DEL PEAK 46(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     20
  WHITE                                                        203
[1] 4 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 46(22Q13.32) MUTATED     5 192
  DEL PEAK 46(22Q13.32) WILD-TYPE   2 190
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 46(22Q13.32) MUTATED      5  192
  DEL PEAK 46(22Q13.32) WILD-TYPE    2  190
                        clus
vv                       DEL PEAK 46(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           192
                        clus
vv                       DEL PEAK 46(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             190
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 47(XP22.2) MUTATION ANALYSIS
D68V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 47(XP22.2) MUTATED    96  39
  DEL PEAK 47(XP22.2) WILD-TYPE 241 115
  DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE 
                          135                           356 
  DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE 
                           39                           115 
$`DEL PEAK 47(XP22.2) MUTATED`
TCGA-05-4382 TCGA-05-4389 TCGA-05-4396 TCGA-05-4397 TCGA-05-4405 TCGA-05-4426 
       19.96        45.01         9.96        24.03        20.05        26.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5428 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       26.01        15.02        22.03         2.04         7.40         5.98 
TCGA-38-6178 TCGA-44-2659 TCGA-44-5643 TCGA-44-5644 TCGA-44-6778 TCGA-44-6779 
       14.73        44.94        33.30        28.37        61.28        16.44 
TCGA-44-7660 TCGA-44-8117 TCGA-44-8120 TCGA-49-4490 TCGA-49-4505 TCGA-49-4512 
       19.46        12.66         8.55        12.66        14.07        29.75 
TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARQ TCGA-50-5066 TCGA-50-5068 
       22.26        63.95        62.24       211.82        31.04        49.28 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5946 TCGA-50-6593 
       40.60        78.67         8.45        18.64        22.55        11.05 
TCGA-50-6594 TCGA-50-6597 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-55-1592 
       12.16        41.69        10.13        34.29        30.54        23.05 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6979 
       45.21         2.86         0.07         0.79        42.51         7.79 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7726 TCGA-55-7903 TCGA-55-7994 
       70.26         0.59         0.20         1.28        18.64        19.82 
TCGA-55-8090 TCGA-55-8094 TCGA-55-8203 TCGA-55-8301 TCGA-55-8510 TCGA-55-8616 
       19.66         0.13        17.98         1.45        17.72         1.58 
TCGA-55-A48X TCGA-55-A48Z TCGA-55-A492 TCGA-55-A4DG TCGA-62-8397 TCGA-62-A46O 
       22.65        21.40        19.59        19.99        42.38        47.80 
TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-5778 TCGA-64-5815 
       67.96        29.92        56.81        39.09        42.90        28.47 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-6217 TCGA-69-7764 TCGA-69-7765 
        1.02        18.84        14.04        13.87        13.61         5.42 
TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-7499 
        2.93         7.04         2.01        26.30        15.35        23.51 
TCGA-73-A9RS TCGA-78-7146 TCGA-78-7154 TCGA-78-7160 TCGA-78-7166 TCGA-78-7535 
       11.18         5.69        19.50        22.29         8.48        31.20 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-78-8660 TCGA-86-7954 TCGA-86-7955 
       10.55       214.62        77.59        10.55        19.89        16.70 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8358 TCGA-86-8359 TCGA-86-8673 
       24.49         4.08        15.75        21.47        14.60        14.96 
TCGA-86-A4P7 TCGA-91-6848 TCGA-91-7771 TCGA-91-8496 TCGA-93-A4JO TCGA-93-A4JQ 
       13.64         7.36        16.18        16.60         1.08        17.29 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-97-7554 
        1.12         1.22        18.67        27.29         2.76        25.48 
TCGA-97-7937 TCGA-97-8172 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M6 
        5.95        17.92        14.30        21.60        21.44        18.67 
TCGA-97-A4M7 TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N5 
       20.68        19.00         0.20        14.53        12.59         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TI TCGA-NJ-A4YI 
       86.14        58.45        37.35        86.04        14.10         0.13 
TCGA-NJ-A55A TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.26         9.70        16.87 

$`DEL PEAK 47(XP22.2) WILD-TYPE`
TCGA-05-4249 TCGA-05-4250 TCGA-05-4384 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 
       50.07         3.98        14.01        37.02         0.00        47.05 
TCGA-05-4402 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 TCGA-05-4420 
        8.02        19.00         2.99        14.96         9.01        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       12.00        30.02        21.99        25.02        25.02        24.00 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-35-3615 TCGA-35-5375 
       15.02         4.96        29.00         9.04         0.46         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4630 
       97.74       120.79        37.71        49.05        28.41        35.28 
TCGA-38-4631 TCGA-38-4632 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 
       11.64        44.61        26.30         4.37        43.53        46.98 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2662 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       13.15        24.36        42.08        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       37.15        38.24        38.89        34.06         6.25        26.56 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
       12.59        23.77        10.78         9.93        27.78        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7661 
       21.63        23.18        63.72        32.45        14.60        12.03 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
        7.17        36.07        18.87        29.00        17.59        23.64 
TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
        3.25        15.98        15.32         9.44        11.08        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 
       13.64        13.45        76.21        28.11        28.57        35.54 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6742 
       46.72        32.84         8.81        29.46        55.89        14.63 
TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAQV TCGA-49-AAR0 
       12.13        29.26        17.16        11.64        22.26       153.04 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARN TCGA-49-AARO TCGA-49-AARR 
       28.90         8.55        40.41        37.32       123.58       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
