[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/22506767/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LUAD-TP/22531212/transformed.cor.cli.txt"

nPatients in clinical file=522, in cluster file=516, common to both=516
[1]  75 516
[1] "AMP PEAK  1(1P34.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          137                           379 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          137                           379 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          377                           139 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          377                           139 
[1] "AMP PEAK  3(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                          169                           347 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                          169                           347 
[1] "AMP PEAK  4(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                         96                         420 
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                         96                         420 
[1] "AMP PEAK  5(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           333                            183 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           333                            183 
[1] "AMP PEAK  6(5P13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          304                           212 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          304                           212 
[1] "AMP PEAK  7(5Q35.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE 
                          126                           390 
  AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE 
                          126                           390 
[1] "AMP PEAK  8(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                          189                           327 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                          189                           327 
[1] "AMP PEAK  9(7P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE 
                          284                           232 
  AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE 
                          284                           232 
[1] "AMP PEAK 10(7P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          274                           242 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          274                           242 
[1] "AMP PEAK 11(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          218                           298 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          218                           298 
[1] "AMP PEAK 12(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           175                            341 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           175                            341 
[1] "AMP PEAK 13(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           325                            191 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           325                            191 
[1] "AMP PEAK 14(10P15.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE 
                           142                            374 
  AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE 
                           142                            374 
[1] "AMP PEAK 15(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           172                            344 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           172                            344 
[1] "AMP PEAK 16(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                           178                            338 
  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                           178                            338 
[1] "AMP PEAK 17(12Q14.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE 
                           169                            347 
  AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE 
                           169                            347 
[1] "AMP PEAK 18(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE 
                         169                          347 
  AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE 
                         169                          347 
[1] "AMP PEAK 19(13Q33.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                            76                            440 
  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                            76                            440 
[1] "AMP PEAK 20(14Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE 
                           233                            283 
  AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE 
                           233                            283 
[1] "AMP PEAK 21(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE 
                           167                            349 
  AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE 
                           167                            349 
[1] "AMP PEAK 22(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                         227                          289 
  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                         227                          289 
[1] "AMP PEAK 23(17Q23.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE 
                           249                            267 
  AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE 
                           249                            267 
[1] "AMP PEAK 24(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           105                            411 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           105                            411 
[1] "AMP PEAK 25(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         139                          377 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         139                          377 
[1] "AMP PEAK 26(20P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE 
                            201                             315 
  AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE 
                            201                             315 
[1] "AMP PEAK 27(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                            251                             265 
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                            251                             265 
[1] "AMP PEAK 28(22Q11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                             90                             426 
  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                             90                             426 
[1] "AMP PEAK 29(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        159                         357 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        159                         357 
[1] "DEL PEAK  1(1P36.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                           122                            394 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                           122                            394 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          151                           365 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          151                           365 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           46                           470 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           46                           470 
[1] "DEL PEAK  4(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                          233                           283 
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                          233                           283 
[1] "DEL PEAK  5(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                           248                            268 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                           248                            268 
[1] "DEL PEAK  6(3Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                          141                           375 
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                          141                           375 
[1] "DEL PEAK  7(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                        136                         380 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                        136                         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                           386 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                          130                           386 
[1] "DEL PEAK  9(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                          158                           358 
  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                          158                           358 
[1] "DEL PEAK 10(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                          187                           329 
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                          187                           329 
[1] "DEL PEAK 11(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                          179                           337 
  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                          179                           337 
[1] "DEL PEAK 12(5Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE 
                          211                           305 
  DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE 
                          211                           305 
[1] "DEL PEAK 13(6Q14.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE 
                          253                           263 
  DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE 
                          253                           263 
[1] "DEL PEAK 14(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                        258                         258 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                        258                         258 
[1] "DEL PEAK 15(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          254                           262 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          254                           262 
[1] "DEL PEAK 16(8P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                           125                            391 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                           125                            391 
[1] "DEL PEAK 17(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                        287                         229 
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                        287                         229 
[1] "DEL PEAK 18(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          294                           222 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          294                           222 
[1] "DEL PEAK 19(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                           258                            258 
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                           258                            258 
[1] "DEL PEAK 20(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           131                            385 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           131                            385 
[1] "DEL PEAK 21(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                           148                            368 
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                           148                            368 
[1] "DEL PEAK 22(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                           143                            373 
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                           143                            373 
[1] "DEL PEAK 23(11Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE 
                           120                            396 
  DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE 
                           120                            396 
[1] "DEL PEAK 24(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                         115                          401 
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                         115                          401 
[1] "DEL PEAK 25(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                           140                            376 
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                           140                            376 
[1] "DEL PEAK 26(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                          99                          417 
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                          99                          417 
[1] "DEL PEAK 27(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                            133                             383 
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                            133                             383 
[1] "DEL PEAK 28(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                            293                             223 
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                            293                             223 
[1] "DEL PEAK 29(13Q34) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE 
                         241                          275 
  DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE 
                         241                          275 
[1] "DEL PEAK 30(14Q32.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE 
                            150                             366 
  DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE 
                            150                             366 
[1] "DEL PEAK 31(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                           263                            253 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                           263                            253 
[1] "DEL PEAK 32(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                           275                            241 
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                           275                            241 
[1] "DEL PEAK 33(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                           111                            405 
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                           111                            405 
[1] "DEL PEAK 34(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                           169                            347 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                           169                            347 
[1] "DEL PEAK 35(16Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE 
                           188                            328 
  DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE 
                           188                            328 
[1] "DEL PEAK 36(17P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                           281                            235 
  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                           281                            235 
[1] "DEL PEAK 37(18Q21.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                            255                             261 
  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                            255                             261 
[1] "DEL PEAK 38(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE 
                         249                          267 
  DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE 
                         249                          267 
[1] "DEL PEAK 39(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE 
                           276                            240 
  DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE 
                           276                            240 
[1] "DEL PEAK 40(19P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                           269                            247 
  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                           269                            247 
[1] "DEL PEAK 41(19Q13.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE 
                            195                             321 
  DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE 
                            195                             321 
[1] "DEL PEAK 42(20P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE 
                         130                          386 
  DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE 
                         130                          386 
[1] "DEL PEAK 43(20Q13.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE 
                             82                             434 
  DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE 
                             82                             434 
[1] "DEL PEAK 44(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                           179                            337 
  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                           179                            337 
[1] "DEL PEAK 45(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                            250                             266 
  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                            250                             266 
[1] "DEL PEAK 46(XP22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          145                           371 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          145                           371 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RESIDUAL_TUMOR"                      
[19] "RACE"                                
[20] "ETHNICITY"                           

Input Data has 20 rows and 516 columns.

[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=174,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=286,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=94,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 516 columns, 1 survival variables, and 14 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "KARNOFSKY_PERFORMANCE_SCORE"  
 [9] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RESIDUAL_TUMOR"               
[13] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=52, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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 
171 278  46  19 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
171 278  46  19 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
171 278  46  19 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
171 278  46  19 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
333  96  74   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  333    96    76 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
333  96  74   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  333    96    76 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=9, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=12, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=94, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=59, binary=FALSE, numeric=TRUE
RESIDUAL_TUMOR, 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(1P34.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P34.3) MUTATED    86  50
  AMP PEAK  1(1P34.3) WILD-TYPE 237 131
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                          136                           368 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                           50                           131 
$`AMP PEAK  1(1P34.3) MUTATED`
TCGA-05-4402 TCGA-05-4427 TCGA-38-4630 TCGA-38-6178 TCGA-44-8119 TCGA-49-4501 
        8.02        26.01        35.28        14.73         9.37        46.72 
TCGA-49-6742 TCGA-49-AAR0 TCGA-50-6597 TCGA-55-1592 TCGA-55-6979 TCGA-55-7573 
       16.04       156.66        41.69        23.05         7.79        16.01 
TCGA-55-8091 TCGA-55-A48X TCGA-55-A4DF TCGA-67-6217 TCGA-80-5611 TCGA-91-7771 
       19.73        22.65        20.19        13.87        85.32        16.18 
TCGA-95-7562 TCGA-J2-8192 TCGA-MN-A4N1 TCGA-05-4420 TCGA-05-4432 TCGA-05-5428 
        2.86        24.30        27.19        29.98        25.02        22.03 
TCGA-05-5429 TCGA-38-4628 TCGA-44-2657 TCGA-44-2659 TCGA-44-3917 TCGA-44-5644 
        9.04        49.05        44.42        44.94        38.89        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       28.01        23.77        23.18        61.28        16.44        19.46 
TCGA-44-7669 TCGA-44-A47A TCGA-44-A4SU TCGA-49-4490 TCGA-49-4505 TCGA-49-4510 
       18.87        15.32        13.45        12.66        14.07        29.46 
TCGA-49-4512 TCGA-49-6744 TCGA-49-AAR4 TCGA-49-AARQ TCGA-50-5044 TCGA-50-5045 
       29.75        55.33        28.90       221.33        20.52        71.47 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
       49.28         8.22        14.27        48.46        57.53        53.16 
TCGA-50-6591 TCGA-53-7624 TCGA-55-6712 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 
        3.91        34.29         5.62        40.73        53.65        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6987 TCGA-55-7281 TCGA-55-7576 TCGA-55-8096 
       45.34        32.71        70.26        28.67        22.03        23.64 
TCGA-55-8206 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-A4DG TCGA-55-A57B 
       29.19        13.74        20.28        17.10        19.99        17.95 
TCGA-62-8394 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46V TCGA-64-1676 TCGA-64-1681 
        4.57        88.64        47.80        72.30        56.81        38.37 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3772 TCGA-69-7760 TCGA-69-7980 
       28.41        51.25        20.05        18.84         6.64        13.51 
TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4676 TCGA-75-5147 TCGA-75-6206 
       13.45        19.43         8.42         9.24        43.82        85.15 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7155 TCGA-78-7161 
      108.66        27.16        19.27       129.53        38.50         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-7542 TCGA-78-8655 
      104.19       238.29        88.14        31.20        10.55        77.59 
TCGA-78-8662 TCGA-86-7713 TCGA-86-7953 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 
      110.50        38.04        32.78         4.08         0.79        22.82 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-A456 TCGA-86-A4P7 
       31.20        23.05        21.47        13.91        29.46        13.64 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-93-A4JN 
       10.19        12.23        27.68         7.36        16.60        23.61 
TCGA-95-7039 TCGA-95-7944 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8176 
       41.82        12.39        42.25        61.48        18.54        15.39 
TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M1 TCGA-99-7458 TCGA-J2-A4AG TCGA-L9-A5IP 
       16.41        20.58        19.76        24.56        32.48         1.91 
TCGA-L9-A7SV TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-NJ-A55O 
       18.58        58.45        58.85         0.43 

$`AMP PEAK  1(1P34.3) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 
       19.96        14.01         9.96        20.05         9.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       15.02        28.41        11.64        26.30        43.53        38.10 
TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       42.08        23.93        27.78        86.01        18.31        29.00 
TCGA-44-7671 TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 
       29.23        11.08        17.16        11.64        37.32        40.60 
TCGA-50-5935 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 
       21.47        48.62         5.79         7.99        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
       21.44         6.15        19.66        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 
       32.12        18.15        13.68        16.93        20.58        19.59 
TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       20.65        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       10.55        13.71         1.45         6.12        17.29        16.54 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       20.52        17.75        20.68        23.80         6.35        10.09 
TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
       21.83         5.29        31.23         2.43        10.09        50.07 
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-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       19.00         2.99        14.96        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5715 
       26.01        25.02        24.00         4.96        29.00         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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2665 TCGA-44-2666 
       37.71        44.61         4.37        46.98        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        33.73        26.56 
TCGA-44-5643 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-7659 
       33.30        19.56        23.15        21.63        32.45        22.72 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
        7.17        36.07        23.64        12.66         8.55        15.98 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
        9.44        11.54        13.64        76.21        28.11        28.57 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 TCGA-49-6767 
       35.54        32.84         8.81        55.89        53.29        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
       22.26        73.12        62.24         8.55        40.41       123.58 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
      164.12         9.86       101.72        15.72        60.16        47.41 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 
        9.27        78.67         8.45        15.12        60.72        42.35 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.99        36.79        27.25        30.54        13.94        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
       38.73        67.89        30.58        14.30        80.52        42.51 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       15.25        46.03         3.88        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 
      107.21        20.02        27.09        32.71         3.91        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       25.41        18.64        11.28        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       19.82        29.23        29.72        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       17.79        15.65        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
       14.47         0.36        17.72        19.96        26.01        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 
        0.92        15.81        39.98        42.38        14.60        49.25 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        54.35        67.96        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
       40.96        29.92        39.09        81.80        37.02        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 
        2.04        42.90        28.47        20.05        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
       14.73         5.72         4.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
        5.42         7.56         6.05         4.41        13.41        14.01 
TCGA-69-8255 TCGA-69-8453 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        4.24        26.73        23.38        26.30        15.35         4.31 
TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 
       30.31         1.25        50.33        11.18        66.64        77.85 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7146 TCGA-78-7148 
       49.84        36.66       100.57       163.10         5.69        20.58 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95       119.51        19.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       64.90        22.92        26.53         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.35       232.18        39.75        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
        5.88        31.13        34.39        20.55        19.89        35.24 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 
       37.74         4.57        24.33        32.65        31.04        14.60 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       11.61        30.84        27.58         0.62        28.34        26.50 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
        3.81        24.23        26.47        10.62        41.36         1.97 
TCGA-91-6835 TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        2.60         1.15        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 
       17.46         1.08        19.00        18.67        27.29         2.76 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 
       19.89        64.60        63.52        25.48         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 
       18.67         5.39        18.12        14.30        21.60        21.44 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.84        18.67        34.85        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W 
       21.63        18.08        35.47        19.00        14.30        14.53 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 
       15.65        38.63         2.76        86.14        49.35        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        24.36 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.10        11.15        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.13         1.64        47.08         0.49        19.82        20.28 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                         0.43                          0.00 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                       238.29                        232.18 
  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE 
                       23.705                        20.695 
[1] "0.4 - 238.3 (23.7)" "0.0 - 232.2 (20.7)"
[1] "hr=" "1.2"
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  1(1P34.3) MUTATED         3       31       39        0        19
  AMP PEAK  1(1P34.3) WILD-TYPE       2      102      100        1        31
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  1(1P34.3) MUTATED          18         15          3        7
  AMP PEAK  1(1P34.3) WILD-TYPE        54         57          8       18
D1V3, multiclass
            clus
vv           AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            31                           102
  STAGE IB                            39                           100
  STAGE II                             0                             1
  STAGE IIA                           19                            31
  STAGE IIB                           18                            54
  STAGE IIIA                          15                            57
  STAGE IIIB                           3                             8
  STAGE IV                             7                            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  1(1P34.3) MUTATED    40  82  10   5
  AMP PEAK  1(1P34.3) WILD-TYPE 131 196  36  14
D1V4, multiclass
    clus
vv   AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  T1                          40                           131
  T2                          82                           196
  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
  AMP PEAK  1(1P34.3) MUTATED    84  33    15
  AMP PEAK  1(1P34.3) WILD-TYPE 249  63    61
D1V5, multiclass
       clus
vv      AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  N0                             84                           249
  N1                             33                            63
  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"
D1V6, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED    90   7
  AMP PEAK  1(1P34.3) WILD-TYPE 259  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED     90    7
  AMP PEAK  1(1P34.3) WILD-TYPE  259   18
   clus
vv  AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  0                          90                           259
  1                           7                            18
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED    79  58
  AMP PEAK  1(1P34.3) WILD-TYPE 197 182
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED     79   58
  AMP PEAK  1(1P34.3) WILD-TYPE  197  182
        clus
vv       AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  FEMALE                          79                           197
  MALE                            58                           182
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P34.3) MUTATED   116  14
  AMP PEAK  1(1P34.3) WILD-TYPE 294  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED    116   14
  AMP PEAK  1(1P34.3) WILD-TYPE  294   46
     clus
vv    AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  NO                          116                           294
  YES                          14                            46
[1] 2 2
[1] FALSE
D1V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  1(1P34.3) MUTATED                            5
  AMP PEAK  1(1P34.3) WILD-TYPE                         13
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  1(1P34.3) MUTATED                                  20
  AMP PEAK  1(1P34.3) WILD-TYPE                                87
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  1(1P34.3) MUTATED                                                   94
  AMP PEAK  1(1P34.3) WILD-TYPE                                                227
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  1(1P34.3) MUTATED                                            1
  AMP PEAK  1(1P34.3) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  1(1P34.3) MUTATED                                               6
  AMP PEAK  1(1P34.3) WILD-TYPE                                            13
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  1(1P34.3) MUTATED                                0
  AMP PEAK  1(1P34.3) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  1(1P34.3) MUTATED                                    1
  AMP PEAK  1(1P34.3) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  1(1P34.3) MUTATED                              0
  AMP PEAK  1(1P34.3) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  1(1P34.3) MUTATED                               6
  AMP PEAK  1(1P34.3) WILD-TYPE                            17
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  1(1P34.3) MUTATED                                 0
  AMP PEAK  1(1P34.3) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  1(1P34.3) MUTATED                                               1
  AMP PEAK  1(1P34.3) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  1(1P34.3) MUTATED                              3
  AMP PEAK  1(1P34.3) WILD-TYPE                            7
D1V10, multiclass
                                                    clus
vv                                                   AMP PEAK  1(1P34.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          94
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                6
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           1
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                6
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  MUCINOUS (COLLOID) CARCINOMA                                                 3
                                                    clus
vv                                                   AMP PEAK  1(1P34.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             87
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           227
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 13
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 17
  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"
D1V11, continuous
D1V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1P34.3) MUTATED    84   7   1   6
  AMP PEAK  1(1P34.3) WILD-TYPE 260   6   3  20
D1V13, multiclass
    clus
vv   AMP PEAK  1(1P34.3) MUTATED AMP PEAK  1(1P34.3) WILD-TYPE
  R0                          84                           260
  R1                           7                             6
  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  1(1P34.3) MUTATED                                  0     2
  AMP PEAK  1(1P34.3) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P34.3) MUTATED                          17   105
  AMP PEAK  1(1P34.3) WILD-TYPE                        35   285
D1V14, multiclass
                                  clus
vv                                 AMP PEAK  1(1P34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    105
                                  clus
vv                                 AMP PEAK  1(1P34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   35
  WHITE                                                      285
[1] 4 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(1P34.3) MUTATED     2  99
  AMP PEAK  1(1P34.3) WILD-TYPE   5 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.3) MUTATED      2   99
  AMP PEAK  1(1P34.3) WILD-TYPE    5  285
                        clus
vv                       AMP PEAK  1(1P34.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          99
                        clus
vv                       AMP PEAK  1(1P34.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           285
[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   233 138
  AMP PEAK  2(1Q21.3) WILD-TYPE  90  43
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          371                           133 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                          138                            43 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-5420 TCGA-38-4629 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       26.01        15.02        28.41        14.73        26.30        43.53 
TCGA-44-2662 TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 
       42.08        27.78        86.01        29.00        29.23         9.37 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN 
       11.08        46.72        16.04        11.64       156.66        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6979 
       40.60        21.47        41.69        23.05        48.62         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 TCGA-55-7914 TCGA-55-8203 TCGA-55-8207 
        7.99        16.01        14.53         6.15        17.98        32.12 
TCGA-55-8511 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-4658 
       18.15        22.65        19.59        20.19        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 
       82.68        39.09         8.48        50.24        85.32        13.71 
TCGA-91-7771 TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK 
       16.18         6.12        16.54         2.86        15.68        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 
       18.18        17.92        20.19        17.75        20.68        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC 
        6.35        10.09        21.83        27.19         5.29         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4430 
       47.05         2.99        14.96        12.00        30.02        25.02 
TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 
       25.02         4.96        29.00        22.03         9.04         2.04 
TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 
        0.46         5.98         8.68        97.74        49.05        44.61 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2665 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 
       46.98        44.94        42.77        25.02        38.89        34.06 
TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6775 TCGA-44-6777 
       26.56        28.37        28.01        23.77        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 
       61.28        16.44        22.72        19.46         7.17        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SS TCGA-44-A4SU 
       23.64        12.66        15.32         9.44        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 
       32.84         8.81        29.46        29.75        53.29        55.33 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
       22.26        22.26        62.24        28.90         8.55        40.41 
TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      123.58       221.33         9.86        20.52        71.47       101.72 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       15.72        47.41        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
       78.67         8.45        48.46        57.53        53.16         3.91 
TCGA-50-6593 TCGA-50-7109 TCGA-50-8457 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       11.05        10.13        36.99        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       13.94        35.21        30.58        80.52         5.62        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       15.25        46.03        53.65        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 
       92.81        24.99        70.26        28.67        20.02        32.71 
TCGA-55-7576 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 
       22.03        25.41        18.64        11.28        34.19        18.44 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 TCGA-55-8301 TCGA-55-8507 TCGA-55-8508 
       23.64        29.19        22.16        17.56        13.74        20.28 
TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z 
       17.72        17.10        14.66         1.58        20.71        21.40 
TCGA-55-A490 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 
        3.25        15.81        19.99        17.95         4.57        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-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       72.30        39.25        56.81        81.80        37.02        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 
       87.98        42.90        28.41        51.25        20.05        18.84 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       12.66        14.73         5.72         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
       13.61         5.42         7.56        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       13.45        19.43         8.42        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS 
        4.31        30.31         9.24         1.25        50.33        11.18 
TCGA-75-5147 TCGA-75-6206 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7146 
       43.82        85.15       108.66       100.57       163.10         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       19.27        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
      104.19       238.29        88.14        26.53        31.20         8.02 
TCGA-78-7537 TCGA-78-7539 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       53.33        26.01       232.18        77.59       110.50        93.11 
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        38.04        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        35.24        37.74         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       22.82        32.65        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       14.60        11.61        30.84         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6829 
       29.46         3.81        24.23        13.64        10.62        41.36 
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-91-8497 TCGA-91-8499 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       14.27         1.18        17.46        23.61         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       41.82        18.67        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       42.25        64.60        61.48        25.48        18.54         0.59 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       18.67         5.39        15.39        14.30        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A5IP 
        1.45        21.57        18.08        32.48        19.00         1.91 
TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T6 
       18.58        38.63         2.76        86.14        58.45        58.85 
TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK 
        5.49        29.46        11.05        24.36        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        74.33         0.13         1.64        47.08 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.43        19.82        20.28        59.11        16.87 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-05-4434 TCGA-38-4630 TCGA-38-4631 TCGA-44-2661 TCGA-44-6146 TCGA-44-7661 
       15.02        35.28        11.64        38.10        23.93        18.31 
TCGA-49-6745 TCGA-55-6978 TCGA-55-7724 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 
       17.16         5.79        23.18        21.44        19.66        19.73 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8619 TCGA-55-8621 TCGA-55-A491 TCGA-64-1677 
       16.93        19.69        13.68        16.93        20.58        20.65 
TCGA-78-8660 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7948 TCGA-97-A4M2 TCGA-J2-8192 
       10.55         1.45        17.29        15.65        20.52        24.30 
TCGA-MP-A4TA TCGA-05-4397 TCGA-05-4403 TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 
       31.23        24.03        19.00        29.98        21.99        26.01 
TCGA-05-4433 TCGA-35-4122 TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F TCGA-44-2657 
       24.00         7.40       120.79        37.71         4.37        44.42 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-5643 TCGA-44-6145 
        3.19        37.15        38.24        33.73        33.30        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-7667 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G 
       23.15        21.63        36.07         8.55        15.98        11.54 
TCGA-49-4514 TCGA-49-AAR2 TCGA-49-AARR TCGA-50-5055 TCGA-50-5939 TCGA-50-5942 
       55.89        73.12       164.12        60.16        15.12        60.72 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8459 
       42.35        25.55        12.16         6.21         0.72        36.79 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6968 TCGA-55-6975 TCGA-55-6985 
       38.73        67.89        14.30        42.51         3.88        40.54 
TCGA-55-6986 TCGA-55-7570 TCGA-55-7727 TCGA-55-7728 TCGA-55-7911 TCGA-55-7994 
      107.21        27.09         3.91        23.15        17.65        19.82 
TCGA-55-8097 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8512 
       15.65        15.42        15.72        14.47         0.36        19.96 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8620 TCGA-55-A493 TCGA-62-8395 TCGA-62-8397 
       26.01        17.62        12.33         0.92        39.98        42.38 
TCGA-62-8402 TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-5775 
       49.25        13.61        40.96        29.92        39.09         2.04 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-6216 TCGA-69-7974 TCGA-69-7978 
       28.47        20.05        14.04         4.64         6.05         4.41 
TCGA-69-8255 TCGA-69-8453 TCGA-75-5125 TCGA-75-5146 TCGA-75-6212 TCGA-75-6214 
        4.24        26.73        66.64        77.85        49.84        36.66 
TCGA-78-7145 TCGA-78-7155 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-83-5908 
       27.16        38.50        39.35        10.55        39.75        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-A4BD TCGA-93-7347 TCGA-97-7552 TCGA-97-7941 TCGA-97-8175 
        7.36        19.82        22.45        63.52        15.91        18.12 
TCGA-97-8177 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A50W 
       16.41        36.76        21.63        35.47        14.30        14.53 
TCGA-L9-A8F4 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TI 
       15.65        49.35        37.35        86.04        41.59        14.10 
TCGA-NJ-A55A 
        0.49 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.00                          0.36 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       238.29                        164.12 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        21.83                         21.44 
[1] "0.0 - 238.3 (21.8)" "0.4 - 164.1 (21.4)"
[1] "hr=" "1"  
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  2(1Q21.3) MUTATED         4       99      100        1        40
  AMP PEAK  2(1Q21.3) WILD-TYPE       1       34       39        0        10
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  2(1Q21.3) MUTATED          46         51         11       19
  AMP PEAK  2(1Q21.3) WILD-TYPE        26         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                            34
  STAGE IB                           100                            39
  STAGE II                             1                             0
  STAGE IIA                           40                            10
  STAGE IIB                           46                            26
  STAGE IIIA                          51                            21
  STAGE IIIB                          11                             0
  STAGE IV                            19                             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   123 205  31  16
  AMP PEAK  2(1Q21.3) WILD-TYPE  48  73  15   3
D2V4, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  T1                         123                            48
  T2                         205                            73
  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   239  72    56
  AMP PEAK  2(1Q21.3) WILD-TYPE  94  24    20
D2V5, multiclass
       clus
vv      AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  N0                            239                            94
  N1                             72                            24
  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   259  19
  AMP PEAK  2(1Q21.3) WILD-TYPE  90   6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    259   19
  AMP PEAK  2(1Q21.3) WILD-TYPE   90    6
   clus
vv  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  0                         259                            90
  1                          19                             6
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED   195 182
  AMP PEAK  2(1Q21.3) WILD-TYPE  81  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    195  182
  AMP PEAK  2(1Q21.3) WILD-TYPE   81   58
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                         195                            81
  MALE                           182                            58
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED   301  46
  AMP PEAK  2(1Q21.3) WILD-TYPE 109  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED    301   46
  AMP PEAK  2(1Q21.3) WILD-TYPE  109   14
     clus
vv    AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  NO                          301                           109
  YES                          46                            14
[1] 2 2
[1] FALSE
D2V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  2(1Q21.3) MUTATED                           15
  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                                                  230
  AMP PEAK  2(1Q21.3) WILD-TYPE                                                 91
                               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
D2V10, multiclass
                                                    clus
vv                                                   AMP PEAK  2(1Q21.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         230
  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)                            91
  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"
D2V11, continuous
D2V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(1Q21.3) MUTATED   246  10   2  22
  AMP PEAK  2(1Q21.3) WILD-TYPE  98   3   2   4
D2V13, multiclass
    clus
vv   AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  R0                         246                            98
  R1                          10                             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                          40   283
  AMP PEAK  2(1Q21.3) WILD-TYPE                        12   107
D2V14, multiclass
                                  clus
vv                                 AMP PEAK  2(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 40
  WHITE                                                    283
                                  clus
vv                                 AMP PEAK  2(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                      107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V15, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     5 278
  AMP PEAK  2(1Q21.3) WILD-TYPE   2 106
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      5  278
  AMP PEAK  2(1Q21.3) WILD-TYPE    2  106
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         278
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           106
[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    99  69
  AMP PEAK  3(3Q26.2) WILD-TYPE 224 112
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                          168                           336 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                           69                           112 
$`AMP PEAK  3(3Q26.2) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 
       19.96         8.02        26.01        15.02        15.02        35.28 
TCGA-38-4631 TCGA-44-2662 TCGA-44-7670 TCGA-49-AAR0 TCGA-49-AARN TCGA-55-7284 
       11.64        42.08        29.00       156.66        37.32         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-8205 TCGA-55-A491 TCGA-55-A4DF 
       16.01        23.18        21.44        19.69        20.58        20.19 
TCGA-64-1677 TCGA-80-5611 TCGA-91-7771 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       20.65        85.32        16.18         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-97-A4LX TCGA-L9-A443 TCGA-L9-A444 TCGA-05-4250 
        2.86        15.68        20.19         6.35        10.09         3.98 
TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4417 TCGA-05-4420 
       45.01         0.00        24.03        47.05        14.96        29.98 
TCGA-05-4424 TCGA-05-4430 TCGA-05-5425 TCGA-05-5429 TCGA-35-4122 TCGA-35-5375 
       30.02        25.02        29.00         9.04         7.40         8.68 
TCGA-38-4626 TCGA-38-4628 TCGA-44-2668 TCGA-44-3918 TCGA-44-5643 TCGA-44-6145 
      120.79        49.05        25.02        34.06        33.30        19.56 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7669 TCGA-44-7672 TCGA-44-A47B TCGA-49-4487 
       16.44        19.46        18.87        23.64         9.44        28.11 
TCGA-49-4488 TCGA-49-4507 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAR9 
       28.57         8.81        53.29        55.33        22.26         8.55 
TCGA-49-AARQ TCGA-50-5055 TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 TCGA-50-5946 
      221.33        60.16         8.22        14.27        48.46        53.16 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1594 
        3.91        25.55         6.21        34.29        35.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6972 
       67.89        30.58        80.52        42.51        40.73        53.65 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 
       24.99        40.54        70.26        25.41        11.28        34.19 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8094 TCGA-55-8208 
       18.44        19.82        29.23        29.72        17.79        22.16 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8614 TCGA-55-8620 TCGA-55-A490 TCGA-55-A493 
       13.74        20.28        17.62        12.33         3.25         0.92 
TCGA-62-8394 TCGA-62-A46O TCGA-62-A46P TCGA-62-A470 TCGA-64-1676 TCGA-64-1679 
        4.57        47.80        19.53        39.25        56.81        81.80 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-69-7760 TCGA-69-7761 TCGA-69-7978 
       51.25        28.47        20.05         6.64         6.12         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 
       13.41        13.51        19.43         8.42        23.38        26.30 
TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5147 
       15.35         9.24        50.33        11.18        66.64        43.82 
TCGA-75-6214 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7154 
       36.66       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        26.01        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        32.78         4.08 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8358 TCGA-86-8669 TCGA-86-8673 
        0.79        22.82        31.04        21.47        30.84        28.34 
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-91-8497 TCGA-91-8499 TCGA-93-A4JN TCGA-95-7039 TCGA-95-7567 TCGA-95-8494 
       14.27         1.18        23.61        41.82        18.67         2.76 
TCGA-97-7553 TCGA-97-8176 TCGA-J2-A4AD TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV 
       61.48        15.39        18.08        15.65        38.63        86.14 
TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-O1-A52J TCGA-S2-AA1A 
       11.05        11.15        19.13        71.05        59.11        16.87 

$`AMP PEAK  3(3Q26.2) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-38-4629 TCGA-38-6178 
       14.01         9.96        20.05         9.01        28.41        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       26.30        43.53        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       18.31        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 
       48.62         5.79         7.79        14.53         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       19.73        17.98        16.93        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       16.93        22.65        19.59        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-6836 TCGA-91-A4BC 
       39.09         8.48        50.24        10.55        13.71         1.45 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 
       15.65        21.40        18.18        17.92        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 
       20.68        24.30        23.80        21.83        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4390 TCGA-05-4403 
       31.23         2.43        10.09        50.07        37.02        19.00 
TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4432 TCGA-05-4433 
        2.99        12.00        21.99        26.01        25.02        24.00 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4625 
        4.96        22.03         2.04         0.46         5.98        97.74 
TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       37.71        44.61         4.37        46.98        44.42        44.94 
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        33.73 
TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6148 TCGA-44-6774 
       26.56        28.37        28.01        23.77        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 
       23.18        32.45        61.28        22.72         7.17        36.07 
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-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       13.45        76.21        12.66        35.54        14.07        32.84 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       29.46        29.75        55.89        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       28.90        40.41       123.58       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
       71.47       101.72        15.72        47.41        49.28         9.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
       78.67         8.45        15.12        60.72        57.53        42.35 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       11.05        12.16         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-6543 TCGA-55-6712 TCGA-55-6970 
       27.25        30.54        13.94        14.30         5.62        15.25 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       46.03         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
      107.21        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7911 TCGA-55-8087 TCGA-55-8089 
        3.91        23.15        18.64        17.65        15.19        23.08 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 
        5.06        23.64        15.65        29.19        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
       15.72        14.47         0.36        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A494 
       17.10        14.66         1.58        20.71        21.40        15.81 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
       19.99        17.95        39.98        42.38        14.60        88.64 
TCGA-62-8402 TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       49.25        56.71        54.35        67.96        72.30        13.61 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       40.96        29.92        39.09        37.02        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
        2.04        42.90        28.41        20.05        18.84        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-7764 
       12.66        14.73         5.72         4.64        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        5.42         7.56         6.05        14.01        13.45         4.24 
TCGA-69-8453 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-75-5146 TCGA-75-6206 
       26.73         4.31        30.31         1.25        77.85        85.15 
TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 
       49.84       108.66       100.57        20.58       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
       39.95       119.51        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
        9.57       104.19       238.29        88.14        31.20         8.02 
TCGA-78-7537 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 
       53.33        10.55       232.18        39.75        77.59        93.11 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 
       38.04        20.55        19.89        35.24        37.74         4.57 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
       24.33        32.65        31.20        23.05        14.60        11.61 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       13.91        27.58         0.62        26.50        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6831 TCGA-91-6847 TCGA-91-6849 
       24.23        13.64        26.47        10.19        27.68         1.15 
TCGA-91-8496 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP 
       16.60        19.82        22.45        17.46         1.08        19.00 
TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       12.39        27.29        19.89        42.25        64.60        63.52 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       25.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       18.12        16.41        14.30        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        21.63        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4SW 
       14.30        14.53         1.91        18.58         2.76        58.45 
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-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       29.46        24.36        14.10        73.91        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        47.08         0.49         0.43        19.82        20.28 

  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                         0.00                          0.13 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                       221.33                        238.29 
  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE 
                       21.455                        21.630 
[1] "0.0 - 221.3 (21.5)" "0.1 - 238.3 (21.6)"
[1] "hr=" "1.3"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  3(3Q26.2) MUTATED         2       42       43        0        21
  AMP PEAK  3(3Q26.2) WILD-TYPE       3       91       96        1        29
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  3(3Q26.2) MUTATED          25         20          3       11
  AMP PEAK  3(3Q26.2) WILD-TYPE        47         52          8       14
D3V3, multiclass
            clus
vv           AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            42                            91
  STAGE IB                            43                            96
  STAGE II                             0                             1
  STAGE IIA                           21                            29
  STAGE IIB                           25                            47
  STAGE IIIA                          20                            52
  STAGE IIIB                           3                             8
  STAGE IV                            11                            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  3(3Q26.2) MUTATED    55  94  15   5
  AMP PEAK  3(3Q26.2) WILD-TYPE 116 184  31  14
D3V4, multiclass
    clus
vv   AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  T1                          55                           116
  T2                          94                           184
  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 223  58    56
D3V5, multiclass
       clus
vv      AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  N0                            110                           223
  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   109  11
  AMP PEAK  3(3Q26.2) WILD-TYPE 240  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q26.2) MUTATED    109   11
  AMP PEAK  3(3Q26.2) WILD-TYPE  240   14
   clus
vv  AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  0                         109                           240
  1                          11                            14
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(3Q26.2) MUTATED    91  78
  AMP PEAK  3(3Q26.2) WILD-TYPE 185 162
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q26.2) MUTATED     91   78
  AMP PEAK  3(3Q26.2) WILD-TYPE  185  162
        clus
vv       AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  FEMALE                          91                           185
  MALE                            78                           162
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(3Q26.2) MUTATED   132  19
  AMP PEAK  3(3Q26.2) WILD-TYPE 278  41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q26.2) MUTATED    132   19
  AMP PEAK  3(3Q26.2) WILD-TYPE  278   41
     clus
vv    AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  NO                          132                           278
  YES                          19                            41
[1] 2 2
[1] FALSE
D3V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  3(3Q26.2) MUTATED                            7
  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                                                209
                               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
D3V10, multiclass
                                                    clus
vv                                                   AMP PEAK  3(3Q26.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   7
  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)                           209
  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"
D3V11, continuous
D3V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(3Q26.2) MUTATED   115   3   3   9
  AMP PEAK  3(3Q26.2) WILD-TYPE 229  10   1  17
D3V13, multiclass
    clus
vv   AMP PEAK  3(3Q26.2) MUTATED AMP PEAK  3(3Q26.2) WILD-TYPE
  R0                         115                           229
  R1                           3                            10
  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
  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                          16   123
  AMP PEAK  3(3Q26.2) WILD-TYPE                        36   267
D3V14, multiclass
                                  clus
vv                                 AMP PEAK  3(3Q26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    123
                                  clus
vv                                 AMP PEAK  3(3Q26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   36
  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"
D3V15, binary
                               cls
clus                              0   1
  AMP PEAK  3(3Q26.2) MUTATED     4 121
  AMP PEAK  3(3Q26.2) WILD-TYPE   3 263
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q26.2) MUTATED      4  121
  AMP PEAK  3(3Q26.2) WILD-TYPE    3  263
                        clus
vv                       AMP PEAK  3(3Q26.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         121
                        clus
vv                       AMP PEAK  3(3Q26.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           263
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(4Q12) MUTATION ANALYSIS
D4V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  4(4Q12) MUTATED    59  34
  AMP PEAK  4(4Q12) WILD-TYPE 264 147
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                         93                         411 
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                         34                         147 
$`AMP PEAK  4(4Q12) MUTATED`
TCGA-38-4629 TCGA-38-6178 TCGA-44-2662 TCGA-44-7661 TCGA-44-7670 TCGA-55-1592 
       28.41        14.73        42.08        18.31        29.00        23.05 
TCGA-55-1595 TCGA-55-7573 TCGA-55-8091 TCGA-55-A4DF TCGA-73-4662 TCGA-80-5611 
       48.62        16.01        19.73        20.19        82.68        85.32 
TCGA-95-7948 TCGA-J2-8194 TCGA-05-4420 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 
       15.65        23.80        29.98        25.02         4.96        29.00 
TCGA-38-4628 TCGA-44-2656 TCGA-44-2659 TCGA-44-4112 TCGA-44-5645 TCGA-44-6775 
       49.05        46.98        44.94        26.56        28.01        23.18 
TCGA-44-6778 TCGA-44-8117 TCGA-44-A4SU TCGA-49-4507 TCGA-49-AARQ TCGA-50-6590 
       61.28        12.66        13.45         8.81       221.33        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 
        3.91        25.55        12.16        34.29        13.94        38.73 
TCGA-55-1596 TCGA-55-6712 TCGA-55-7283 TCGA-55-7576 TCGA-55-7995 TCGA-55-8089 
       67.89         5.62        20.02        22.03        29.23        23.08 
TCGA-55-8092 TCGA-55-8620 TCGA-55-A490 TCGA-55-A493 TCGA-55-A57B TCGA-62-8402 
        5.06        12.33         3.25         0.92        17.95        49.25 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1680 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
       40.96        56.81        37.02        13.41        13.51        14.01 
TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6214 TCGA-78-7143 
       11.18        77.85        43.82        85.15        36.66       163.10 
TCGA-78-7145 TCGA-78-7150 TCGA-78-7154 TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 
       27.16        21.90        19.50         9.57       238.29        31.20 
TCGA-78-7542 TCGA-78-8662 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8074 
       10.55       110.50        32.78        35.24        37.74         0.79 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8669 TCGA-86-8673 TCGA-86-A456 TCGA-91-6848 
       31.04        31.20        30.84        28.34        29.46         7.36 
TCGA-91-8499 TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-8494 TCGA-97-7937 
        1.18        19.00        41.82        18.67         2.76        18.54 
TCGA-97-8179 TCGA-L4-A4E5 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T6 
       14.30        19.00         2.76        58.45        49.35        58.85 
TCGA-MP-A4TF TCGA-MP-A4TK TCGA-NJ-A4YF 
       11.05        19.13        71.05 