        9.86        20.52        71.47        70.55        15.72        60.16 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 TCGA-50-5939 TCGA-50-5942 
        8.22         9.27        14.27        21.47        15.12        29.03 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 
       25.12        42.35         3.91        25.55         6.21         0.72 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       25.61         7.59        27.25        13.94         9.21        38.73 
TCGA-55-1595 TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       48.62        32.65        40.73        15.25         0.82        48.49 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
        3.88         5.49         2.20        45.34        32.71        60.03 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 TCGA-55-7284 TCGA-55-7573 
       24.99        40.54       107.21         1.15         7.99         0.13 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7728 
        3.12         1.32        23.18         1.28         1.12         0.79 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 TCGA-55-7995 
        1.78         0.53         6.48        17.65         6.15         0.16 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8091 TCGA-55-8092 TCGA-55-8096 
       29.72        15.19         3.29        19.73         5.06        23.64 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
       15.65         1.08         1.51         2.17        22.16        15.42 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 
        0.76         0.95         0.36         0.26         0.49         0.30 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8619 
        0.10         4.80         6.64        17.62         0.49         1.61 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
        2.17        16.93        20.71         1.58        20.58         0.92 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 
       15.81        20.19        17.95         4.57        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V 
       88.64        49.25        19.53        56.71        54.35        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1677 TCGA-64-1679 TCGA-64-1680 
       13.61        39.25        40.96        20.65        55.43        37.02 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 
       38.37        87.98         2.04        28.41        51.25        20.05 
TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       12.66         5.72         4.64         6.64         6.12        22.68 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        7.56         6.05         2.30        12.56        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4670 
        4.24        26.73        52.60        23.38        29.98         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-78-7143 TCGA-78-7145 
        1.32         5.39         1.25        39.09       163.10        27.16 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58        35.93        21.90        39.52        24.99 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 
       38.50        32.09         5.88        64.90         7.07       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
      223.96        88.14        26.53         8.02        53.33        10.75 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.35        32.68        39.75       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
        5.88        31.13        34.39        13.87        20.55        19.43 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57        24.33         0.79        16.08        15.65        15.85 
TCGA-86-8280 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       23.05         1.15        13.91        30.84        27.58         0.62 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 
       13.32        13.32         3.81        17.62        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
       41.36         1.97        10.19         2.60        13.71        12.23 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
       27.68         1.15        14.27         1.18         1.45        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7562 
        9.76         4.18         6.12        23.61        19.00         2.86 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
       12.39        15.68        15.65        21.40        18.18        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 
       31.69        64.60        63.52        43.79         0.59         0.72 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8552 
       18.67         5.39        18.12        15.39        16.41        20.58 
TCGA-97-A4LX TCGA-97-A4M1 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M5 TCGA-99-7458 
       20.19        19.76        20.52        17.75        20.84        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-8192 
       34.85        36.76         1.45         5.59        21.63        24.30 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A443 
       23.80        18.08        35.47        16.44        14.30         3.81 
TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MP-A4SY 
        1.91        17.46        11.87        27.19        38.63        49.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC 
       58.85         5.49         5.29        41.59        31.23         2.43 
TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK 
       10.09        29.46        11.05        14.66        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O 
       73.91        71.05        62.60         1.64        29.13         0.43 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

  DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE 
                         0.07                          0.00 
  DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE 
                       214.62                        223.96 
  DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE 
                       18.640                        18.425 
[1] "0.1 - 214.6 (18.6)" "0.0 - 224.0 (18.4)"
[1] "hr=" "1.1"
D68V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 47(XP22.2) MUTATED         2       33       40        0        12
  DEL PEAK 47(XP22.2) WILD-TYPE       3      102      100        1        39
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 47(XP22.2) MUTATED          28         17          3        8
  DEL PEAK 47(XP22.2) WILD-TYPE        45         55          8       18
D68V3, multiclass
            clus
vv           DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            33                           102
  STAGE IB                            40                           100
  STAGE II                             0                             1
  STAGE IIA                           12                            39
  STAGE IIB                           28                            45
  STAGE IIIA                          17                            55
  STAGE IIIB                           3                             8