$`AMP PEAK  4(4Q12) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 
       26.01        15.02        15.02        35.28        11.64        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7671 
       43.53        38.10        23.93        27.78        86.01        29.23 
TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 
        9.37        11.08        46.72        16.04        17.16        11.64 
TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-6978 
      156.66        37.32        40.60        21.47        41.69         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.79         7.99        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
       19.66        17.98        16.93        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 
       13.68        16.93        22.65        20.58        19.59        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       13.87        52.60        39.09         8.48        50.24        10.55 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
        2.86        15.68        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A444 
       20.52        17.75        20.68        24.30         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       21.83        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       50.07         3.98        45.01        37.02         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
       47.05        19.00         2.99        14.96        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5428 TCGA-05-5429 
       21.99        26.01        25.02        24.00        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        2.04         0.46         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 
      120.79        37.71        44.61         4.37        44.42        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-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.73        33.30        28.37        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       21.63        32.45        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       36.07        18.87        23.64         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
        9.44        11.54        13.64        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 
       12.66        35.54        14.07        32.84        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 
       55.89        53.29        55.33        22.26        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARR 
       62.24        28.90         8.55        40.41       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       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
        8.45        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       11.05         6.21         0.72        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       27.25        30.54        35.21        30.58        14.30        80.52 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 
      107.21        70.26        28.67        27.09        32.71         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       23.15        25.41        18.64        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8094 TCGA-55-8096 
       18.44        19.82        29.72        15.19        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       14.47         0.36        13.74        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y 
       26.01        17.10        17.62        14.66         1.58        20.71 
TCGA-55-A48Z TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       21.40        15.81        19.99         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       14.60        88.64        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1678 
       67.96        72.30        13.61        39.25        29.92        39.09 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       51.25        28.47        20.05        20.05        18.84        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       12.66        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
       22.68        13.61         5.42         7.56         6.05         4.41 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
       13.45         4.24        26.73        19.43         8.42        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.30        15.35         4.31        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 
       50.33        66.64        49.84       108.66       100.57         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
       19.27        20.58       129.53        39.95       119.51        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7167 
       32.09         5.88        64.90        22.92       104.19        88.14 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8640 
       26.53         8.02        53.33        26.01        39.35       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       39.75        77.59        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8055 
       31.13        34.39        38.04        20.55        19.89         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8280 TCGA-86-8358 
        4.57        24.33        22.82        32.65        23.05        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
       14.60        11.61        13.91        27.58         0.62        26.50 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
        3.81        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
        1.97        10.19         2.60        12.23        27.68         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       16.60        14.27        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
        1.08        12.39        27.29        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       63.52        61.48        25.48         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 
        5.39        18.12        15.39        16.41        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         1.45        21.57        21.63        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
       32.48        14.30        14.53         1.91        18.58        15.65 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
       38.63        86.14        37.35        86.04         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG 
       29.46        24.36        14.10        11.15        73.91        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                       0.79                        0.00 
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                     238.29                      232.18 
  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE 
                      25.55                       21.40 
[1] "0.8 - 238.3 (25.6)" "0.0 - 232.2 (21.4)"
[1] "hr=" "1.1"
D4V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  4(4Q12) MUTATED         3       19       28        0         8
  AMP PEAK  4(4Q12) WILD-TYPE       2      114      111        1        42
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  4(4Q12) MUTATED          21         10          1        6
  AMP PEAK  4(4Q12) WILD-TYPE        51         62         10       19
D4V3, multiclass
            clus
vv           AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  STAGE I                            3                           2
  STAGE IA                          19                         114
  STAGE IB                          28                         111
  STAGE II                           0                           1
  STAGE IIA                          8                          42
  STAGE IIB                         21                          51
  STAGE IIIA                        10                          62
  STAGE IIIB                         1                          10
  STAGE IV                           6                          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  4(4Q12) MUTATED    26  56  11   2
  AMP PEAK  4(4Q12) WILD-TYPE 145 222  35  17
D4V4, multiclass
    clus
vv   AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  T1                        26                         145
  T2                        56                         222
  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
  AMP PEAK  4(4Q12) MUTATED    61  23    10
  AMP PEAK  4(4Q12) WILD-TYPE 272  73    66
D4V5, multiclass
       clus
vv      AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  N0                           61                         272
  N1                           23                          73
  N2+N3                        10                          66
[1] 3 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(4Q12) MUTATED    68   6
  AMP PEAK  4(4Q12) WILD-TYPE 281  19
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(4Q12) MUTATED     68    6
  AMP PEAK  4(4Q12) WILD-TYPE  281   19
   clus
vv  AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  0                        68                         281
  1                         6                          19
[1] 2 2
[1] FALSE
D4V7, binary
                             cls
clus                            0   1
  AMP PEAK  4(4Q12) MUTATED    49  47
  AMP PEAK  4(4Q12) WILD-TYPE 227 193
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(4Q12) MUTATED     49   47
  AMP PEAK  4(4Q12) WILD-TYPE  227  193
        clus
vv       AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  FEMALE                        49                         227
  MALE                          47                         193
[1] 2 2
[1] FALSE
D4V8, binary
                             cls
clus                            0   1
  AMP PEAK  4(4Q12) MUTATED    81   9
  AMP PEAK  4(4Q12) WILD-TYPE 329  51
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(4Q12) MUTATED     81    9
  AMP PEAK  4(4Q12) WILD-TYPE  329   51
     clus
vv    AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  NO                         81                         329
  YES                         9                          51
[1] 2 2
[1] FALSE
D4V9, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  4(4Q12) MUTATED                            3
  AMP PEAK  4(4Q12) WILD-TYPE                         15
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  4(4Q12) MUTATED                                  13
  AMP PEAK  4(4Q12) WILD-TYPE                                94
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  4(4Q12) MUTATED                                                   71
  AMP PEAK  4(4Q12) WILD-TYPE                                                250
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  4(4Q12) MUTATED                                            0
  AMP PEAK  4(4Q12) WILD-TYPE                                          5
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  4(4Q12) MUTATED                                               4
  AMP PEAK  4(4Q12) WILD-TYPE                                            15
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  4(4Q12) MUTATED                                1
  AMP PEAK  4(4Q12) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  4(4Q12) MUTATED                                    1
  AMP PEAK  4(4Q12) WILD-TYPE                                  2
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  4(4Q12) MUTATED                              0
  AMP PEAK  4(4Q12) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  4(4Q12) MUTATED                               2
  AMP PEAK  4(4Q12) WILD-TYPE                            21
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  4(4Q12) MUTATED                                 0
  AMP PEAK  4(4Q12) WILD-TYPE                               1
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  4(4Q12) MUTATED                                               1
  AMP PEAK  4(4Q12) WILD-TYPE                                             4
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  4(4Q12) MUTATED                              0
  AMP PEAK  4(4Q12) WILD-TYPE                           10
D4V10, multiclass
                                                    clus
vv                                                   AMP PEAK  4(4Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         13
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        71
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                 0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                              4
  LUNG CLEAR CELL ADENOCARCINOMA                                             1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                         1
  LUNG MUCINOUS ADENOCARCINOMA                                               0
  LUNG PAPILLARY ADENOCARCINOMA                                              2
  LUNG SIGNET RING ADENOCARCINOMA                                            0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                              1
  MUCINOUS (COLLOID) CARCINOMA                                               0
                                                    clus
vv                                                   AMP PEAK  4(4Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                  15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           94
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         250
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               15
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 2
  LUNG PAPILLARY ADENOCARCINOMA                                               21
  LUNG SIGNET RING ADENOCARCINOMA                                              1
  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"
D4V11, continuous
D4V12, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  4(4Q12) MUTATED    62   4   0   4
  AMP PEAK  4(4Q12) WILD-TYPE 282   9   4  22
D4V13, multiclass
    clus
vv   AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  R0                        62                         282
  R1                         4                           9
  R2                         0                           4
  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
  AMP PEAK  4(4Q12) MUTATED                                  0     4
  AMP PEAK  4(4Q12) WILD-TYPE                                1     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(4Q12) MUTATED                           9    69
  AMP PEAK  4(4Q12) WILD-TYPE                        43   321
D4V14, multiclass
                                  clus
vv                                 AMP PEAK  4(4Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                                9
  WHITE                                                   69
                                  clus
vv                                 AMP PEAK  4(4Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 43
  WHITE                                                    321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V15, binary
                             cls
clus                            0   1
  AMP PEAK  4(4Q12) MUTATED     3  68
  AMP PEAK  4(4Q12) WILD-TYPE   4 316
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(4Q12) MUTATED      3   68
  AMP PEAK  4(4Q12) WILD-TYPE    4  316
                        clus
vv                       AMP PEAK  4(4Q12) MUTATED AMP PEAK  4(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             3                           4
  NOT HISPANIC OR LATINO                        68                         316
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(5P15.33) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  5(5P15.33) MUTATED   211 113
  AMP PEAK  5(5P15.33) WILD-TYPE 112  68
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           324                            180 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                           113                             68 
$`AMP PEAK  5(5P15.33) MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-38-4629 TCGA-38-4631 
       19.96         9.96         8.02        20.05        28.41        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2662 TCGA-44-6147 TCGA-44-7670 
       14.73        26.30        43.53        42.08        27.78        29.00 
TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN 
        9.37        11.08        46.72        11.64       156.66        37.32 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6979 TCGA-55-7573 
       21.47        41.69        23.05        48.62         7.79        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-8091 TCGA-55-8204 TCGA-55-8207 
       23.18        14.53        21.44        19.73        16.93        32.12 
TCGA-55-8511 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       18.15        22.65        20.58        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 
       52.60        82.68         8.48        50.24        85.32        13.71 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
        1.45         6.12        17.29        16.54         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A444 
       15.65        21.40        17.92        20.68        24.30        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD 
       21.83        27.19         5.29        31.23         2.43        10.09 
TCGA-05-4389 TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 
       45.01         0.00        47.05         2.99        29.98        12.00 
TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       30.02        26.01        25.02         4.96        29.00        22.03 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
        2.04         0.46         5.98         8.68       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2668 
       49.05        44.61        46.98        44.42        44.94        25.02 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 
       38.24        34.06        33.73        26.56        28.37        28.01 
TCGA-44-6144 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 
       23.77        21.63        23.18        32.45        61.28        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-A47A TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       15.32        13.64        76.21        28.11        28.57        12.66 
TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
       14.07        29.46        29.75        55.89        53.29        55.33 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO 
       22.26        22.26        73.12        28.90         8.55       123.58 
TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
      221.33         9.86        71.47       101.72        15.72        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 
       49.28         8.22         9.27        14.27        78.67        48.46 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       57.53        53.16         3.91        25.55        11.05        12.16 
TCGA-50-7109 TCGA-50-8457 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 
       10.13        36.99        34.29        30.54        13.94        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
       67.89        30.58        14.30         5.62        40.73        15.25 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 
       53.65        69.34        45.34        32.71        92.81        40.54 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7903 
       70.26        28.67        27.09        32.71         3.91        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 
       34.19        17.65        19.82        17.79        23.64        29.19 
TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       22.16        17.56        15.72         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       17.72        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 
       20.71         3.25         0.92        15.81        19.99         4.57 
TCGA-62-8395 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y 
       39.98        88.64        49.25        54.35        67.96        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        81.80        37.02        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-67-3770 TCGA-67-6215 TCGA-67-6216 
       87.98        42.90        51.25        20.05         5.72         4.64 
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 
       13.41        13.51        14.01         4.24        19.43         8.42 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       15.35        30.31         9.24        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6214 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       43.82        36.66       163.10        27.16         5.69        19.27 
TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 
      129.53       119.51        19.50        38.50        64.90        22.92 
TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 
      238.29        26.53        31.20         8.02        26.01       232.18 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        38.04        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 
        4.08        24.33         0.79        22.82        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       21.47        14.60        11.61        27.58         0.62        28.34 
TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6840 TCGA-91-6848 
        3.81        10.62        41.36         1.97        12.23         7.36 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP 
        1.18        19.82        22.45        17.46         1.08        19.00 
TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 
       41.82        18.67        27.29         2.76        42.25        64.60 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8171 TCGA-97-8174 
       61.48        25.48        18.54         0.59        18.67         5.39 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       15.39        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AD 
       18.67        24.56        34.85        36.76        21.57        18.08 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       35.47        19.00         1.91        18.58        15.65        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
        2.76        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-NJ-A4YF 
        5.49        41.59        11.05        24.36        19.13        71.05 
TCGA-NJ-A4YG TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       74.33         0.43        19.82        20.28        59.11        16.87 

$`AMP PEAK  5(5P15.33) WILD-TYPE`
TCGA-05-4384 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 
       14.01         9.01        26.01        15.02        15.02        35.28 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-49-6742 
       38.10        23.93        86.01        18.31        29.23        16.04 
TCGA-49-6745 TCGA-50-5932 TCGA-55-6978 TCGA-55-7284 TCGA-55-7914 TCGA-55-8090 
       17.16        40.60         5.79         7.99         6.15        19.66 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8619 TCGA-55-8621 TCGA-55-A492 TCGA-73-7498 
       17.98        19.69        13.68        16.93        19.59        39.09 
TCGA-78-8660 TCGA-91-7771 TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       10.55        16.18        18.18        20.19        20.52        17.75 
TCGA-J2-8194 TCGA-L9-A443 TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4397 
       23.80         6.35        50.07         3.98        37.02        24.03 
TCGA-05-4403 TCGA-05-4417 TCGA-05-4425 TCGA-05-4432 TCGA-05-4433 TCGA-05-5429 
       19.00        14.96        21.99        25.02        24.00         9.04 
TCGA-35-4122 TCGA-38-4625 TCGA-38-A44F TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 
        7.40        97.74         4.37        42.77         3.19        37.15 
TCGA-44-3917 TCGA-44-5643 TCGA-44-6145 TCGA-44-6148 TCGA-44-6779 TCGA-44-8120 
       38.89        33.30        19.56        23.15        16.44         8.55 
TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU TCGA-49-4494 TCGA-49-4506 
       15.98         9.44        11.54        13.45        35.54        32.84 
TCGA-49-4507 TCGA-49-AAR3 TCGA-49-AARE TCGA-49-AARR TCGA-50-5044 TCGA-50-5055 
        8.81        62.24        40.41       164.12        20.52        60.16 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 TCGA-50-6595 TCGA-50-6673 
        8.45        15.12        60.72        42.35         6.21         0.72 
TCGA-50-8459 TCGA-50-8460 TCGA-53-A4EZ TCGA-55-6642 TCGA-55-6968 TCGA-55-6971 
       36.79        27.25        35.21        80.52        42.51        46.03 
TCGA-55-6975 TCGA-55-6984 TCGA-55-6986 TCGA-55-7283 TCGA-55-7576 TCGA-55-7728 
        3.88        24.99       107.21        20.02        22.03        23.15 
TCGA-55-7815 TCGA-55-7907 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       25.41        11.28        18.44        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8097 TCGA-55-8299 TCGA-55-8505 TCGA-55-8512 
       23.08         5.06        15.65        15.42        14.47        19.96 
TCGA-55-8513 TCGA-55-A48Z TCGA-55-A57B TCGA-62-8397 TCGA-62-8398 TCGA-62-A46O 
       26.01        21.40        17.95        42.38        14.60        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46V TCGA-64-1676 TCGA-64-1678 TCGA-64-5775 
       19.53        56.71        72.30        56.81        39.09         2.04 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       28.41        28.47        20.05        18.84        14.04        12.66 
TCGA-67-4679 TCGA-69-7761 TCGA-69-7978 TCGA-69-8254 TCGA-69-8453 TCGA-73-4659 
       14.73         6.12         4.41        13.45        26.73        23.38 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4677 TCGA-73-A9RS TCGA-75-6206 TCGA-75-6212 
       26.30         4.31         1.25        11.18        85.15        49.84 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7156 
      108.66       100.57        20.58        21.90        39.95        32.09 
TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 
        5.88         9.57       104.19        88.14        53.33        39.35 
TCGA-78-7542 TCGA-78-8648 TCGA-86-7701 TCGA-86-7714 TCGA-86-8056 TCGA-86-8076 
       10.55        39.75        31.13        20.55         4.57        32.65 
TCGA-86-8278 TCGA-86-8668 TCGA-86-8669 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF 
       31.04        13.91        30.84        26.50        29.46        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 
       13.64        26.47        10.19         2.60        27.68         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-93-A4JN TCGA-95-7944 TCGA-95-A4VP TCGA-97-7552 
       16.60        14.27        23.61        12.39        19.89        63.52 
TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 TCGA-97-A4M5 TCGA-99-8032 TCGA-99-AA5R 
       15.91        18.12        16.41        20.84         1.45        21.63 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-MP-A4SV TCGA-MP-A4TE TCGA-MP-A4TI 
       32.48        14.30        14.53        86.14        29.46        14.10 
TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       11.15        73.91         0.13         1.64        47.08         0.49 

  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                          0.00                           0.13 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                        238.29                         164.12 
  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE 
                        22.355                         20.355 
[1] "0.0 - 238.3 (22.4)" "0.1 - 164.1 (20.4)"
[1] "hr=" "1.2"
D5V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  5(5P15.33) MUTATED         4       88       88        1        38
  AMP PEAK  5(5P15.33) WILD-TYPE       1       45       51        0        12
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  5(5P15.33) MUTATED          39         48          8       15
  AMP PEAK  5(5P15.33) WILD-TYPE        33         24          3       10
D5V3, multiclass
            clus
vv           AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                             88                             45
  STAGE IB                             88                             51
  STAGE II                              1                              0
  STAGE IIA                            38                             12
  STAGE IIB                            39                             33
  STAGE IIIA                           48                             24
  STAGE IIIB                            8                              3
  STAGE IV                             15                             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  5(5P15.33) MUTATED   115 179  24  13
  AMP PEAK  5(5P15.33) WILD-TYPE  56  99  22   6
D5V4, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  T1                          115                             56
  T2                          179                             99
  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  5(5P15.33) MUTATED   208  63    54
  AMP PEAK  5(5P15.33) WILD-TYPE 125  33    22
D5V5, multiclass
       clus
vv      AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  N0                             208                            125
  N1                              63                             33
  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"
D5V6, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED   222  15
  AMP PEAK  5(5P15.33) WILD-TYPE 127  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED    222   15
  AMP PEAK  5(5P15.33) WILD-TYPE  127   10
   clus
vv  AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  0                          222                            127
  1                           15                             10
[1] 2 2
[1] FALSE
D5V7, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED   184 149
  AMP PEAK  5(5P15.33) WILD-TYPE  92  91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED    184  149
  AMP PEAK  5(5P15.33) WILD-TYPE   92   91
        clus
vv       AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  FEMALE                          184                             92
  MALE                            149                             91
[1] 2 2
[1] FALSE
D5V8, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED   267  41
  AMP PEAK  5(5P15.33) WILD-TYPE 143  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED    267   41
  AMP PEAK  5(5P15.33) WILD-TYPE  143   19
     clus
vv    AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  NO                           267                            143
  YES                           41                             19
[1] 2 2
[1] FALSE
D5V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  5(5P15.33) MUTATED                           12
  AMP PEAK  5(5P15.33) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  5(5P15.33) MUTATED                                  65
  AMP PEAK  5(5P15.33) WILD-TYPE                                42
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  5(5P15.33) MUTATED                                                  217
  AMP PEAK  5(5P15.33) WILD-TYPE                                                104
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  5(5P15.33) MUTATED                                            2
  AMP PEAK  5(5P15.33) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  5(5P15.33) MUTATED                                              13
  AMP PEAK  5(5P15.33) WILD-TYPE                                             6
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  5(5P15.33) MUTATED                                2
  AMP PEAK  5(5P15.33) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  5(5P15.33) MUTATED                                    2
  AMP PEAK  5(5P15.33) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  5(5P15.33) MUTATED                              0
  AMP PEAK  5(5P15.33) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  5(5P15.33) MUTATED                              14
  AMP PEAK  5(5P15.33) WILD-TYPE                             9
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  5(5P15.33) MUTATED                                 0
  AMP PEAK  5(5P15.33) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  5(5P15.33) MUTATED                                               3
  AMP PEAK  5(5P15.33) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  5(5P15.33) MUTATED                              3
  AMP PEAK  5(5P15.33) WILD-TYPE                            7
D5V10, multiclass
                                                    clus
vv                                                   AMP PEAK  5(5P15.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          217
  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  5(5P15.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            104
  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"
D5V11, continuous
D5V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  5(5P15.33) MUTATED   221   8   2  19
  AMP PEAK  5(5P15.33) WILD-TYPE 123   5   2   7
D5V13, multiclass
    clus
vv   AMP PEAK  5(5P15.33) MUTATED AMP PEAK  5(5P15.33) WILD-TYPE
  R0                          221                            123
  R1                            8                              5
  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  5(5P15.33) MUTATED                                  1     6
  AMP PEAK  5(5P15.33) WILD-TYPE                                0     1
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(5P15.33) MUTATED                          36   251
  AMP PEAK  5(5P15.33) WILD-TYPE                        16   139
D5V14, multiclass
                                  clus
vv                                 AMP PEAK  5(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  36
  WHITE                                                     251
                                  clus
vv                                 AMP PEAK  5(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         1
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                       139
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V15, binary
                                cls
clus                               0   1
  AMP PEAK  5(5P15.33) MUTATED     5 249
  AMP PEAK  5(5P15.33) WILD-TYPE   2 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(5P15.33) MUTATED      5  249
  AMP PEAK  5(5P15.33) WILD-TYPE    2  135
                        clus
vv                       AMP PEAK  5(5P15.33) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          249
                        clus
vv                       AMP PEAK  5(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            135
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(5P13.1) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(5P13.1) MUTATED   196 100
  AMP PEAK  6(5P13.1) WILD-TYPE 127  81
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          296                           208 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                          100                            81 
$`AMP PEAK  6(5P13.1) MUTATED`
TCGA-05-4396 TCGA-05-4405 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 
        9.96        20.05        28.41        11.64        14.73        26.30 
TCGA-44-2662 TCGA-44-6147 TCGA-44-7670 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       42.08        27.78        29.00         9.37        11.08        46.72 
TCGA-49-6761 TCGA-49-AAR0 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       11.64       156.66        21.47        41.69        23.05        48.62 
TCGA-55-6979 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-8091 
        7.79        16.01        23.18        14.53        21.44        19.73 
TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF 
       16.93        32.12        18.15        22.65        20.58        20.19 
TCGA-67-6217 TCGA-73-4658 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 
       13.87        52.60         8.48        50.24        85.32        13.71 
TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-97-8172 
        1.45        17.29        16.54        15.68        15.65        17.92 
TCGA-97-A4M7 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       20.68        10.09        21.83        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4389 TCGA-05-4395 TCGA-05-4398 TCGA-05-4420 
        2.43        10.09        45.01         0.00        47.05        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-5423 TCGA-05-5425 
       12.00        30.02        26.01        25.02         4.96        29.00 
TCGA-05-5428 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 
       22.03         2.04         0.46         5.98         8.68       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       37.71        49.05        44.61        46.98        44.42        44.94 
TCGA-44-2665 TCGA-44-2668 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       42.77        25.02        38.24        34.06        33.73        26.56 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       28.37        28.01        23.77        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       61.28        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-A47A TCGA-44-A4SS TCGA-49-4487 TCGA-49-4488 
       23.64        12.66        15.32        13.64        28.11        28.57 
TCGA-49-4490 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       12.66        14.07        29.46        29.75        55.89        53.29 
TCGA-49-6744 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ 
       55.33        28.90         8.55        40.41       123.58       221.33 
TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 
        9.86        71.47       101.72        15.72        47.41        49.28 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
        9.27        14.27        48.46        57.53        53.16         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-7109 TCGA-50-8457 TCGA-53-7624 
       25.55        11.05        12.16        10.13        36.99        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 
       30.54        13.94        35.21        38.73        30.58        14.30 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 
       42.51        40.73        15.25        53.65        69.34        45.34 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 
       92.81        40.54        70.26        28.67        27.09        32.71 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 
        3.91        18.64        34.19        17.65        19.82        29.23 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 TCGA-55-8302 TCGA-55-8506 
       17.79        23.64        29.19        22.16        15.72         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       13.74        20.28        17.72        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8399 TCGA-62-8402 
       15.81        19.99         4.57        39.98        88.64        49.25 
TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       47.80        54.35        67.96        13.61        39.25        40.96 
TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 
       39.09        81.80        37.02        87.98        42.90        51.25 
TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 
       14.04         5.72         4.64         6.64        22.68        13.61 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-A59K 
        5.42         7.56        13.51        14.01         4.24        19.43 
TCGA-71-6725 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-5146 
        8.42        15.35        30.31         9.24        50.33        77.85 
TCGA-75-5147 TCGA-75-6214 TCGA-78-7143 TCGA-78-7147 TCGA-78-7149 TCGA-78-7153 
       43.82        36.66       163.10        19.27       129.53       119.51 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 TCGA-78-7220 
       19.50        38.50        64.90        22.92       238.29        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 
       31.20         8.02        26.01       232.18        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
       93.11        27.09        12.36         5.88        34.39        38.04 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 
       32.78        19.89        35.24        37.74         4.08        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
        0.79        22.82        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8672 TCGA-86-8673 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 
       11.61         0.62        28.34         3.81        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BD 
        1.97        10.19        12.23         7.36         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 
       22.45        17.46         1.08        19.00        41.82        27.29 
TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
        2.76        42.25        64.60        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-8174 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        0.59         5.39        15.39        14.30        21.60        20.58 
TCGA-97-A4M0 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
       21.44        34.85        21.57        18.08        35.47        19.00 
TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
        1.91        18.58        15.65        38.63         2.76        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TF 
       49.35        37.35        86.04        58.85         5.49        11.05 
TCGA-MP-A4TH TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A55R TCGA-NJ-A7XG 
       24.36        19.13        71.05        74.33        19.82        20.28 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

$`AMP PEAK  6(5P13.1) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         8.02         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4630 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 
       15.02        35.28        43.53        38.10        23.93        86.01 
TCGA-44-7661 TCGA-44-7671 TCGA-49-6742 TCGA-49-6745 TCGA-49-AARN TCGA-50-5932 
       18.31        29.23        16.04        17.16        37.32        40.60 
TCGA-55-6978 TCGA-55-7284 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8205 
        5.79         7.99         6.15        19.66        17.98        19.69 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A492 TCGA-64-1677 TCGA-73-4662 TCGA-73-7498 
       13.68        16.93        19.59        20.65        82.68        39.09 
TCGA-78-8660 TCGA-91-7771 TCGA-93-8067 TCGA-95-7562 TCGA-95-A4VK TCGA-95-A4VN 
       10.55        16.18         6.12         2.86        21.40        18.18 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.19        20.52        17.75        24.30        23.80         6.35 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4397 TCGA-05-4403 TCGA-05-4415 
       50.07         3.98        37.02        24.03        19.00         2.99 
TCGA-05-4417 TCGA-05-4425 TCGA-05-4432 TCGA-05-4433 TCGA-05-5429 TCGA-35-4122 
       14.96        21.99        25.02        24.00         9.04         7.40 
TCGA-38-4625 TCGA-38-A44F TCGA-44-2666 TCGA-44-3396 TCGA-44-3917 TCGA-44-5643 
       97.74         4.37         3.19        37.15        38.89        33.30 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6779 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       19.56        23.15        16.44         8.55        15.98         9.44 
TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 
       11.54        13.45        76.21        35.54        32.84         8.81 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARR TCGA-50-5044 
       22.26        22.26        73.12        62.24       164.12        20.52 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
       60.16         8.22        78.67         8.45        15.12        60.72 
TCGA-50-6590 TCGA-50-6595 TCGA-50-6673 TCGA-50-8459 TCGA-50-8460 TCGA-55-1596 
       42.35         6.21         0.72        36.79        27.25        67.89 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6975 TCGA-55-6982 TCGA-55-6984 
       80.52         5.62        46.03         3.88        32.71        24.99 
TCGA-55-6986 TCGA-55-7283 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
      107.21        20.02        22.03        23.15        25.41        11.28 
TCGA-55-7913 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8097 
       18.44        29.72        15.19        23.08         5.06        15.65 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 TCGA-55-A57B 
       15.42        17.56        14.47        19.96        26.01        17.95 
TCGA-62-8397 TCGA-62-8398 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46V TCGA-62-A472 
       42.38        14.60        19.53        56.71        72.30        29.92 
TCGA-64-1676 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 
       56.81        38.37         2.04        28.41        28.47        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-4679 TCGA-69-7761 TCGA-69-7974 
       20.05        18.84        12.66        14.73         6.12         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8254 TCGA-69-8453 TCGA-73-4659 TCGA-73-4666 
        4.41        13.41        13.45        26.73        23.38        26.30 
TCGA-73-4670 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5125 TCGA-75-6206 TCGA-75-6212 
        4.31         1.25        11.18        66.64        85.15        49.84 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 
      108.66       100.57        27.16         5.69        20.58        21.90 
TCGA-78-7152 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 
       39.95        32.09         5.88         9.57       104.19        88.14 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-86-7701 TCGA-86-7714 
       53.33        39.35        10.55        39.75        31.13        20.55 
TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
        4.57        32.65        31.04        13.91        30.84        27.58 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 
       26.50        29.46        24.23        13.64        26.47         2.60 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-93-A4JN TCGA-95-7567 
       27.68         1.15        16.60        14.27        23.61        18.67 
TCGA-95-7944 TCGA-95-A4VP TCGA-97-7552 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 
       12.39        19.89        63.52        15.91        18.67        18.12 
TCGA-97-8177 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 
       16.41        19.76        20.84        18.67        24.56        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-MP-A4SV 
        1.45        21.63        32.48        14.30        14.53        86.14 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YI 
       41.59        29.46        14.10        11.15        73.91         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
        1.64        47.08         0.49         0.43 

  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                         0.00                          0.13 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                       238.29                        164.12 
  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE 
                        22.77                         20.12 
[1] "0.0 - 238.3 (22.8)" "0.1 - 164.1 (20.1)"
[1] "hr=" "1.3"
D6V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  6(5P13.1) MUTATED         4       81       86        0        35
  AMP PEAK  6(5P13.1) WILD-TYPE       1       52       53        1        15
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  6(5P13.1) MUTATED          33         40          7       13
  AMP PEAK  6(5P13.1) WILD-TYPE        39         32          4       12
D6V3, multiclass
            clus
vv           AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  STAGE I                              4                             1
  STAGE IA                            81                            52
  STAGE IB                            86                            53
  STAGE II                             0                             1
  STAGE IIA                           35                            15
  STAGE IIB                           33                            39
  STAGE IIIA                          40                            32
  STAGE IIIB                           7                             4
  STAGE IV                            13                            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(5P13.1) MUTATED   108 163  22   9
  AMP PEAK  6(5P13.1) WILD-TYPE  63 115  24  10
D6V4, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  T1                         108                            63
  T2                         163                           115
  T3                          22                            24
  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
  AMP PEAK  6(5P13.1) MUTATED   198  54    45
  AMP PEAK  6(5P13.1) WILD-TYPE 135  42    31
D6V5, multiclass
       clus
vv      AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  N0                            198                           135
  N1                             54                            42
  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"
D6V6, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED   202  13
  AMP PEAK  6(5P13.1) WILD-TYPE 147  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED    202   13
  AMP PEAK  6(5P13.1) WILD-TYPE  147   12
   clus
vv  AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  0                         202                           147
  1                          13                            12
[1] 2 2
[1] FALSE
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED   168 136
  AMP PEAK  6(5P13.1) WILD-TYPE 108 104
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED    168  136
  AMP PEAK  6(5P13.1) WILD-TYPE  108  104
        clus
vv       AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  FEMALE                         168                           108
  MALE                           136                           104
[1] 2 2
[1] FALSE
D6V8, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED   242  38
  AMP PEAK  6(5P13.1) WILD-TYPE 168  22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED    242   38
  AMP PEAK  6(5P13.1) WILD-TYPE  168   22
     clus
vv    AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  NO                          242                           168
  YES                          38                            22
[1] 2 2
[1] FALSE
D6V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  6(5P13.1) MUTATED                           11
  AMP PEAK  6(5P13.1) WILD-TYPE                          7
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  6(5P13.1) MUTATED                                  56
  AMP PEAK  6(5P13.1) WILD-TYPE                                51
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  6(5P13.1) MUTATED                                                  202
  AMP PEAK  6(5P13.1) WILD-TYPE                                                119
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  6(5P13.1) MUTATED                                            2
  AMP PEAK  6(5P13.1) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  6(5P13.1) MUTATED                                              12
  AMP PEAK  6(5P13.1) WILD-TYPE                                             7
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  6(5P13.1) MUTATED                                2
  AMP PEAK  6(5P13.1) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  6(5P13.1) MUTATED                                    2
  AMP PEAK  6(5P13.1) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  6(5P13.1) MUTATED                              0
  AMP PEAK  6(5P13.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  6(5P13.1) MUTATED                              12
  AMP PEAK  6(5P13.1) WILD-TYPE                            11
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  6(5P13.1) MUTATED                                 0
  AMP PEAK  6(5P13.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  6(5P13.1) MUTATED                                               3
  AMP PEAK  6(5P13.1) WILD-TYPE                                             2
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  6(5P13.1) MUTATED                              2
  AMP PEAK  6(5P13.1) WILD-TYPE                            8
D6V10, multiclass
                                                    clus
vv                                                   AMP PEAK  6(5P13.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         202
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               12
  LUNG CLEAR CELL ADENOCARCINOMA                                               2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                               12
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                3
  MUCINOUS (COLLOID) CARCINOMA                                                 2
                                                    clus
vv                                                   AMP PEAK  6(5P13.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           119
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  7
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 11
  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"
D6V11, continuous
D6V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  6(5P13.1) MUTATED   207   6   1  16
  AMP PEAK  6(5P13.1) WILD-TYPE 137   7   3  10
D6V13, multiclass
    clus
vv   AMP PEAK  6(5P13.1) MUTATED AMP PEAK  6(5P13.1) WILD-TYPE
  R0                         207                           137
  R1                           6                             7
  R2                           1                             3
  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
  AMP PEAK  6(5P13.1) MUTATED                                  1     3
  AMP PEAK  6(5P13.1) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(5P13.1) MUTATED                          32   234
  AMP PEAK  6(5P13.1) WILD-TYPE                        20   156
D6V14, multiclass
                                  clus
vv                                 AMP PEAK  6(5P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 32
  WHITE                                                    234
                                  clus
vv                                 AMP PEAK  6(5P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   20
  WHITE                                                      156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V15, binary
                               cls
clus                              0   1
  AMP PEAK  6(5P13.1) MUTATED     6 229
  AMP PEAK  6(5P13.1) WILD-TYPE   1 155
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(5P13.1) MUTATED      6  229
  AMP PEAK  6(5P13.1) WILD-TYPE    1  155
                        clus
vv                       AMP PEAK  6(5P13.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         229
                        clus
vv                       AMP PEAK  6(5P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           155
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(5Q35.1) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  7(5Q35.1) MUTATED    86  37
  AMP PEAK  7(5Q35.1) WILD-TYPE 237 144
  AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE 
                          123                           381 
  AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE 
                           37                           144 
$`AMP PEAK  7(5Q35.1) MUTATED`
TCGA-38-6178 TCGA-44-2662 TCGA-44-A47F TCGA-49-4501 TCGA-49-6761 TCGA-49-AAR0 
       14.73        42.08        11.08        46.72        11.64       156.66 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-7573 TCGA-55-8091 TCGA-55-8207 
       21.47        41.69        48.62        16.01        19.73        32.12 
TCGA-55-A491 TCGA-67-6217 TCGA-78-7633 TCGA-93-A4JQ TCGA-95-7043 TCGA-97-A4M7 
       20.58        13.87        50.24        17.29        16.54        20.68 
TCGA-MP-A4TD TCGA-05-4426 TCGA-05-5423 TCGA-35-3615 TCGA-35-5375 TCGA-44-2657 
       10.09        26.01         4.96         0.46         8.68        44.42 
TCGA-44-2659 TCGA-44-2665 TCGA-44-3398 TCGA-44-4112 TCGA-44-5645 TCGA-44-6777 
       44.94        42.77        38.24        26.56        28.01        32.45 
TCGA-44-7659 TCGA-44-7672 TCGA-44-A47A TCGA-49-4488 TCGA-49-4490 TCGA-49-4512 
       22.72        23.64        15.32        28.57        12.66        29.75 
TCGA-49-6744 TCGA-49-AAQV TCGA-50-5045 TCGA-50-5051 TCGA-50-5068 TCGA-50-5944 
       55.33        22.26        71.47        15.72        49.28        57.53 
TCGA-50-6591 TCGA-50-6594 TCGA-50-8457 TCGA-53-7813 TCGA-55-6543 TCGA-55-6642 
        3.91        12.16        36.99        13.94        14.30        80.52 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6980 TCGA-55-6983 TCGA-55-6987 TCGA-55-7281 
       15.25        53.65        69.34        92.81        70.26        28.67 
TCGA-55-7727 TCGA-55-7911 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        3.91        17.65        29.19        15.42        17.56        15.72 
TCGA-55-8508 TCGA-55-A48Z TCGA-55-A493 TCGA-55-A4DG TCGA-62-A46S TCGA-62-A46U 
       20.28        21.40         0.92        19.99        54.35        67.96 
TCGA-62-A46Y TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 
       13.61        81.80        37.02         2.04        28.47        20.05 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-8253 
        5.72         4.64         6.64        22.68        13.61        14.01 
TCGA-73-4675 TCGA-73-7499 TCGA-75-5147 TCGA-75-6214 TCGA-78-7143 TCGA-78-7147 
       30.31        50.33        43.82        36.66       163.10        19.27 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7163 TCGA-78-7539 TCGA-86-7953 TCGA-86-7954 
      119.51        19.50       238.29        26.01        32.78        19.89 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8280 TCGA-86-8669 TCGA-91-A4BD TCGA-93-7348 
        4.08         4.57        23.05        30.84        19.82        17.46 
TCGA-93-A4JP TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       19.00        27.29         2.76        19.89        42.25        64.60 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M0 
        5.39        15.39        16.41        14.30        20.58        21.44 
TCGA-97-A4M1 TCGA-99-8028 TCGA-99-8032 TCGA-J2-A4AE TCGA-MP-A4SY TCGA-MP-A4T2 
       19.76        36.76         1.45        35.47        49.35        37.35 
TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A55O 
        5.49        11.05        24.36        71.05        74.33         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       19.82        20.28        59.11 

$`AMP PEAK  7(5Q35.1) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       26.30        43.53        38.10        23.93        27.78        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-49-6742 TCGA-49-6745 
       18.31        29.00        29.23         9.37        16.04        17.16 
TCGA-49-AARN TCGA-50-5932 TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       37.32        40.60        23.05         5.79         7.79         7.99 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 
       23.18        14.53        21.44         6.15        19.66        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       16.93        19.69        18.15        13.68        16.93        22.65 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 
       19.59        20.19        20.65        52.60        82.68        39.09 
TCGA-78-7166 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
        8.48        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
        6.12         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 
       17.92        20.19        20.52        17.75        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
        6.35        10.09        21.83        27.19         5.29        31.23 
TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
        2.43        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 
       24.03        47.05        19.00         2.99        14.96        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-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 
       29.00        22.03         9.04         2.04         7.40         5.98 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F 
       97.74       120.79        37.71        49.05        44.61         4.37 
TCGA-44-2656 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 
       46.98         3.19        25.02        37.15        38.89        34.06 
TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.73        33.30        28.37        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 
       21.63        23.18        61.28        16.44        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       36.07        18.87        12.66         8.55        15.98         9.44 
TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 
       11.54        13.64        13.45        76.21        28.11        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 
       14.07        32.84         8.81        29.46        55.89        53.29 
TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
       22.26        73.12        62.24        28.90         8.55        40.41 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5049 
      123.58       221.33       164.12         9.86        20.52       101.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       60.16        47.41         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 
        8.45        15.12        48.46        60.72        53.16        42.35 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 
       25.55        11.05         6.21         0.72        10.13        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 
       27.25        34.29        30.54        35.21        38.73        67.89 
TCGA-55-5899 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6975 
       30.58         5.62        42.51        40.73        46.03         3.88 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 
       45.34        32.71        24.99        40.54       107.21        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       27.09        32.71        22.03        23.15        25.41        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       11.28        34.19        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       15.19        23.08         5.06        17.79        23.64        15.65 
TCGA-55-8208 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 
       22.16        14.47         0.36        13.74        17.72        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       26.01        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
       20.71         3.25        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-A46R TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 
       56.71        72.30        39.25        40.96        29.92        56.81 
TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       39.09        38.37        87.98        42.90        28.41        51.25 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-69-7761 
       20.05        18.84        14.04        12.66        14.73         6.12 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
       13.45         4.24        26.73        19.43         8.42        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-A9RS 
       26.30        15.35         4.31         9.24         1.25        11.18 
TCGA-75-5125 TCGA-75-5146 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 
       66.64        77.85        85.15        49.84       108.66       100.57 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        20.58       129.53        21.90        39.95 
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        22.92         9.57 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      104.19        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 TCGA-86-8073 TCGA-86-8074 
       38.04        20.55        35.24        37.74        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 
       22.82        32.65        31.04        31.20        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       11.61        13.91        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       29.46         3.81        24.23        13.64        26.47        10.62 
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-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-93-7347 
        7.36         1.15        16.60        14.27         1.18        22.45 
TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-97-7552 
       23.61         1.08        41.82        18.67        12.39        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       18.12        21.60        20.84        18.67        24.56        34.85 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        21.63        18.08        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.53         1.91        18.58        15.65        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TE 
       86.14        58.45        86.04        58.85        41.59        29.46 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YP 
       14.10        11.15        19.13        73.91         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-S2-AA1A 
       47.08         0.49        16.87 

  AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE 
                         0.43                          0.00 
  AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE 
                       238.29                        232.18 
  AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE 
                        21.44                         21.63 
[1] "0.4 - 238.3 (21.4)" "0.0 - 232.2 (21.6)"
[1] "hr=" "1.4"
D7V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  7(5Q35.1) MUTATED         1       42       30        1        12
  AMP PEAK  7(5Q35.1) WILD-TYPE       4       91      109        0        38
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  7(5Q35.1) MUTATED          11         21          2        5
  AMP PEAK  7(5Q35.1) WILD-TYPE        61         51          9       20
D7V3, multiclass
            clus
vv           AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                            42                            91
  STAGE IB                            30                           109
  STAGE II                             1                             0
  STAGE IIA                           12                            38
  STAGE IIB                           11                            61
  STAGE IIIA                          21                            51
  STAGE IIIB                           2                             9
  STAGE IV                             5                            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
  AMP PEAK  7(5Q35.1) MUTATED    52  63   6   4
  AMP PEAK  7(5Q35.1) WILD-TYPE 119 215  40  15
D7V4, multiclass
    clus
vv   AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE
  T1                          52                           119
  T2                          63                           215
  T3                           6                            40
  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  7(5Q35.1) MUTATED    80  23    19
  AMP PEAK  7(5Q35.1) WILD-TYPE 253  73    57
D7V5, multiclass
       clus
vv      AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE
  N0                             80                           253
  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"
D7V6, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.1) MUTATED    82   5
  AMP PEAK  7(5Q35.1) WILD-TYPE 267  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.1) MUTATED     82    5
  AMP PEAK  7(5Q35.1) WILD-TYPE  267   20
   clus
vv  AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE
  0                          82                           267
  1                           5                            20
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.1) MUTATED    75  51
  AMP PEAK  7(5Q35.1) WILD-TYPE 201 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.1) MUTATED     75   51
  AMP PEAK  7(5Q35.1) WILD-TYPE  201  189
        clus
vv       AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE
  FEMALE                          75                           201
  MALE                            51                           189
[1] 2 2
[1] FALSE
D7V8, binary
                               cls
clus                              0   1
  AMP PEAK  7(5Q35.1) MUTATED   105  11
  AMP PEAK  7(5Q35.1) WILD-TYPE 305  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.1) MUTATED    105   11
  AMP PEAK  7(5Q35.1) WILD-TYPE  305   49
     clus
vv    AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE
  NO                          105                           305
  YES                          11                            49
[1] 2 2
[1] FALSE
D7V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  7(5Q35.1) MUTATED                            8
  AMP PEAK  7(5Q35.1) WILD-TYPE                         10
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  7(5Q35.1) MUTATED                                  25
  AMP PEAK  7(5Q35.1) WILD-TYPE                                82
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  7(5Q35.1) MUTATED                                                   76
  AMP PEAK  7(5Q35.1) WILD-TYPE                                                245
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  7(5Q35.1) MUTATED                                            1
  AMP PEAK  7(5Q35.1) WILD-TYPE                                          4
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  7(5Q35.1) MUTATED                                               6
  AMP PEAK  7(5Q35.1) WILD-TYPE                                            13
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  7(5Q35.1) MUTATED                                1
  AMP PEAK  7(5Q35.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  7(5Q35.1) MUTATED                                    0
  AMP PEAK  7(5Q35.1) WILD-TYPE                                  3
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  7(5Q35.1) MUTATED                              0
  AMP PEAK  7(5Q35.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  7(5Q35.1) MUTATED                               6
  AMP PEAK  7(5Q35.1) WILD-TYPE                            17
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  7(5Q35.1) MUTATED                                 0
  AMP PEAK  7(5Q35.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  7(5Q35.1) MUTATED                                               0
  AMP PEAK  7(5Q35.1) WILD-TYPE                                             5
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  7(5Q35.1) MUTATED                              3
  AMP PEAK  7(5Q35.1) WILD-TYPE                            7
D7V10, multiclass
                                                    clus
vv                                                   AMP PEAK  7(5Q35.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          76
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                6
  LUNG CLEAR CELL ADENOCARCINOMA                                               1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           0
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                                6
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                0
  MUCINOUS (COLLOID) CARCINOMA                                                 3
                                                    clus
vv                                                   AMP PEAK  7(5Q35.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           245
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 13
  LUNG CLEAR CELL ADENOCARCINOMA                                                 1
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             3
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 17
  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"
D7V11, continuous
D7V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  7(5Q35.1) MUTATED    78   3   0   8
  AMP PEAK  7(5Q35.1) WILD-TYPE 266  10   4  18
D7V13, multiclass
    clus
vv   AMP PEAK  7(5Q35.1) MUTATED AMP PEAK  7(5Q35.1) WILD-TYPE
  R0                          78                           266
  R1                           3                            10
  R2                           0                             4
  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  7(5Q35.1) MUTATED                                  0     2
  AMP PEAK  7(5Q35.1) WILD-TYPE                                1     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(5Q35.1) MUTATED                          11   105
  AMP PEAK  7(5Q35.1) WILD-TYPE                        41   285
D7V14, multiclass
                                  clus
vv                                 AMP PEAK  7(5Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    105
                                  clus
vv                                 AMP PEAK  7(5Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   41
  WHITE                                                      285
[1] 4 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(5Q35.1) MUTATED     0  99
  AMP PEAK  7(5Q35.1) WILD-TYPE   7 285
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(5Q35.1) MUTATED      0   99
  AMP PEAK  7(5Q35.1) WILD-TYPE    7  285
                        clus
vv                       AMP PEAK  7(5Q35.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          99
                        clus
vv                       AMP PEAK  7(5Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 7
  NOT HISPANIC OR LATINO                           285
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(6P21.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(6P21.1) MUTATED   125  61
  AMP PEAK  8(6P21.1) WILD-TYPE 198 120
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                          186                           318 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                           61                           120 
$`AMP PEAK  8(6P21.1) MUTATED`
TCGA-05-4427 TCGA-38-6178 TCGA-44-6147 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 
       26.01        14.73        27.78        29.00        29.23         9.37 
TCGA-44-A47F TCGA-49-6742 TCGA-49-6761 TCGA-49-AAR0 TCGA-50-5932 TCGA-50-5935 
       11.08        16.04        11.64       156.66        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-7573 TCGA-55-7914 TCGA-55-8203 
       41.69        23.05        48.62        16.01         6.15        17.98 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-A48X TCGA-64-1677 TCGA-73-4662 
       19.69        32.12        18.15        22.65        20.65        82.68 
TCGA-73-7498 TCGA-78-7633 TCGA-95-7562 TCGA-95-7948 TCGA-97-A4M2 TCGA-97-A4M7 
       39.09        50.24         2.86        15.65        20.52        20.68 
TCGA-J2-8194 TCGA-L9-A444 TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4389 TCGA-05-4420 
       23.80        10.09        10.09        50.07        45.01        29.98 
TCGA-05-4430 TCGA-05-5425 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 
       25.02        29.00         0.46         8.68        97.74        49.05 
TCGA-44-2656 TCGA-44-2659 TCGA-44-3918 TCGA-44-6774 TCGA-44-7660 TCGA-44-7662 
       46.98        44.94        34.06        21.63        19.46         7.17 
TCGA-44-7667 TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4510 
       36.07        13.45        28.11        28.57        12.66        29.46 
TCGA-49-4512 TCGA-49-6767 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 
       29.75        22.26        14.27        78.67        48.46        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6673 TCGA-50-7109 
       53.16        42.35         3.91        25.55         0.72        10.13 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 
       34.29        13.94        35.21        67.89        30.58        80.52 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6985 TCGA-55-7283 TCGA-55-7576 TCGA-55-7815 
       15.25        53.65        40.54        20.02        22.03        25.41 
TCGA-55-7903 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8097 TCGA-55-8206 
       18.64        19.82        29.23        29.72        15.65        29.19 
TCGA-55-8208 TCGA-55-8507 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       22.16        13.74        19.96        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A494 TCGA-62-8394 
        1.58        12.33        20.71         3.25        15.81         4.57 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U 
       14.60        88.64        49.25        19.53        54.35        67.96 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 
       72.30        39.25        40.96        37.02        87.98        28.41 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
       14.04        14.73         5.72        22.68        13.61         5.42 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 
       13.41        13.51         4.24         8.42        26.30        15.35 
TCGA-73-4670 TCGA-73-4677 TCGA-73-7499 TCGA-75-6206 TCGA-75-6214 TCGA-78-7145 
        4.31         1.25        50.33        85.15        36.66        27.16 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 
       19.27       129.53        38.50         5.88        64.90         9.57 
TCGA-78-7162 TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 
      104.19        26.53        26.01        10.55        77.59       110.50 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7713 TCGA-86-7954 TCGA-86-8074 TCGA-86-8075 
       93.11         5.88        38.04        19.89         0.79        22.82 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8672 TCGA-86-8674 
       31.20        23.05        21.47        14.60         0.62        26.50 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 
       10.19         2.60        12.23        27.68         7.36         1.18 
TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-97-7546 TCGA-97-7553 
       23.61        19.00        18.67        12.39        42.25        61.48 
TCGA-97-7554 TCGA-97-7938 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 
       25.48         0.59        18.67         5.39        15.39        16.41 
TCGA-97-8179 TCGA-97-A4M1 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L9-A7SV 
       14.30        19.76        21.57        18.08        35.47        18.58 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T6 TCGA-MP-A4TE TCGA-MP-A4TF 
       38.63         2.76        86.14        58.85        29.46        11.05 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A7XG TCGA-O1-A52J 
       73.91        71.05         1.64         0.49        20.28        59.11 