  STAGE IV                             8                            18
[1] 9 2
[1] 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(XP22.2) MUTATED    44  80  13   6
  DEL PEAK 47(XP22.2) WILD-TYPE 126 198  33  13
D68V4, multiclass
    clus
vv   DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE
  T1                          44                           126
  T2                          80                           198
  T3                          13                            33
  T4                           6                            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 47(XP22.2) MUTATED    86  35    20
  DEL PEAK 47(XP22.2) WILD-TYPE 246  61    56
D68V5, multiclass
       clus
vv      DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE
  N0                             86                           246
  N1                             35                            61
  N2+N3                          20                            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"
D68V6, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP22.2) MUTATED    98   7
  DEL PEAK 47(XP22.2) WILD-TYPE 250  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP22.2) MUTATED     98    7
  DEL PEAK 47(XP22.2) WILD-TYPE  250   18
   clus
vv  DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE
  0                          98                           250
  1                           7                            18
[1] 2 2
[1] FALSE
D68V7, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP22.2) MUTATED    65  78
  DEL PEAK 47(XP22.2) WILD-TYPE 210 162
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP22.2) MUTATED     65   78
  DEL PEAK 47(XP22.2) WILD-TYPE  210  162
        clus
vv       DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE
  FEMALE                          65                           210
  MALE                            78                           162
[1] 2 2
[1] FALSE
D68V8, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 47(XP22.2) MUTATED                            7
  DEL PEAK 47(XP22.2) WILD-TYPE                         12
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 47(XP22.2) MUTATED                                  33
  DEL PEAK 47(XP22.2) WILD-TYPE                                74
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 47(XP22.2) MUTATED                                                   91
  DEL PEAK 47(XP22.2) WILD-TYPE                                                228
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 47(XP22.2) MUTATED                                            2
  DEL PEAK 47(XP22.2) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 47(XP22.2) MUTATED                                               4
  DEL PEAK 47(XP22.2) WILD-TYPE                                            15
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 47(XP22.2) MUTATED                                0
  DEL PEAK 47(XP22.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 47(XP22.2) MUTATED                                    2
  DEL PEAK 47(XP22.2) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 47(XP22.2) MUTATED                              0
  DEL PEAK 47(XP22.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 47(XP22.2) MUTATED                               3
  DEL PEAK 47(XP22.2) WILD-TYPE                            20
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 47(XP22.2) MUTATED                                 0
  DEL PEAK 47(XP22.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 47(XP22.2) MUTATED                                               0
  DEL PEAK 47(XP22.2) WILD-TYPE                                             5
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 47(XP22.2) MUTATED                              1
  DEL PEAK 47(XP22.2) WILD-TYPE                            9
D68V9, multiclass
                                                    clus
vv                                                   DEL PEAK 47(XP22.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          91
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                4
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                3
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                0
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   DEL PEAK 47(XP22.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           228
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 15
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 20
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  5
  MUCINOUS (COLLOID) CARCINOMA                                                   9
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP22.2) MUTATED     4 139
  DEL PEAK 47(XP22.2) WILD-TYPE  17 355
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP22.2) MUTATED      4  139
  DEL PEAK 47(XP22.2) WILD-TYPE   17  355
     clus
vv    DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE
  NO                            4                            17
  YES                         139                           355
[1] 2 2
[1] FALSE
D68V11, continuous
D68V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 47(XP22.2) MUTATED    91   2   1   6
  DEL PEAK 47(XP22.2) WILD-TYPE 252  10   3  20
D68V13, multiclass
    clus
vv   DEL PEAK 47(XP22.2) MUTATED DEL PEAK 47(XP22.2) WILD-TYPE
  R0                          91                           252
  R1                           2                            10
  R2                           1                             3
  RX                           6                            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                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 47(XP22.2) MUTATED                                  1     2
  DEL PEAK 47(XP22.2) WILD-TYPE                                0     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 47(XP22.2) MUTATED                          16   103
  DEL PEAK 47(XP22.2) WILD-TYPE                        35   286
D68V14, multiclass
                                  clus
vv                                 DEL PEAK 47(XP22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    103
                                  clus
vv                                 DEL PEAK 47(XP22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   35
  WHITE                                                      286
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V15, binary
                               cls
clus                              0   1
  DEL PEAK 47(XP22.2) MUTATED     1 103
  DEL PEAK 47(XP22.2) WILD-TYPE   6 279
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 47(XP22.2) MUTATED      1  103
  DEL PEAK 47(XP22.2) WILD-TYPE    6  279
                        clus
vv                       DEL PEAK 47(XP22.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         103
                        clus
vv                       DEL PEAK 47(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           279
[1] 2 2
[1] FALSE