$`AMP PEAK  8(6P21.1) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 
       15.02        15.02        28.41        35.28        11.64        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 
       43.53        38.10        42.08        23.93        86.01        18.31 
TCGA-49-4501 TCGA-49-6745 TCGA-49-AARN TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       46.72        17.16        37.32         5.79         7.79         7.99 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 
       23.18        14.53        21.44        19.66        19.73        16.93 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 
       13.68        16.93        20.58        19.59        20.19        13.87 
TCGA-73-4658 TCGA-78-7166 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 
       52.60         8.48        10.55        85.32        13.71        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VK 
        1.45         6.12        17.29        16.54        15.68        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M3 TCGA-J2-8192 TCGA-L9-A443 
       18.18        17.92        20.19        17.75        24.30         6.35 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4250 
       21.83        27.19         5.29        31.23         2.43         3.98 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4432 
       14.96        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 
       24.00         4.96        22.03         9.04         2.04         7.40 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 
        5.98       120.79        37.71        44.61         4.37        44.42 
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-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 
       33.73        26.56        33.30        28.37        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       19.56        23.15        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       22.72        18.87        23.64        12.66         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-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 
       14.07        32.84         8.81        55.89        53.29        55.33 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
       22.26        73.12        62.24        28.90         8.55        40.41 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
      123.58       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6593 TCGA-50-6594 
        9.27         8.45        15.12        60.72        11.05        12.16 
TCGA-50-6595 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1594 
        6.21        36.99        36.79        27.25        30.54        38.73 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6975 
       14.30         5.62        42.51        40.73        46.03         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 
       69.34        45.34        32.71        92.81        24.99       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 
       70.26        28.67        27.09        32.71         3.91        23.15 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-8087 TCGA-55-8089 
       11.28        34.19        17.65        18.44        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
        5.06        17.79        23.64        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8513 TCGA-55-A48Z 
       14.47         0.36        20.28        17.72        26.01        21.40 
TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-A46O 
        0.92        19.99        17.95        39.98        42.38        47.80 
TCGA-62-A46R TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       56.71        13.61        29.92        56.81        39.09        81.80 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       38.37         2.04        42.90        51.25        28.47        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       20.05        18.84        12.66         4.64         6.64         6.12 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        7.56         6.05         4.41        14.01        13.45        26.73 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS TCGA-75-5125 
       19.43        23.38        30.31         9.24        11.18        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       77.85        43.82        49.84       108.66       100.57       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        39.95       119.51        19.50 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 
       32.09        22.92       238.29        88.14        31.20         8.02 
TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-83-5908 TCGA-86-6562 
       53.33        39.35       232.18        39.75        27.09        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 
       31.13        34.39        20.55        32.78        35.24        37.74 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8585 
        4.08         4.57        24.33        32.65        31.04        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 
       13.91        30.84        27.58        28.34        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
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        22.45        17.46 
TCGA-93-A4JO TCGA-95-7039 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 
        1.08        41.82        27.29         2.76        19.89        64.60 
TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 TCGA-97-8175 TCGA-97-8547 TCGA-97-8552 
       63.52        18.54        15.91        18.12        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       21.44        20.84        18.67        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W 
        1.45        21.63        32.48        19.00        14.30        14.53 
TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
        1.91        15.65        58.45        49.35        37.35        86.04 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
        5.49        41.59        24.36        14.10        11.15        19.13 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
       74.33         0.13        47.08         0.43        19.82        16.87 

  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                         0.46                          0.00 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                       156.66                        238.29 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                        21.83                         21.52 
[1] "0.5 - 156.7 (21.8)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.2"
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  8(6P21.1) MUTATED         2       50       52        0        20
  AMP PEAK  8(6P21.1) WILD-TYPE       3       83       87        1        30
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  8(6P21.1) MUTATED          20         24          5       12
  AMP PEAK  8(6P21.1) WILD-TYPE        52         48          6       13
D8V3, multiclass
            clus
vv           AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            50                            83
  STAGE IB                            52                            87
  STAGE II                             0                             1
  STAGE IIA                           20                            30
  STAGE IIB                           20                            52
  STAGE IIIA                          24                            48
  STAGE IIIB                           5                             6
  STAGE IV                            12                            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  8(6P21.1) MUTATED    64 102  13   8
  AMP PEAK  8(6P21.1) WILD-TYPE 107 176  33  11
D8V4, multiclass
    clus
vv   AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  T1                          64                           107
  T2                         102                           176
  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  8(6P21.1) MUTATED   127  30    27
  AMP PEAK  8(6P21.1) WILD-TYPE 206  66    49
D8V5, multiclass
       clus
vv      AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  N0                            127                           206
  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"
D8V6, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P21.1) MUTATED   131  12
  AMP PEAK  8(6P21.1) WILD-TYPE 218  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P21.1) MUTATED    131   12
  AMP PEAK  8(6P21.1) WILD-TYPE  218   13
   clus
vv  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  0                         131                           218
  1                          12                            13
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P21.1) MUTATED   100  89
  AMP PEAK  8(6P21.1) WILD-TYPE 176 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P21.1) MUTATED    100   89
  AMP PEAK  8(6P21.1) WILD-TYPE  176  151
        clus
vv       AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  FEMALE                         100                           176
  MALE                            89                           151
[1] 2 2
[1] FALSE
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P21.1) MUTATED   153  22
  AMP PEAK  8(6P21.1) WILD-TYPE 257  38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P21.1) MUTATED    153   22
  AMP PEAK  8(6P21.1) WILD-TYPE  257   38
     clus
vv    AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  NO                          153                           257
  YES                          22                            38
[1] 2 2
[1] FALSE
D8V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                           10
  AMP PEAK  8(6P21.1) WILD-TYPE                          8
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  8(6P21.1) MUTATED                                  37
  AMP PEAK  8(6P21.1) WILD-TYPE                                70
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  8(6P21.1) MUTATED                                                  118
  AMP PEAK  8(6P21.1) WILD-TYPE                                                203
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  8(6P21.1) MUTATED                                            0
  AMP PEAK  8(6P21.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  8(6P21.1) MUTATED                                               8
  AMP PEAK  8(6P21.1) WILD-TYPE                                            11
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                                1
  AMP PEAK  8(6P21.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                                    1
  AMP PEAK  8(6P21.1) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                              0
  AMP PEAK  8(6P21.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                              12
  AMP PEAK  8(6P21.1) WILD-TYPE                            11
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                                 0
  AMP PEAK  8(6P21.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                                               1
  AMP PEAK  8(6P21.1) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  8(6P21.1) MUTATED                              1
  AMP PEAK  8(6P21.1) WILD-TYPE                            9
D8V10, multiclass
                                                    clus
vv                                                   AMP PEAK  8(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                                               12
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                1
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   AMP PEAK  8(6P21.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           203
  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                                                 11
  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"
D8V11, continuous
D8V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(6P21.1) MUTATED   125   6   0   9
  AMP PEAK  8(6P21.1) WILD-TYPE 219   7   4  17
D8V13, multiclass
    clus
vv   AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  R0                         125                           219
  R1                           6                             7
  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  8(6P21.1) MUTATED                                  1     5
  AMP PEAK  8(6P21.1) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(6P21.1) MUTATED                          10   158
  AMP PEAK  8(6P21.1) WILD-TYPE                        42   232
D8V14, multiclass
                                  clus
vv                                 AMP PEAK  8(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                    158
                                  clus
vv                                 AMP PEAK  8(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   42
  WHITE                                                      232
[1] 4 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(6P21.1) MUTATED     4 149
  AMP PEAK  8(6P21.1) WILD-TYPE   3 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P21.1) MUTATED      4  149
  AMP PEAK  8(6P21.1) WILD-TYPE    3  235
                        clus
vv                       AMP PEAK  8(6P21.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         149
                        clus
vv                       AMP PEAK  8(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           235
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(7P21.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(7P21.1) MUTATED   170 107
  AMP PEAK  9(7P21.1) WILD-TYPE 153  74
  AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE 
                          277                           227 
  AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE 
                          107                            74 
$`AMP PEAK  9(7P21.1) MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-38-4629 
       19.96        14.01         8.02        20.05         9.01        28.41 
TCGA-38-4631 TCGA-38-6178 TCGA-44-2661 TCGA-44-2662 TCGA-44-6147 TCGA-44-7661 
       11.64        14.73        38.10        42.08        27.78        18.31 
TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 
        9.37        11.08        46.72        16.04        17.16        11.64 
TCGA-49-AAR0 TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
      156.66        41.69        48.62         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8205 
       16.01        23.18        21.44        19.66        19.73        19.69 
TCGA-55-8511 TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       18.15        20.58        19.59        13.87        52.60        82.68 
TCGA-80-5611 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VN 
       85.32         1.45        17.29         2.86        15.68        18.18 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
       20.68        24.30        23.80         6.35        10.09        21.83 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 
       27.19         5.29        31.23         2.43        10.09         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 
       45.01        37.02         0.00        47.05         2.99        14.96 
TCGA-05-4420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-35-4123 TCGA-38-4627 
       29.98         4.96        29.00        22.03         5.98        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-3396 
       49.05        44.61        46.98        44.42        44.94        37.15 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 
       38.89        34.06        33.73        26.56        28.37        28.01 
TCGA-44-6144 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 
       23.77        23.18        32.45        16.44        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G 
       36.07        18.87        12.66         8.55        15.98        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       13.64        13.45        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV 
       32.84        29.46        29.75        55.33        22.26        22.26 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 
       28.90        40.41       221.33         9.86        71.47       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5933 TCGA-50-5936 
       15.72        60.16        47.41         8.22        78.67         8.45 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 
       48.46        57.53        53.16        42.35         3.91        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-53-7624 TCGA-55-1596 TCGA-55-5899 
       12.16         6.21         0.72        34.29        67.89        30.58 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       14.30         5.62        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7576 
       45.34        32.71        40.54        70.26        20.02        22.03 
TCGA-55-7727 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 TCGA-55-7994 
        3.91        25.41        11.28        34.19        18.44        19.82 
TCGA-55-8085 TCGA-55-8092 TCGA-55-8096 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 
       29.72         5.06        23.64        29.19        17.56        15.72 
TCGA-55-8505 TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y 
       14.47        17.72        17.10        14.66         1.58        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B 
       21.40         3.25         0.92        15.81        19.99        17.95 
TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
        4.57        42.38        14.60        88.64        49.25        19.53 
TCGA-62-A46R TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       56.71        13.61        29.92        56.81        39.09        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 
       37.02        38.37        28.41        51.25        20.05        20.05 
TCGA-67-3772 TCGA-69-7760 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 
       18.84         6.64        13.61         5.42         6.05        13.41 
TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 
       13.51         4.24        19.43         8.42        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-6214 
       30.31         9.24        50.33        11.18        66.64        36.66 
TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7154 
      108.66       163.10        27.16        19.27        21.90        19.50 
TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 TCGA-78-7539 
       38.50        22.92         9.57       238.29        31.20        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       39.35        10.55        77.59       110.50        27.09        12.36 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 
       31.13        38.04        32.78        35.24         4.08        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
        0.79        22.82        31.04        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8668 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6829 
       14.60        13.91        28.34        29.46        13.64        41.36 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-93-7348 
       10.19         2.60        27.68         7.36        16.60        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
       23.61         1.08        19.00        18.67        12.39        27.29 
TCGA-95-8494 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 
        2.76        61.48        25.48        18.54        18.67        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 
       15.39        16.41        14.30        21.60        20.58        19.76 
TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A50W 
       34.85        21.57        18.08        35.47        19.00        14.53 
TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T2 
        1.91        18.58        38.63         2.76        49.35        37.35 
TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A55O TCGA-O1-A52J 
       58.85        41.59        19.13        71.05         0.43        59.11 
TCGA-S2-AA1A 
       16.87 

$`AMP PEAK  9(7P21.1) WILD-TYPE`
TCGA-05-4396 TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-7271 
        9.96        26.01        15.02        15.02        35.28        26.30 
TCGA-44-2655 TCGA-44-6146 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 TCGA-49-AARN 
       43.53        23.93        86.01        29.00        29.23        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 TCGA-55-7725 TCGA-55-7914 TCGA-55-8203 
       40.60        21.47        23.05        14.53         6.15        17.98 
TCGA-55-8204 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A4DF 
       16.93        32.12        13.68        16.93        22.65        20.19 
TCGA-64-1677 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-6836 
       20.65        39.09         8.48        50.24        10.55        13.71 
TCGA-91-7771 TCGA-93-8067 TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 
       16.18         6.12        16.54        15.65        21.40        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-05-4249 TCGA-05-4397 TCGA-05-4403 
       20.19        20.52        17.75        50.07        24.03        19.00 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-5375 
       24.00         9.04         2.04         0.46         7.40         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-A44F TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       97.74       120.79         4.37        42.77         3.19        25.02 
TCGA-44-3398 TCGA-44-5643 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6778 
       38.24        33.30        19.56        23.15        21.63        61.28 
TCGA-44-7659 TCGA-44-7672 TCGA-44-A47A TCGA-44-A47B TCGA-49-4486 TCGA-49-4487 
       22.72        23.64        15.32         9.44        76.21        28.11 
TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 
        8.81        55.89        53.29        73.12        62.24         8.55 
TCGA-49-AARO TCGA-49-AARR TCGA-50-5044 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
      123.58       164.12        20.52        49.28         9.27        14.27 
TCGA-50-5939 TCGA-50-5942 TCGA-50-6592 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 
       15.12        60.72        25.55        10.13        36.99        36.79 
TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6642 
       27.25        30.54        13.94        35.21        38.73        80.52 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 
       42.51        40.73        15.25        92.81        24.99       107.21 
TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7728 TCGA-55-7903 TCGA-55-7911 
       28.67        27.09        32.71        23.15        18.64        17.65 
TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8097 TCGA-55-8208 
       29.23        15.19        23.08        17.79        15.65        22.16 
TCGA-55-8299 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
       15.42         0.36        13.74        20.28        19.96        26.01 
TCGA-55-8614 TCGA-55-8620 TCGA-62-8395 TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U 
       17.62        12.33        39.98        47.80        54.35        67.96 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       72.30        39.25        40.96        87.98         2.04        42.90 
TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       28.47        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 
        6.12        22.68         7.56         4.41        14.01        13.45 
TCGA-69-8453 TCGA-73-4659 TCGA-73-4666 TCGA-73-4677 TCGA-75-5146 TCGA-75-5147 
       26.73        23.38        26.30         1.25        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
       85.15        49.84       100.57         5.69        20.58       129.53 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 
       39.95       119.51        32.09         5.88        64.90       104.19 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-8640 TCGA-78-8648 
       88.14        26.53         8.02        53.33       232.18        39.75 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
       93.11         5.88        34.39        20.55        19.89        37.74 
TCGA-86-8056 TCGA-86-8076 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
        4.57        32.65        11.61        30.84        27.58         0.62 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
       26.50         3.81        24.23        26.47        10.62         1.97 
TCGA-91-6840 TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
       12.23         1.15        14.27         1.18        19.82        22.45 
TCGA-95-7039 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 
       41.82        19.89        42.25        64.60        63.52         0.59 
TCGA-97-7941 TCGA-97-8174 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       15.91         5.39        21.44        20.84        18.67        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A8F4 
       36.76         1.45        21.63        32.48        14.30        15.65 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.14        58.45        86.04         5.49        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       24.36        14.10        11.15        73.91        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG 
        1.64        47.08         0.49        19.82        20.28 

  AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE 
                         0.00                          0.13 
  AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE 
                       238.29                        232.18 
  AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE 
                        20.58                         22.72 
[1] "0.0 - 238.3 (20.6)" "0.1 - 232.2 (22.7)"
[1] "hr=" "1.3"
D9V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK  9(7P21.1) MUTATED         5       66       73        1        32
  AMP PEAK  9(7P21.1) WILD-TYPE       0       67       66        0        18
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK  9(7P21.1) MUTATED          35         47          6       15
  AMP PEAK  9(7P21.1) WILD-TYPE        37         25          5       10
D9V3, multiclass
            clus
vv           AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE
  STAGE I                              5                             0
  STAGE IA                            66                            67
  STAGE IB                            73                            66
  STAGE II                             1                             0
  STAGE IIA                           32                            18
  STAGE IIB                           35                            37
  STAGE IIIA                          47                            25
  STAGE IIIB                           6                             5
  STAGE IV                            15                            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  9(7P21.1) MUTATED    88 158  28   8
  AMP PEAK  9(7P21.1) WILD-TYPE  83 120  18  11
D9V4, multiclass
    clus
vv   AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE
  T1                          88                            83
  T2                         158                           120
  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  9(7P21.1) MUTATED   169  52    55
  AMP PEAK  9(7P21.1) WILD-TYPE 164  44    21
D9V5, multiclass
       clus
vv      AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE
  N0                            169                           164
  N1                             52                            44
  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"
D9V6, binary
                               cls
clus                              0   1
  AMP PEAK  9(7P21.1) MUTATED   187  15
  AMP PEAK  9(7P21.1) WILD-TYPE 162  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P21.1) MUTATED    187   15
  AMP PEAK  9(7P21.1) WILD-TYPE  162   10
   clus
vv  AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE
  0                         187                           162
  1                          15                            10
[1] 2 2
[1] FALSE
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(7P21.1) MUTATED   156 128
  AMP PEAK  9(7P21.1) WILD-TYPE 120 112
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P21.1) MUTATED    156  128
  AMP PEAK  9(7P21.1) WILD-TYPE  120  112
        clus
vv       AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE
  FEMALE                         156                           120
  MALE                           128                           112
[1] 2 2
[1] FALSE
D9V8, binary
                               cls
clus                              0   1
  AMP PEAK  9(7P21.1) MUTATED   231  33
  AMP PEAK  9(7P21.1) WILD-TYPE 179  27
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P21.1) MUTATED    231   33
  AMP PEAK  9(7P21.1) WILD-TYPE  179   27
     clus
vv    AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE
  NO                          231                           179
  YES                          33                            27
[1] 2 2
[1] FALSE
D9V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK  9(7P21.1) MUTATED                            8
  AMP PEAK  9(7P21.1) WILD-TYPE                         10
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK  9(7P21.1) MUTATED                                  55
  AMP PEAK  9(7P21.1) WILD-TYPE                                52
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK  9(7P21.1) MUTATED                                                  187
  AMP PEAK  9(7P21.1) WILD-TYPE                                                134
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK  9(7P21.1) MUTATED                                            4
  AMP PEAK  9(7P21.1) WILD-TYPE                                          1
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK  9(7P21.1) MUTATED                                              11
  AMP PEAK  9(7P21.1) WILD-TYPE                                             8
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK  9(7P21.1) MUTATED                                1
  AMP PEAK  9(7P21.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK  9(7P21.1) MUTATED                                    2
  AMP PEAK  9(7P21.1) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK  9(7P21.1) MUTATED                              0
  AMP PEAK  9(7P21.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK  9(7P21.1) MUTATED                               9
  AMP PEAK  9(7P21.1) WILD-TYPE                            14
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK  9(7P21.1) MUTATED                                 0
  AMP PEAK  9(7P21.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK  9(7P21.1) MUTATED                                               4
  AMP PEAK  9(7P21.1) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK  9(7P21.1) MUTATED                              3
  AMP PEAK  9(7P21.1) WILD-TYPE                            7
D9V10, multiclass
                                                    clus
vv                                                   AMP PEAK  9(7P21.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         187
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               11
  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                                4
  MUCINOUS (COLLOID) CARCINOMA                                                 3
                                                    clus
vv                                                   AMP PEAK  9(7P21.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           134
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  8
  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                                  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"
D9V11, continuous
D9V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  9(7P21.1) MUTATED   187   7   3  18
  AMP PEAK  9(7P21.1) WILD-TYPE 157   6   1   8
D9V13, multiclass
    clus
vv   AMP PEAK  9(7P21.1) MUTATED AMP PEAK  9(7P21.1) WILD-TYPE
  R0                         187                           157
  R1                           7                             6
  R2                           3                             1
  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
  AMP PEAK  9(7P21.1) MUTATED                                  1     6
  AMP PEAK  9(7P21.1) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(7P21.1) MUTATED                          33   211
  AMP PEAK  9(7P21.1) WILD-TYPE                        19   179
D9V14, multiclass
                                  clus
vv                                 AMP PEAK  9(7P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 33
  WHITE                                                    211
                                  clus
vv                                 AMP PEAK  9(7P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      179
[1] 4 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(7P21.1) MUTATED     3 217
  AMP PEAK  9(7P21.1) WILD-TYPE   4 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(7P21.1) MUTATED      3  217
  AMP PEAK  9(7P21.1) WILD-TYPE    4  167
                        clus
vv                       AMP PEAK  9(7P21.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         217
                        clus
vv                       AMP PEAK  9(7P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           167
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7P11.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7P11.2) MUTATED   158 109
  AMP PEAK 10(7P11.2) WILD-TYPE 165  72
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          267                           237 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                          109                            72 
$`AMP PEAK 10(7P11.2) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-38-4629 TCGA-38-4631 
       19.96         8.02        20.05         9.01        28.41        11.64 
TCGA-38-6178 TCGA-44-2661 TCGA-44-2662 TCGA-44-6147 TCGA-44-7661 TCGA-44-A47F 
       14.73        38.10        42.08        27.78        18.31        11.08 
TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-55-6978 
       46.72        16.04        17.16        11.64       156.66         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 TCGA-55-8091 TCGA-55-8205 
        7.79         7.99        23.18        21.44        19.73        19.69 
TCGA-55-8511 TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       18.15        20.58        19.59        13.87        52.60        82.68 
TCGA-80-5611 TCGA-91-A4BC TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VN TCGA-97-A4M7 
       85.32         1.45         2.86        15.68        18.18        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 
       31.23         2.43        10.09         3.98        37.02         0.00 
TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-5423 TCGA-05-5425 
       47.05         2.99        14.96        29.98         4.96        29.00 
TCGA-05-5428 TCGA-35-4123 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 
       22.03         5.98        37.71        49.05        44.61        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       44.42        44.94        37.15        38.89        34.06        33.73 
TCGA-44-4112 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6775 TCGA-44-6777 
       26.56        28.37        28.01        23.77        23.18        32.45 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 
       16.44        19.46         7.17        36.07        18.87        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4488 
        8.55        15.98        11.54        13.64        13.45        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 
       12.66        35.54        14.07        32.84        29.46        29.75 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ 
       22.26        22.26        28.90        40.41       123.58       221.33 
TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 
        9.86        71.47       101.72        60.16        47.41         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        48.46        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       53.16        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        35.21        38.73        67.89        30.58 
TCGA-55-6543 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       14.30         5.62        46.03        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7576 
       45.34        32.71        40.54        70.26        20.02        22.03 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 
        3.91        11.28        34.19        18.44        19.82        29.72 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 
       23.08         5.06        23.64        29.19        17.56        15.72 
TCGA-55-8505 TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Z 
       14.47        17.72        17.10        14.66         1.58        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
        3.25         0.92        15.81        19.99        17.95         4.57 
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-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       13.61        29.92        56.81        81.80        37.02        38.37 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-69-7760 
       28.41        51.25        20.05        20.05        18.84         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         4.41        13.41        13.51 
TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 
        4.24        19.43         8.42        23.38        15.35         4.31 
TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-6214 
       30.31         9.24        50.33        11.18        66.64        36.66 
TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 
      108.66       163.10        27.16         5.69        19.27        21.90 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 
       19.50        38.50        22.92         9.57       238.29        31.20 
TCGA-78-7540 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       39.35        77.59       110.50        27.09        12.36        31.13 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 
       38.04        32.78        35.24         4.08        24.33         0.79 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8668 
       22.82        31.04        31.20        23.05        14.60        13.91 
TCGA-86-8673 TCGA-86-A456 TCGA-86-A4P7 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 
       28.34        29.46        13.64        10.19         2.60        27.68 
TCGA-91-6848 TCGA-91-8496 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
        7.36        16.60        17.46         1.08        19.00        41.82 
TCGA-95-7944 TCGA-95-8494 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 
       12.39         2.76        61.48        25.48        18.54        18.67 
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-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
       19.76        34.85        21.57        18.08        35.47        19.00 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
       14.53         1.91        18.58        38.63         2.76        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TK 
       49.35        37.35        58.85        41.59        11.05        19.13 
TCGA-NJ-A4YF TCGA-O1-A52J TCGA-S2-AA1A 
       71.05        59.11        16.87 

$`AMP PEAK 10(7P11.2) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 
       14.01         9.96        26.01        15.02        15.02        35.28 
TCGA-38-7271 TCGA-44-2655 TCGA-44-6146 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 
       26.30        43.53        23.93        86.01        29.00        29.23 
TCGA-44-8119 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
        9.37        37.32        40.60        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-7573 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 
       48.62        16.01        14.53         6.15        19.66        17.98 
TCGA-55-8204 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A4DF 
       16.93        32.12        13.68        16.93        22.65        20.19 
TCGA-64-1677 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-6836 
       20.65        39.09         8.48        50.24        10.55        13.71 
TCGA-91-7771 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VK 
       16.18         6.12        17.29        16.54        15.65        21.40 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-L9-A743 TCGA-05-4249 
       17.92        20.19        20.52        17.75        21.83        50.07 
TCGA-05-4389 TCGA-05-4397 TCGA-05-4403 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       45.01        24.03        19.00        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5429 TCGA-05-5715 
       26.01        25.02        25.02        24.00         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-A44F 
        0.46         7.40         8.68        97.74       120.79         4.37 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 TCGA-44-5643 TCGA-44-6145 
       42.77         3.19        25.02        38.24        33.30        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6778 TCGA-44-7659 TCGA-44-7672 TCGA-44-A47A 
       23.15        21.63        61.28        22.72        23.64        15.32 
TCGA-44-A47B TCGA-49-4486 TCGA-49-4487 TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 
        9.44        76.21        28.11         8.81        55.89        53.29 
TCGA-49-6744 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARR TCGA-50-5044 
       55.33        73.12        62.24         8.55       164.12        20.52 
TCGA-50-5051 TCGA-50-5068 TCGA-50-5931 TCGA-50-5942 TCGA-50-6592 TCGA-50-7109 
       15.72        49.28        14.27        60.72        25.55        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-55-6642 
       36.99        36.79        27.25        30.54        13.94        80.52 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 
       42.51        40.73        15.25        92.81        24.99       107.21 
TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       28.67        27.09        32.71        23.15        25.41        18.64 
TCGA-55-7911 TCGA-55-7995 TCGA-55-8087 TCGA-55-8094 TCGA-55-8097 TCGA-55-8208 
       17.65        29.23        15.19        17.79        15.65        22.16 
TCGA-55-8299 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
       15.42         0.36        13.74        20.28        19.96        26.01 
TCGA-55-8614 TCGA-55-8620 TCGA-55-A48Y TCGA-62-8395 TCGA-62-8402 TCGA-62-A46S 
       17.62        12.33        20.71        39.98        49.25        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 TCGA-64-5774 
       67.96        72.30        39.25        40.96        39.09        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
        2.04        42.90        28.47        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-8253 
        5.72         4.64         6.12        22.68         7.56        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-73-4666 TCGA-73-4677 TCGA-75-5146 TCGA-75-5147 
       13.45        26.73        26.30         1.25        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
       85.15        49.84       100.57        20.58       129.53        39.95 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7167 
      119.51        32.09         5.88        64.90       104.19        88.14 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 
       26.53         8.02        53.33        26.01        10.55       232.18 
TCGA-78-8648 TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 
       39.75        93.11         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 
       37.74         4.57        32.65        21.47        11.61        30.84 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 
       27.58         0.62        26.50         3.81        24.23        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6840 TCGA-91-6849 TCGA-91-8497 
       10.62        41.36         1.97        12.23         1.15        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-95-7567 TCGA-95-8039 
        1.18        19.82        22.45        23.61        18.67        27.29 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 TCGA-97-7941 
       19.89        42.25        64.60        63.52         0.59        15.91 
TCGA-97-8174 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 
        5.39        21.44        20.84        18.67        24.56        36.76 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A8F4 TCGA-MP-A4SV 
        1.45        21.63        32.48        14.30        15.65        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        24.36        14.10        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.43        19.82        20.28 

  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                         0.00                          0.13 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                       238.29                        232.18 
  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE 
                        20.58                         22.65 
[1] "0.0 - 238.3 (20.6)" "0.1 - 232.2 (22.6)"
[1] "hr=" "1.5"
D10V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 10(7P11.2) MUTATED         5       62       71        1        29
  AMP PEAK 10(7P11.2) WILD-TYPE       0       71       68        0        21
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 10(7P11.2) MUTATED          36         48          6       13
  AMP PEAK 10(7P11.2) WILD-TYPE        36         24          5       12
D10V3, multiclass
            clus
vv           AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  STAGE I                              5                             0
  STAGE IA                            62                            71
  STAGE IB                            71                            68
  STAGE II                             1                             0
  STAGE IIA                           29                            21
  STAGE IIB                           36                            36
  STAGE IIIA                          48                            24
  STAGE IIIB                           6                             5
  STAGE IV                            13                            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 10(7P11.2) MUTATED    83 153  28   8
  AMP PEAK 10(7P11.2) WILD-TYPE  88 125  18  11
D10V4, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  T1                          83                            88
  T2                         153                           125
  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 10(7P11.2) MUTATED   160  51    55
  AMP PEAK 10(7P11.2) WILD-TYPE 173  45    21
D10V5, multiclass
       clus
vv      AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  N0                            160                           173
  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"
D10V6, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED   181  13
  AMP PEAK 10(7P11.2) WILD-TYPE 168  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED    181   13
  AMP PEAK 10(7P11.2) WILD-TYPE  168   12
   clus
vv  AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  0                         181                           168
  1                          13                            12
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED   153 121
  AMP PEAK 10(7P11.2) WILD-TYPE 123 119
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED    153  121
  AMP PEAK 10(7P11.2) WILD-TYPE  123  119
        clus
vv       AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  FEMALE                         153                           123
  MALE                           121                           119
[1] 2 2
[1] FALSE
D10V8, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED   221  34
  AMP PEAK 10(7P11.2) WILD-TYPE 189  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED    221   34
  AMP PEAK 10(7P11.2) WILD-TYPE  189   26
     clus
vv    AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  NO                          221                           189
  YES                          34                            26
[1] 2 2
[1] FALSE
D10V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                            6
  AMP PEAK 10(7P11.2) WILD-TYPE                         12
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 10(7P11.2) MUTATED                                  53
  AMP PEAK 10(7P11.2) WILD-TYPE                                54
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 10(7P11.2) MUTATED                                                  183
  AMP PEAK 10(7P11.2) WILD-TYPE                                                138
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 10(7P11.2) MUTATED                                            4
  AMP PEAK 10(7P11.2) WILD-TYPE                                          1
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 10(7P11.2) MUTATED                                              10
  AMP PEAK 10(7P11.2) WILD-TYPE                                             9
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                                0
  AMP PEAK 10(7P11.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                                    2
  AMP PEAK 10(7P11.2) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                              0
  AMP PEAK 10(7P11.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                              10
  AMP PEAK 10(7P11.2) WILD-TYPE                            13
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                                 0
  AMP PEAK 10(7P11.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                                               4
  AMP PEAK 10(7P11.2) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 10(7P11.2) MUTATED                              2
  AMP PEAK 10(7P11.2) WILD-TYPE                            8
D10V10, multiclass
                                                    clus
vv                                                   AMP PEAK 10(7P11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         183
  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 10(7P11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           138
  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"
D10V11, continuous
D10V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 10(7P11.2) MUTATED   182   7   3  14
  AMP PEAK 10(7P11.2) WILD-TYPE 162   6   1  12
D10V13, multiclass
    clus
vv   AMP PEAK 10(7P11.2) MUTATED AMP PEAK 10(7P11.2) WILD-TYPE
  R0                         182                           162
  R1                           7                             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 10(7P11.2) MUTATED                                  1     5
  AMP PEAK 10(7P11.2) WILD-TYPE                                0     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7P11.2) MUTATED                          33   205
  AMP PEAK 10(7P11.2) WILD-TYPE                        19   185
D10V14, multiclass
                                  clus
vv                                 AMP PEAK 10(7P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 33
  WHITE                                                    205
                                  clus
vv                                 AMP PEAK 10(7P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                      185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V15, binary
                               cls
clus                              0   1
  AMP PEAK 10(7P11.2) MUTATED     4 210
  AMP PEAK 10(7P11.2) WILD-TYPE   3 174
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7P11.2) MUTATED      4  210
  AMP PEAK 10(7P11.2) WILD-TYPE    3  174
                        clus
vv                       AMP PEAK 10(7P11.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         210
                        clus
vv                       AMP PEAK 10(7P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           174
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(7Q31.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(7Q31.2) MUTATED   129  84
  AMP PEAK 11(7Q31.2) WILD-TYPE 194  97
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                          213                           291 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                           84                            97 
$`AMP PEAK 11(7Q31.2) MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 TCGA-38-4631 
        8.02        20.05         9.01        26.01        28.41        11.64 
TCGA-38-6178 TCGA-44-2662 TCGA-44-6147 TCGA-44-7661 TCGA-44-A47F TCGA-49-6745 
       14.73        42.08        27.78        18.31        11.08        17.16 
TCGA-50-5935 TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 
       21.47        23.05         5.79         7.79         7.99        23.18 
TCGA-55-7726 TCGA-55-8091 TCGA-55-8205 TCGA-55-8511 TCGA-55-A492 TCGA-73-4658 
       21.44        19.73        19.69        18.15        19.59        52.60 
TCGA-73-4662 TCGA-91-6836 TCGA-91-A4BC TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
       82.68        13.71         1.45        16.54         2.86        15.68 
TCGA-J2-8192 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       24.30        10.09        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4398 TCGA-05-4420 TCGA-05-5423 TCGA-05-5425 
       10.09         3.98        47.05        29.98         4.96        29.00 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
       22.03         7.40         5.98         8.68        97.74        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-3396 
       49.05        44.61        46.98        44.42        44.94        37.15 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 
       38.89        34.06        33.73        26.56        28.01        23.77 
TCGA-44-6145 TCGA-44-6777 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 
       19.56        32.45        61.28        19.46         7.17        18.87 
TCGA-44-8117 TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
       12.66        13.64        13.45        28.57        12.66        35.54 
TCGA-49-4505 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 
       14.07        29.75        22.26        22.26        62.24        28.90 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 
       40.41       123.58       221.33         9.86        71.47       101.72 
TCGA-50-5066 TCGA-50-5930 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       47.41         9.27        48.46        57.53        53.16        42.35 
TCGA-50-6593 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 
       11.05        35.21        67.89        14.30         5.62        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6983 
       15.25        46.03        53.65         3.88        69.34        92.81 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7576 TCGA-55-7907 TCGA-55-7910 
       40.54        70.26        20.02        22.03        11.28        34.19 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8092 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 
       19.82        29.23         5.06        29.19        17.56        15.72 
TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 
       14.47        13.74        17.72        17.10         1.58        12.33 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 
        3.25         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 
       81.80        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         4.41        13.41        19.43         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
       23.38        26.30         4.31        30.31         9.24        50.33 
TCGA-75-5125 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7154 TCGA-78-7160 
       66.64       163.10        27.16        19.27        19.50        22.92 
TCGA-78-7163 TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
      238.29        26.53         8.02        39.35        10.55       232.18 
TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 
       77.59        27.09        12.36        31.13        38.04        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8280 
       19.89        35.24         4.08        24.33        22.82        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8672 TCGA-86-8673 TCGA-86-A4P7 TCGA-91-6835 
       21.47        14.60         0.62        28.34        13.64         2.60 
TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
       27.68         7.36        16.60        17.46        23.61         1.08 
TCGA-95-7039 TCGA-95-7944 TCGA-95-8494 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       41.82        12.39         2.76        61.48        25.48        18.54 
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-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV 
       21.57        19.00        14.53        18.58        38.63        86.14 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TK 
       49.35        37.35        86.04        58.85        41.59        19.13 
TCGA-NJ-A4YF TCGA-O1-A52J TCGA-S2-AA1A 
       71.05        59.11        16.87 

$`AMP PEAK 11(7Q31.2) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 
       19.96        14.01         9.96        15.02        15.02        35.28 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 TCGA-44-7670 
       26.30        43.53        38.10        23.93        86.01        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-6761 TCGA-49-AAR0 
       29.23         9.37        46.72        16.04        11.64       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-6597 TCGA-55-1595 TCGA-55-7573 TCGA-55-7725 
       37.32        40.60        41.69        48.62        16.01        14.53 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-8619 
        6.15        19.66        17.98        16.93        32.12        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       16.93        22.65        20.58        20.19        20.65        13.87 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-7771 
       39.09         8.48        50.24        10.55        85.32        16.18 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        6.12        17.29        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A443 
       20.19        20.52        17.75        20.68        23.80         6.35 
TCGA-L9-A743 TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       21.83        50.07        45.01        37.02         0.00        24.03 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       19.00         2.99        14.96        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5429 TCGA-05-5715 
       26.01        25.02        25.02        24.00         9.04         2.04 
TCGA-35-3615 TCGA-38-4626 TCGA-38-A44F TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        0.46       120.79         4.37        42.77         3.19        25.02 
TCGA-44-3398 TCGA-44-5643 TCGA-44-5644 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       38.24        33.30        28.37        23.15        21.63        23.18 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7667 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 
       16.44        22.72        36.07        23.64         8.55        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 TCGA-49-4487 TCGA-49-4506 
       15.32         9.44        11.54        76.21        28.11        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR2 
        8.81        29.46        55.89        53.29        55.33        73.12 
TCGA-49-AAR9 TCGA-49-AARR TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 
        8.55       164.12        20.52        15.72        60.16        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
        8.22        14.27        78.67         8.45        15.12        60.72 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
        3.91        25.55        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-55-1594 TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 TCGA-55-6981 TCGA-55-6982 
       38.73        30.58        80.52        42.51        45.34        32.71 
TCGA-55-6984 TCGA-55-6986 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 
       24.99       107.21        28.67        27.09        32.71         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 TCGA-55-8085 
       23.15        25.41        18.64        17.65        18.44        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8208 
       15.19        23.08        17.79        23.64        15.65        22.16 
TCGA-55-8299 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
       15.42         0.36        20.28        19.96        26.01        17.62 
TCGA-55-8615 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 
       14.66        20.71        21.40        19.99        17.95        39.98 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 
       49.25        19.53        54.35        67.96        72.30        39.25 
TCGA-62-A471 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       40.96        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-67-4679 
       28.47        20.05        20.05        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 
        5.72         4.64         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 
       13.51        14.01        13.45         4.24        26.73        15.35 
TCGA-73-4677 TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
        1.25        11.18        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
       36.66       108.66       100.57         5.69        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95       119.51        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7535 TCGA-78-7537 
       64.90         9.57       104.19        88.14        31.20        53.33 
TCGA-78-7539 TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 TCGA-86-7711 
       26.01        39.75       110.50        93.11         5.88        34.39 
TCGA-86-7714 TCGA-86-8054 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 
       20.55        37.74         4.57         0.79        32.65        31.04 
TCGA-86-8279 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 
       31.20        11.61        13.91        30.84        27.58        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       29.46         3.81        24.23        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 
        1.97        10.19        12.23         1.15        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JP TCGA-95-7567 TCGA-95-8039 TCGA-95-A4VP 
       19.82        22.45        19.00        18.67        27.29        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 
       42.25        64.60        63.52         0.59        15.91         5.39 
TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       16.41        21.60        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE 
       24.56        36.76         1.45        21.63        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW 
       32.48        14.30         1.91        15.65         2.76        58.45 
TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
        5.49        29.46        11.05        24.36        14.10        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.43        19.82        20.28 

  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                         0.62                          0.00 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                       238.29                        164.12 
  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE 
                        22.03                         21.44 
[1] "0.6 - 238.3 (22.0)" "0.0 - 164.1 (21.4)"
[1] "hr=" "1.1"
D11V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 11(7Q31.2) MUTATED         3       50       58        1        23
  AMP PEAK 11(7Q31.2) WILD-TYPE       2       83       81        0        27
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 11(7Q31.2) MUTATED          28         39          2       12
  AMP PEAK 11(7Q31.2) WILD-TYPE        44         33          9       13
D11V3, multiclass
            clus
vv           AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            50                            83
  STAGE IB                            58                            81
  STAGE II                             1                             0
  STAGE IIA                           23                            27
  STAGE IIB                           28                            44
  STAGE IIIA                          39                            33
  STAGE IIIB                           2                             9
  STAGE IV                            12                            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 11(7Q31.2) MUTATED    64 127  21   5
  AMP PEAK 11(7Q31.2) WILD-TYPE 107 151  25  14
D11V4, multiclass
    clus
vv   AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  T1                          64                           107
  T2                         127                           151
  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 11(7Q31.2) MUTATED   128  42    41
  AMP PEAK 11(7Q31.2) WILD-TYPE 205  54    35
D11V5, multiclass
       clus
vv      AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  N0                            128                           205
  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"
D11V6, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q31.2) MUTATED   140  12
  AMP PEAK 11(7Q31.2) WILD-TYPE 209  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED    140   12
  AMP PEAK 11(7Q31.2) WILD-TYPE  209   13
   clus
vv  AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  0                         140                           209
  1                          12                            13
[1] 2 2
[1] FALSE
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q31.2) MUTATED   115 103
  AMP PEAK 11(7Q31.2) WILD-TYPE 161 137
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED    115  103
  AMP PEAK 11(7Q31.2) WILD-TYPE  161  137
        clus
vv       AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  FEMALE                         115                           161
  MALE                           103                           137
[1] 2 2
[1] FALSE
D11V8, binary
                               cls
clus                              0   1
  AMP PEAK 11(7Q31.2) MUTATED   174  27
  AMP PEAK 11(7Q31.2) WILD-TYPE 236  33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED    174   27
  AMP PEAK 11(7Q31.2) WILD-TYPE  236   33
     clus
vv    AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  NO                          174                           236
  YES                          27                            33
[1] 2 2
[1] FALSE
D11V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 11(7Q31.2) MUTATED                            6
  AMP PEAK 11(7Q31.2) WILD-TYPE                         12
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 11(7Q31.2) MUTATED                                  38
  AMP PEAK 11(7Q31.2) WILD-TYPE                                69
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 11(7Q31.2) MUTATED                                                  149
  AMP PEAK 11(7Q31.2) WILD-TYPE                                                172
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 11(7Q31.2) MUTATED                                            3
  AMP PEAK 11(7Q31.2) WILD-TYPE                                          2
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 11(7Q31.2) MUTATED                                              11
  AMP PEAK 11(7Q31.2) WILD-TYPE                                             8
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 11(7Q31.2) MUTATED                                0
  AMP PEAK 11(7Q31.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 11(7Q31.2) MUTATED                                    1
  AMP PEAK 11(7Q31.2) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(7Q31.2) MUTATED                              0
  AMP PEAK 11(7Q31.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 11(7Q31.2) MUTATED                               8
  AMP PEAK 11(7Q31.2) WILD-TYPE                            15
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 11(7Q31.2) MUTATED                                 0
  AMP PEAK 11(7Q31.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 11(7Q31.2) MUTATED                                               1
  AMP PEAK 11(7Q31.2) WILD-TYPE                                             4
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 11(7Q31.2) MUTATED                              1
  AMP PEAK 11(7Q31.2) WILD-TYPE                            9
D11V10, multiclass
                                                    clus
vv                                                   AMP PEAK 11(7Q31.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           38
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         149
  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 11(7Q31.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             69
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           172
  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"
D11V11, continuous
D11V12, continuous
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK 11(7Q31.2) MUTATED   145   5   3  12
  AMP PEAK 11(7Q31.2) WILD-TYPE 199   8   1  14
D11V13, multiclass
    clus
vv   AMP PEAK 11(7Q31.2) MUTATED AMP PEAK 11(7Q31.2) WILD-TYPE
  R0                         145                           199
  R1                           5                             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 11(7Q31.2) MUTATED                                  0     3
  AMP PEAK 11(7Q31.2) WILD-TYPE                                1     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(7Q31.2) MUTATED                          25   169
  AMP PEAK 11(7Q31.2) WILD-TYPE                        27   221
D11V14, multiclass
                                  clus
vv                                 AMP PEAK 11(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 25
  WHITE                                                    169
                                  clus
vv                                 AMP PEAK 11(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      221
[1] 4 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(7Q31.2) MUTATED     1 168
  AMP PEAK 11(7Q31.2) WILD-TYPE   6 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(7Q31.2) MUTATED      1  168
  AMP PEAK 11(7Q31.2) WILD-TYPE    6  216
                        clus
vv                       AMP PEAK 11(7Q31.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         168
                        clus
vv                       AMP PEAK 11(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           216
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8P11.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8P11.21) MUTATED   110  61
  AMP PEAK 12(8P11.21) WILD-TYPE 213 120
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                           171                            333 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                            61                            120 
$`AMP PEAK 12(8P11.21) MUTATED`
TCGA-05-4405 TCGA-05-4418 TCGA-38-4629 TCGA-44-6147 TCGA-44-7670 TCGA-44-7671 
       20.05         9.01        28.41        27.78        29.00        29.23 
TCGA-44-8119 TCGA-44-A47F TCGA-55-1592 TCGA-55-6978 TCGA-55-7724 TCGA-55-8203 
        9.37        11.08        23.05         5.79        23.18        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-A491 TCGA-73-4658 TCGA-78-8660 TCGA-80-5611 
       16.93        19.69        20.58        52.60        10.55        85.32 
TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VN 
       13.71         1.45         6.12        16.54        15.65        18.18 
TCGA-97-8172 TCGA-97-A4M2 TCGA-L9-A444 TCGA-MP-A4TA TCGA-05-4250 TCGA-05-4389 
       17.92        20.52        10.09        31.23         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 
       37.02         0.00        47.05        14.96        29.98        30.02 
TCGA-05-4432 TCGA-05-5428 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 
       25.02        22.03         7.40         8.68        97.74        49.05 
TCGA-44-3917 TCGA-44-3918 TCGA-44-6774 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 
       38.89        34.06        21.63        61.28        19.46         7.17 
TCGA-44-7669 TCGA-44-A47B TCGA-49-4488 TCGA-49-4510 TCGA-49-4512 TCGA-49-6767 
       18.87         9.44        28.57        29.46        29.75        22.26 
TCGA-49-AARE TCGA-49-AARO TCGA-4B-A93V TCGA-50-5051 TCGA-50-5066 TCGA-50-5072 
       40.41       123.58         9.86        15.72        47.41         8.22 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 
       14.27        78.67        48.46        57.53        53.16        25.55 
TCGA-50-6593 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-53-A4EZ TCGA-55-5899 
       11.05         6.21        10.13        36.99        35.21        30.58 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-7570 TCGA-55-7903 
       80.52        40.73        15.25        46.03        27.09        18.64 
TCGA-55-7907 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8301 
       11.28         5.06        17.79        23.64        29.19        17.56 
TCGA-55-8507 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       13.74        17.10        17.62         1.58        12.33        20.71 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8398 TCGA-62-A46P 
        0.92        15.81        17.95        39.98        14.60        19.53 
TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1680 TCGA-64-5775 
       54.35        39.25        40.96        56.81        37.02         2.04 
TCGA-64-5779 TCGA-67-3771 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
       28.41        20.05         6.64        22.68        13.61         7.56 
TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 TCGA-73-4659 TCGA-73-4675 TCGA-73-4676 
        6.05        13.41         4.24        23.38        30.31         9.24 
TCGA-73-4677 TCGA-75-5147 TCGA-75-6206 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 
        1.25        43.82        85.15        36.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7155 TCGA-78-7158 
       27.16        20.58       129.53       119.51        38.50         5.88 
TCGA-78-7159 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 TCGA-78-8662 
       64.90        26.53        31.20         8.02        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        35.24        31.20        11.61 
TCGA-86-8669 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 
       30.84        28.34        26.50         3.81        13.64        10.62 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-93-7347 TCGA-93-A4JO 
       10.19        12.23         7.36         1.18        22.45         1.08 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-8176 
       19.89        64.60        61.48        25.48        18.67        15.39 
TCGA-97-8179 TCGA-97-8552 TCGA-99-8032 TCGA-99-8033 TCGA-MN-A4N5 TCGA-MP-A4SY 
       14.30        20.58         1.45        21.57         2.76        49.35 
TCGA-MP-A4T2 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK 
       37.35        29.46        11.05        24.36        11.15        19.13 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI 
       71.05        74.33         0.13 

$`AMP PEAK 12(8P11.21) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96         8.02        26.01        15.02 
TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       15.02        35.28        11.64        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-49-4501 
       38.10        42.08        23.93        86.01        18.31        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       16.04        17.16        11.64       156.66        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       21.47        41.69        48.62         7.79         7.99        16.01 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 
       14.53        21.44         6.15        19.66        19.73        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF 
       18.15        13.68        16.93        22.65        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       20.65        13.87        82.68        39.09         8.48        50.24 
TCGA-91-7771 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-97-A4LX 
       16.18        17.29         2.86        15.68        21.40        20.19 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A743 
       17.75        20.68        24.30        23.80         6.35        21.83 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4397 
       27.19         5.29         2.43        10.09        50.07        24.03 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       19.00         2.99        12.00        21.99        26.01        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       24.00         4.96        29.00         9.04         2.04         0.46 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 
        5.98       120.79        37.71        44.61         4.37        46.98 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       38.24        33.73        26.56        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 
       23.77        19.56        23.15        23.18        32.45        16.44 
TCGA-44-7659 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       22.72        36.07        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
       15.32        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 
       12.66        35.54        14.07        32.84         8.81        55.89 
TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       53.29        55.33        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
        8.55       221.33       164.12        20.52        71.47       101.72 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
       60.16        49.28         9.27         8.45        15.12        60.72 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6594 TCGA-50-6673 TCGA-50-8459 TCGA-50-8460 
       42.35         3.91        12.16         0.72        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 
       34.29        30.54        13.94        38.73        67.89        14.30 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
        5.62        42.51        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       28.67        20.02        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       25.41        34.19        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 
       29.72        15.19        23.08        15.65        22.16        15.42 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       15.72        14.47         0.36        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-8615 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A4DG TCGA-62-8394 
       26.01        14.66        21.40         3.25        19.99         4.57 
TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46U 
       42.38        88.64        49.25        47.80        56.71        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
       72.30        13.61        29.92        39.09        81.80        38.37 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 
       87.98        42.90        51.25        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 
       14.04        12.66        14.73         5.72         4.64         6.12 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        5.42         4.41        13.51        14.01        13.45        26.73 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-7499 
       19.43         8.42        26.30        15.35         4.31        50.33 
TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-6212 TCGA-75-7025 TCGA-78-7146 
       11.18        66.64        77.85        49.84       108.66         5.69 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7156 TCGA-78-7160 
       19.27        21.90        39.95        19.50        32.09        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 
        9.57       104.19       238.29        88.14        53.33        26.01 
TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 
       39.35       232.18        39.75        77.59        93.11        27.09 
TCGA-86-6562 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 
       12.36        34.39        38.04        20.55        32.78        37.74 
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        22.82        32.65 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 
       31.04        23.05        21.47        14.60        13.91        27.58 
TCGA-86-8672 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
        0.62        29.46        24.23        26.47        41.36         1.97 
TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
        2.60        27.68         1.15        16.60        14.27        19.82 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       17.46        23.61        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7552 TCGA-97-7937 TCGA-97-7938 
       27.29         2.76        42.25        63.52        18.54         0.59 
TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M0 
       15.91         5.39        18.12        16.41        21.60        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       19.76        20.84        18.67        24.56        34.85        36.76 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.63        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV 
       14.53         1.91        18.58        15.65        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TI 
       58.45        86.04        58.85         5.49        41.59        14.10 
TCGA-MP-A5C7 TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       73.91         1.64        47.08         0.49         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                          0.00                           0.36 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                        163.10                         238.29 
  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE 
                         20.58                          21.99 
[1] "0.0 - 163.1 (20.6)" "0.4 - 238.3 (22.0)"
[1] "hr=" "1.1"
D12V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 12(8P11.21) MUTATED         1       45       55        0        17
  AMP PEAK 12(8P11.21) WILD-TYPE       4       88       84        1        33
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 12(8P11.21) MUTATED          17         25          5        8
  AMP PEAK 12(8P11.21) WILD-TYPE        55         47          6       17
D12V3, multiclass
            clus
vv           AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             45                             88
  STAGE IB                             55                             84
  STAGE II                              0                              1
  STAGE IIA                            17                             33
  STAGE IIB                            17                             55
  STAGE IIIA                           25                             47
  STAGE IIIB                            5                              6
  STAGE IV                              8                             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 12(8P11.21) MUTATED    53 103  11   7
  AMP PEAK 12(8P11.21) WILD-TYPE 118 175  35  12
D12V4, multiclass
    clus
vv   AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  T1                           53                            118
  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 12(8P11.21) MUTATED   118  26    28
  AMP PEAK 12(8P11.21) WILD-TYPE 215  70    48
D12V5, multiclass
       clus
vv      AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  N0                             118                            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"
D12V6, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.21) MUTATED   122   8
  AMP PEAK 12(8P11.21) WILD-TYPE 227  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED    122    8
  AMP PEAK 12(8P11.21) WILD-TYPE  227   17
   clus
vv  AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  0                          122                            227
  1                            8                             17
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.21) MUTATED    82  93
  AMP PEAK 12(8P11.21) WILD-TYPE 194 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED     82   93
  AMP PEAK 12(8P11.21) WILD-TYPE  194  147
        clus
vv       AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  FEMALE                           82                            194
  MALE                             93                            147
[1] 2 2
[1] FALSE
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.21) MUTATED   134  27
  AMP PEAK 12(8P11.21) WILD-TYPE 276  33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED    134   27
  AMP PEAK 12(8P11.21) WILD-TYPE  276   33
     clus
vv    AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  NO                           134                            276
  YES                           27                             33
[1] 2 2
[1] FALSE
D12V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                            9
  AMP PEAK 12(8P11.21) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 12(8P11.21) MUTATED                                  40
  AMP PEAK 12(8P11.21) WILD-TYPE                                67
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 12(8P11.21) MUTATED                                                  108
  AMP PEAK 12(8P11.21) WILD-TYPE                                                213
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 12(8P11.21) MUTATED                                            0
  AMP PEAK 12(8P11.21) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 12(8P11.21) MUTATED                                               5
  AMP PEAK 12(8P11.21) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                                0
  AMP PEAK 12(8P11.21) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                                    0
  AMP PEAK 12(8P11.21) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                              0
  AMP PEAK 12(8P11.21) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                               8
  AMP PEAK 12(8P11.21) WILD-TYPE                            15
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                                 1
  AMP PEAK 12(8P11.21) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                                               4
  AMP PEAK 12(8P11.21) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 12(8P11.21) MUTATED                              0
  AMP PEAK 12(8P11.21) WILD-TYPE                           10
D12V10, multiclass
                                                    clus
vv                                                   AMP PEAK 12(8P11.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            40
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          108
  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 12(8P11.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              67
  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"
D12V11, continuous
D12V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 12(8P11.21) MUTATED   117   5   1   7
  AMP PEAK 12(8P11.21) WILD-TYPE 227   8   3  19
D12V13, multiclass
    clus
vv   AMP PEAK 12(8P11.21) MUTATED AMP PEAK 12(8P11.21) WILD-TYPE
  R0                          117                            227
  R1                            5                              8
  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 12(8P11.21) MUTATED                                  0     2
  AMP PEAK 12(8P11.21) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8P11.21) MUTATED                          14   134
  AMP PEAK 12(8P11.21) WILD-TYPE                        38   256
D12V14, multiclass
                                  clus
vv                                 AMP PEAK 12(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     134
                                  clus
vv                                 AMP PEAK 12(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    38
  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"
D12V15, binary
                                cls
clus                               0   1
  AMP PEAK 12(8P11.21) MUTATED     3 123
  AMP PEAK 12(8P11.21) WILD-TYPE   4 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8P11.21) MUTATED      3  123
  AMP PEAK 12(8P11.21) WILD-TYPE    4  261
                        clus
vv                       AMP PEAK 12(8P11.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          123
                        clus
vv                       AMP PEAK 12(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            261
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(8Q24.21) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(8Q24.21) MUTATED   190 126
  AMP PEAK 13(8Q24.21) WILD-TYPE 133  55
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           316                            188 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                           126                             55 
$`AMP PEAK 13(8Q24.21) MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 
        8.02        20.05         9.01        15.02        15.02        28.41 
TCGA-38-4631 TCGA-38-6178 TCGA-44-2662 TCGA-44-6147 TCGA-44-7661 TCGA-44-7670 
       11.64        14.73        42.08        27.78        18.31        29.00 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 
       29.23         9.37        11.08        46.72        17.16        11.64 
TCGA-49-AAR0 TCGA-50-5932 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 
      156.66        40.60        41.69        23.05        48.62         5.79 
TCGA-55-6979 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8203 
        7.79        23.18        14.53        21.44         6.15        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-8621 TCGA-55-A491 TCGA-64-1677 
       16.93        19.69        18.15        16.93        20.58        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-8660 
       13.87        52.60        82.68        39.09         8.48        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       85.32        13.71        16.18         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
        2.86        15.65        18.18        17.92        20.19        20.52 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 
       23.80         6.35        10.09        21.83        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
       31.23         2.43        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       37.02         0.00        47.05        14.96        29.98        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4432 TCGA-05-5423 TCGA-05-5428 TCGA-35-4122 
       30.02        21.99        25.02         4.96        22.03         7.40 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 
        8.68        97.74        49.05        44.61        46.98        44.42 
TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       42.77        25.02        37.15        38.89        34.06        33.73 
TCGA-44-4112 TCGA-44-5644 TCGA-44-6144 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       26.56        28.37        23.77        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       61.28        16.44         7.17        36.07        18.87        23.64 
TCGA-44-8120 TCGA-44-A47B TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 
        8.55         9.44        13.45        76.21        28.57        12.66 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAQV 
       14.07         8.81        29.46        29.75        22.26        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARE TCGA-49-AARO TCGA-4B-A93V TCGA-50-5049 
       73.12        62.24        40.41       123.58         9.86       101.72 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 
       15.72        47.41        49.28         8.22        14.27        78.67 
TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       48.46        57.53        53.16        42.35         3.91        25.55 
TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-53-7813 
       11.05         6.21         0.72        10.13        36.99        13.94 
TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       35.21        67.89        30.58        14.30        80.52         5.62 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6981 TCGA-55-6982 
       40.73        15.25        46.03        53.65        45.34        32.71 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7574 TCGA-55-7576 TCGA-55-7903 TCGA-55-7907 
       40.54       107.21        32.71        22.03        18.64        11.28 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 
       17.65        18.44        19.82        29.72        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 
       17.79        23.64        15.65        29.19        17.56        15.72 
TCGA-55-8507 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       13.74        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       20.71        21.40         3.25         0.92        15.81        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O 
       17.95         4.57        39.98        14.60        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       19.53        56.71        54.35        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 
       56.81        39.09        37.02        87.98         2.04        28.41 
TCGA-67-3770 TCGA-67-3771 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
       20.05        20.05         6.64        22.68        13.61         7.56 
TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
        6.05        13.41         4.24        19.43         8.42        23.38 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       15.35         4.31        30.31         9.24         1.25        50.33 
TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 
       66.64        43.82        85.15        36.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 
       27.16         5.69        19.27        20.58       129.53        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 TCGA-78-7161 
      119.51        19.50        38.50         5.88        64.90         9.57 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
      104.19        88.14        26.53        31.20         8.02        26.01 
TCGA-78-7542 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
       10.55       110.50        93.11        27.09         5.88        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        38.04        20.55        19.89        35.24        37.74 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       24.33         0.79        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       11.61        30.84         0.62        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 
        3.81        13.64        10.62        10.19        12.23        27.68 
TCGA-91-8499 TCGA-93-7347 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-8494 
        1.18        22.45         1.08        19.00        18.67         2.76 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       19.89        64.60        61.48        25.48        18.54         0.59 
TCGA-97-8171 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       18.67        15.39        14.30        21.60        20.58        21.44 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85        36.76         1.45        21.57        18.08        35.47 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.53         1.91        18.58        15.65        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
       86.14        58.45        49.35        37.35        86.04         5.49 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
       29.46        11.05        24.36        14.10        11.15        19.13 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A7XG 
       71.05        74.33         1.64        20.28 

$`AMP PEAK 13(8Q24.21) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4427 TCGA-38-4630 TCGA-38-7271 
       19.96        14.01         9.96        26.01        35.28        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 TCGA-49-6742 TCGA-49-AARN 
       43.53        38.10        23.93        86.01        16.04        37.32 
TCGA-50-5935 TCGA-55-7284 TCGA-55-7573 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 
       21.47         7.99        16.01        19.66        19.73        32.12 
TCGA-55-8619 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-78-7633 TCGA-91-A4BC 
       13.68        22.65        19.59        20.19        50.24         1.45 
TCGA-95-7947 TCGA-95-A4VK TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-05-4397 
       15.68        21.40        17.75        20.68        24.30        24.03 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5425 
       19.00         2.99        26.01        25.02        24.00        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-A44F TCGA-44-2659 TCGA-44-2666 TCGA-44-3398 TCGA-44-5643 TCGA-44-5645 
        4.37        44.94         3.19        38.24        33.30        28.01 
TCGA-44-6145 TCGA-44-6148 TCGA-44-7659 TCGA-44-7660 TCGA-44-8117 TCGA-44-A479 
       19.56        23.15        22.72        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-49-6743 TCGA-49-6744 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARQ 
       55.89        53.29        55.33        28.90         8.55       221.33 
TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5930 TCGA-50-5936 
      164.12        20.52        71.47        60.16         9.27         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-6594 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
       15.12        60.72        12.16        36.79        27.25        34.29 
TCGA-53-7626 TCGA-55-1594 TCGA-55-6968 TCGA-55-6975 TCGA-55-6980 TCGA-55-6983 
       30.54        38.73        42.51         3.88        69.34        92.81 
TCGA-55-6984 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7727 
       24.99        70.26        28.67        20.02        27.09         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7995 TCGA-55-8087 TCGA-55-8208 
       23.15        25.41        34.19        29.23        15.19        22.16 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       15.42        14.47         0.36        20.28        17.72        19.96 
TCGA-55-8513 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       26.01        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 
       81.80        38.37        42.90        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 
       14.04        12.66        14.73         5.72         4.64         6.12 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        5.42         4.41        13.51        14.01        13.45        26.73 
TCGA-73-4666 TCGA-73-A9RS TCGA-75-5146 TCGA-75-6212 TCGA-75-7025 TCGA-78-7150 
       26.30        11.18        77.85        49.84       108.66        21.90 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7163 TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 
       32.09        22.92       238.29        53.33        39.35       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-86-6562 TCGA-86-7953 TCGA-86-8055 TCGA-86-8056 
       39.75        77.59        12.36        32.78         4.08         4.57 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8668 TCGA-86-8671 TCGA-86-A4JF 
       22.82        32.65        31.04        13.91        27.58        24.23 
TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 
       26.47        41.36         1.97         2.60         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JN TCGA-95-7039 
       16.60        14.27        19.82        17.46        23.61        41.82 
TCGA-95-7944 TCGA-95-8039 TCGA-97-7546 TCGA-97-7552 TCGA-97-7941 TCGA-97-8174 
       12.39        27.29        42.25        63.52        15.91         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       18.12        16.41        19.76        20.84        18.67        24.56 
TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-MP-A4T6 TCGA-MP-A4T9 
       21.63        32.48        19.00        14.30        58.85        41.59 
TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       73.91         0.13        47.08         0.49         0.43        19.82 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                          0.00                           0.13 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                        163.10                         238.29 
  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE 
                         21.42                          22.77 
[1] "0.0 - 163.1 (21.4)" "0.1 - 238.3 (22.8)"
[1] "hr=" "1.4"
D13V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 13(8Q24.21) MUTATED         2       76       96        1        32
  AMP PEAK 13(8Q24.21) WILD-TYPE       3       57       43        0        18
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 13(8Q24.21) MUTATED          43         46          8       18
  AMP PEAK 13(8Q24.21) WILD-TYPE        29         26          3        7
D13V3, multiclass
            clus
vv           AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             76                             57
  STAGE IB                             96                             43
  STAGE II                              1                              0
  STAGE IIA                            32                             18
  STAGE IIB                            43                             29
  STAGE IIIA                           46                             26
  STAGE IIIB                            8                              3
  STAGE IV                             18                              7
[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(8Q24.21) MUTATED    93 192  27  11
  AMP PEAK 13(8Q24.21) WILD-TYPE  78  86  19   8
D13V4, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  T1                           93                             78
  T2                          192                             86
  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
  AMP PEAK 13(8Q24.21) MUTATED   207  61    50
  AMP PEAK 13(8Q24.21) WILD-TYPE 126  35    26
D13V5, multiclass
       clus
vv      AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  N0                             207                            126
  N1                              61                             35
  N2+N3                           50                             26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED   224  18
  AMP PEAK 13(8Q24.21) WILD-TYPE 125   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED    224   18
  AMP PEAK 13(8Q24.21) WILD-TYPE  125    7
   clus
vv  AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  0                          224                            125
  1                           18                              7
[1] 2 2
[1] FALSE
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED   170 155
  AMP PEAK 13(8Q24.21) WILD-TYPE 106  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED    170  155
  AMP PEAK 13(8Q24.21) WILD-TYPE  106   85
        clus
vv       AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  FEMALE                          170                            106
  MALE                            155                             85
[1] 2 2
[1] FALSE
D13V8, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED   262  39
  AMP PEAK 13(8Q24.21) WILD-TYPE 148  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED    262   39
  AMP PEAK 13(8Q24.21) WILD-TYPE  148   21
     clus
vv    AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  NO                           262                            148
  YES                           39                             21
[1] 2 2
[1] FALSE
D13V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                           12
  AMP PEAK 13(8Q24.21) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 13(8Q24.21) MUTATED                                  65
  AMP PEAK 13(8Q24.21) WILD-TYPE                                42
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 13(8Q24.21) MUTATED                                                  213
  AMP PEAK 13(8Q24.21) WILD-TYPE                                                108
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 13(8Q24.21) MUTATED                                            1
  AMP PEAK 13(8Q24.21) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 13(8Q24.21) MUTATED                                              11
  AMP PEAK 13(8Q24.21) WILD-TYPE                                             8
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                                1
  AMP PEAK 13(8Q24.21) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                                    2
  AMP PEAK 13(8Q24.21) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                              0
  AMP PEAK 13(8Q24.21) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                              15
  AMP PEAK 13(8Q24.21) WILD-TYPE                             8
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                                 1
  AMP PEAK 13(8Q24.21) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                                               4
  AMP PEAK 13(8Q24.21) WILD-TYPE                                             1
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 13(8Q24.21) MUTATED                              0
  AMP PEAK 13(8Q24.21) WILD-TYPE                           10
D13V10, multiclass
                                                    clus
vv                                                   AMP PEAK 13(8Q24.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          213
  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                                                15
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 4
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK 13(8Q24.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            108
  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                                                   8
  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"
D13V11, continuous
D13V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(8Q24.21) MUTATED   220  11   4  16
  AMP PEAK 13(8Q24.21) WILD-TYPE 124   2   0  10
D13V13, multiclass
    clus
vv   AMP PEAK 13(8Q24.21) MUTATED AMP PEAK 13(8Q24.21) WILD-TYPE
  R0                          220                            124
  R1                           11                              2
  R2                            4                              0
  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
  AMP PEAK 13(8Q24.21) MUTATED                                  1     7
  AMP PEAK 13(8Q24.21) WILD-TYPE                                0     0
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(8Q24.21) MUTATED                          33   241
  AMP PEAK 13(8Q24.21) WILD-TYPE                        19   149
D13V14, multiclass
                                  clus
vv                                 AMP PEAK 13(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  33
  WHITE                                                     241
                                  clus
vv                                 AMP PEAK 13(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         0
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                       149
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V15, binary
                                cls
clus                               0   1
  AMP PEAK 13(8Q24.21) MUTATED     5 231
  AMP PEAK 13(8Q24.21) WILD-TYPE   2 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(8Q24.21) MUTATED      5  231
  AMP PEAK 13(8Q24.21) WILD-TYPE    2  153
                        clus
vv                       AMP PEAK 13(8Q24.21) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          231
                        clus
vv                       AMP PEAK 13(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            153
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(10P15.1) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(10P15.1) MUTATED    90  50
  AMP PEAK 14(10P15.1) WILD-TYPE 233 131
  AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE 
                           140                            364 
  AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE 
                            50                            131 
$`AMP PEAK 14(10P15.1) MUTATED`
TCGA-05-4382 TCGA-05-4405 TCGA-05-4427 TCGA-05-5420 TCGA-38-4629 TCGA-38-4631 
       19.96        20.05        26.01        15.02        28.41        11.64 
TCGA-44-7671 TCGA-55-6978 TCGA-55-8511 TCGA-55-A491 TCGA-73-4658 TCGA-73-4662 
       29.23         5.79        18.15        20.58        52.60        82.68 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 
       50.24        10.55        85.32        13.71        16.18         6.12 
TCGA-95-7043 TCGA-95-A4VN TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       16.54        18.18        17.75        23.80         6.35        10.09 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       27.19         5.29        10.09        45.01        37.02         0.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4430 
        2.99        14.96        29.98        12.00        30.02        25.02 
TCGA-05-4432 TCGA-05-5425 TCGA-35-4122 TCGA-38-4625 TCGA-38-4632 TCGA-44-3396 
       25.02        29.00         7.40        97.74        44.61        37.15 
TCGA-44-3917 TCGA-44-3918 TCGA-44-6144 TCGA-44-6145 TCGA-44-6778 TCGA-44-7660 
       38.89        34.06        23.77        19.56        61.28        19.46 
TCGA-44-7662 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-49-4487 TCGA-49-4514 
        7.17        23.64        12.66         8.55        28.11        55.89 
TCGA-49-AAR2 TCGA-49-AARE TCGA-4B-A93V TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 
       73.12        40.41         9.86       101.72        15.72        49.28 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 TCGA-50-7109 
       78.67         8.45        57.53        53.16        25.55        10.13 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-6968 TCGA-55-6969 
       34.29        13.94        35.21        67.89        42.51        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-7574 TCGA-55-7727 TCGA-55-7910 TCGA-55-8085 
       15.25        53.65        32.71         3.91        34.19        29.72 
TCGA-55-8092 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8615 TCGA-55-8620 
        5.06        17.56        15.72         0.36        14.66        12.33 
TCGA-55-A4DG TCGA-62-8398 TCGA-62-8399 TCGA-62-A46S TCGA-62-A470 TCGA-64-1678 
       19.99        14.60        88.64        54.35        39.25        39.09 
TCGA-67-3771 TCGA-69-7763 TCGA-69-7979 TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 
       20.05        22.68        13.41         8.42        15.35         4.31 
TCGA-73-4677 TCGA-73-A9RS TCGA-75-5125 TCGA-75-6206 TCGA-75-6214 TCGA-75-7027 
        1.25        11.18        66.64        85.15        36.66       100.57 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7539 
      129.53        19.50        64.90        22.92         9.57        26.01 
TCGA-78-7542 TCGA-78-8662 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       10.55       110.50        93.11        31.13        34.39        38.04 
TCGA-86-7955 TCGA-86-8585 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 
       35.24        11.61         0.62        28.34        29.46         3.81 
TCGA-86-A4JF TCGA-91-6829 TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VP TCGA-97-7553 
       24.23        41.36        18.67        12.39        19.89        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8179 TCGA-99-8025 TCGA-L9-A7SV TCGA-MN-A4N4 
       25.48        18.54        14.30        34.85        18.58        38.63 
TCGA-MN-A4N5 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-NJ-A4YF 
        2.76        86.04         5.49        29.46        11.05        71.05 
TCGA-NJ-A4YQ TCGA-NJ-A55O 
       47.08         0.43 

$`AMP PEAK 14(10P15.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4434 TCGA-38-4630 
       14.01         9.96         8.02         9.01        15.02        35.28 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       14.73        26.30        43.53        38.10        42.08        23.93 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-44-A47F 
       27.78        86.01        18.31        29.00         9.37        11.08 
TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN 
       46.72        16.04        17.16        11.64       156.66        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6979 
       40.60        21.47        41.69        23.05        48.62         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.99        16.01        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       19.66        19.73        17.98        16.93        19.69        32.12 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       13.68        16.93        22.65        19.59        20.19        20.65 
TCGA-67-6217 TCGA-73-7498 TCGA-78-7166 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7562 
       13.87        39.09         8.48         1.45        17.29         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.68        15.65        21.40        17.92        20.19        20.52 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A743 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4249 
       20.68        24.30        21.83        31.23         2.43        50.07 
TCGA-05-4250 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4425 TCGA-05-4426 
        3.98        24.03        47.05        19.00        21.99        26.01 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       24.00         4.96        22.03         9.04         2.04         0.46 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F 
        5.98         8.68       120.79        37.71        49.05         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       46.98        44.42        44.94        42.77         3.19        25.02 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
       38.24        33.73        26.56        33.30        28.37        28.01 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
       23.15        21.63        23.18        32.45        16.44        22.72 
TCGA-44-7667 TCGA-44-7669 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       36.07        18.87        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-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 
       14.07        32.84         8.81        29.46        29.75        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       55.33        22.26        22.26        62.24        28.90         8.55 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 
      123.58       221.33       164.12        20.52        71.47        60.16 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5939 TCGA-50-5941 
       47.41         8.22         9.27        14.27        15.12        48.46 
TCGA-50-5942 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       60.72        42.35         3.91        11.05        12.16         6.21 
TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1594 
        0.72        36.99        36.79        27.25        30.54        38.73 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6975 
       30.58        14.30        80.52         5.62        46.03         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 
      107.21        70.26        28.67        20.02        27.09        22.03 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7913 
       23.15        25.41        18.64        11.28        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 
       19.82        29.23        15.19        23.08        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 
       15.65        29.19        22.16        15.42        14.47        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
        1.58        20.71        21.40         3.25         0.92        15.81 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46O 
       17.95         4.57        39.98        42.38        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 
       19.53        56.71        67.96        72.30        13.61        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        81.80        37.02        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       18.84        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.64         6.12        13.61         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        4.41        13.51        14.01        13.45         4.24        26.73 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 
       19.43        23.38        26.30        30.31         9.24        50.33 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 
       77.85        43.82        49.84       108.66       163.10        27.16 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27        20.58        21.90        39.95       119.51 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       38.50        32.09         5.88       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 
       26.53        31.20         8.02        53.33        39.35       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7714 
       39.75        77.59        27.09        12.36         5.88        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       32.78        19.89        37.74         4.08         4.57        24.33 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
        0.79        22.82        32.65        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 
       21.47        14.60        13.91        30.84        27.58        26.50 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       13.64        26.47        10.62         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       12.23        27.68         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 
       19.00        41.82        27.29         2.76        42.25        64.60 
TCGA-97-7552 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       63.52         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       15.39        16.41        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.84        18.67        24.56        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.63        18.08        35.47        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       14.53         1.91        15.65        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       37.35        58.85        41.59        24.36        14.10        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A 
       19.13        73.91        74.33         0.13         1.64         0.49 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE 
                          0.00                           0.13 
  AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE 
                        129.53                         238.29 
  AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE 
                        23.785                         21.455 
[1] "0.0 - 129.5 (23.8)" "0.1 - 238.3 (21.5)"
[1] "hr=" "1.1"
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 14(10P15.1) MUTATED         0       35       43        0        13
  AMP PEAK 14(10P15.1) WILD-TYPE       5       98       96        1        37
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 14(10P15.1) MUTATED          20         16          5        8
  AMP PEAK 14(10P15.1) WILD-TYPE        52         56          6       17
D14V3, multiclass
            clus
vv           AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                             35                             98
  STAGE IB                             43                             96
  STAGE II                              0                              1
  STAGE IIA                            13                             37
  STAGE IIB                            20                             52
  STAGE IIIA                           16                             56
  STAGE IIIB                            5                              6
  STAGE IV                              8                             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 14(10P15.1) MUTATED    38  85  13   6
  AMP PEAK 14(10P15.1) WILD-TYPE 133 193  33  13
D14V4, multiclass
    clus
vv   AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE
  T1                           38                            133
  T2                           85                            193
  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
  AMP PEAK 14(10P15.1) MUTATED   103  18    20
  AMP PEAK 14(10P15.1) WILD-TYPE 230  78    56
D14V5, multiclass
       clus
vv      AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE
  N0                             103                            230
  N1                              18                             78
  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"
D14V6, binary
                                cls
clus                               0   1
  AMP PEAK 14(10P15.1) MUTATED   103   8
  AMP PEAK 14(10P15.1) WILD-TYPE 246  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(10P15.1) MUTATED    103    8
  AMP PEAK 14(10P15.1) WILD-TYPE  246   17
   clus
vv  AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE
  0                          103                            246
  1                            8                             17
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(10P15.1) MUTATED    62  80
  AMP PEAK 14(10P15.1) WILD-TYPE 214 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(10P15.1) MUTATED     62   80
  AMP PEAK 14(10P15.1) WILD-TYPE  214  160
        clus
vv       AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE
  FEMALE                           62                            214
  MALE                             80                            160
[1] 2 2
[1] FALSE
D14V8, binary
                                cls
clus                               0   1
  AMP PEAK 14(10P15.1) MUTATED   112  18
  AMP PEAK 14(10P15.1) WILD-TYPE 298  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(10P15.1) MUTATED    112   18
  AMP PEAK 14(10P15.1) WILD-TYPE  298   42
     clus
vv    AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE
  NO                           112                            298
  YES                           18                             42
[1] 2 2
[1] FALSE
D14V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 14(10P15.1) MUTATED                            7
  AMP PEAK 14(10P15.1) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 14(10P15.1) MUTATED                                  31
  AMP PEAK 14(10P15.1) WILD-TYPE                                76
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 14(10P15.1) MUTATED                                                   84
  AMP PEAK 14(10P15.1) WILD-TYPE                                                237
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 14(10P15.1) MUTATED                                            0
  AMP PEAK 14(10P15.1) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 14(10P15.1) MUTATED                                               4
  AMP PEAK 14(10P15.1) WILD-TYPE                                            15
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 14(10P15.1) MUTATED                                0
  AMP PEAK 14(10P15.1) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 14(10P15.1) MUTATED                                    2
  AMP PEAK 14(10P15.1) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(10P15.1) MUTATED                              0
  AMP PEAK 14(10P15.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 14(10P15.1) MUTATED                               9
  AMP PEAK 14(10P15.1) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 14(10P15.1) MUTATED                                 0
  AMP PEAK 14(10P15.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 14(10P15.1) MUTATED                                               3
  AMP PEAK 14(10P15.1) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 14(10P15.1) MUTATED                              2
  AMP PEAK 14(10P15.1) WILD-TYPE                            8
D14V10, multiclass
                                                    clus
vv                                                   AMP PEAK 14(10P15.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            31
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           84
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 4
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 9
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   AMP PEAK 14(10P15.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              76
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            237
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  15
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  14
  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"
D14V11, continuous
D14V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(10P15.1) MUTATED    96   4   0   9
  AMP PEAK 14(10P15.1) WILD-TYPE 248   9   4  17
D14V13, multiclass
    clus
vv   AMP PEAK 14(10P15.1) MUTATED AMP PEAK 14(10P15.1) WILD-TYPE
  R0                           96                            248
  R1                            4                              9
  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 14(10P15.1) MUTATED                                  1     4
  AMP PEAK 14(10P15.1) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(10P15.1) MUTATED                          14    96
  AMP PEAK 14(10P15.1) WILD-TYPE                        38   294
D14V14, multiclass
                                  clus
vv                                 AMP PEAK 14(10P15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                      96
                                  clus
vv                                 AMP PEAK 14(10P15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    38
  WHITE                                                       294
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V15, binary
                                cls
clus                               0   1
  AMP PEAK 14(10P15.1) MUTATED     3  94
  AMP PEAK 14(10P15.1) WILD-TYPE   4 290
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(10P15.1) MUTATED      3   94
  AMP PEAK 14(10P15.1) WILD-TYPE    4  290
                        clus
vv                       AMP PEAK 14(10P15.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           94
                        clus
vv                       AMP PEAK 14(10P15.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            290
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(11Q13.3) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(11Q13.3) MUTATED   105  64
  AMP PEAK 15(11Q13.3) WILD-TYPE 218 117
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                           169                            335 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                            64                            117 
$`AMP PEAK 15(11Q13.3) MUTATED`
TCGA-05-4402 TCGA-05-5420 TCGA-38-4629 TCGA-44-2662 TCGA-44-7661 TCGA-44-8119 
        8.02        15.02        28.41        42.08        18.31         9.37 
TCGA-50-5932 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6979 TCGA-55-8203 
       40.60        41.69        23.05        48.62         7.79        17.98 
TCGA-55-8205 TCGA-55-8511 TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-91-6836 
       19.69        18.15        20.65        52.60        82.68        13.71 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 TCGA-97-A4M3 TCGA-L9-A443 
        1.45         6.12        16.54         2.86        17.75         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4389 TCGA-05-4415 
       10.09        27.19        31.23         2.43        45.01         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       14.96        29.98        21.99        25.02        24.00         4.96 
TCGA-05-5429 TCGA-38-4628 TCGA-38-4632 TCGA-44-2659 TCGA-44-3918 TCGA-44-5644 
        9.04        49.05        44.61        44.94        34.06        28.37 
TCGA-44-5645 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       28.01        21.63        23.18        61.28        16.44        19.46 
TCGA-44-7662 TCGA-44-7669 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
        7.17        18.87        12.66        15.98        15.32         9.44 
TCGA-49-4494 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AARE TCGA-4B-A93V 
       35.54        29.75        22.26        62.24        40.41         9.86 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6593 TCGA-53-7624 TCGA-53-7813 
       78.67        48.46        53.16        11.05        34.29        13.94 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       38.73        67.89        30.58        14.30        80.52         5.62 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6981 TCGA-55-7576 TCGA-55-7910 TCGA-55-7994 
       46.03         3.88        45.34        22.03        34.19        19.82 
TCGA-55-7995 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8506 TCGA-55-8507 
       29.23         5.06        17.79        23.64         0.36        13.74 
TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A490 TCGA-55-A494 
       17.72        17.10        14.66         1.58         3.25        15.81 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       19.99        17.95         4.57        88.64        49.25        47.80 
TCGA-62-A470 TCGA-64-1676 TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       39.25        56.81        39.09        38.37        87.98         2.04 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-6215 TCGA-69-7973 
       28.41        28.47        20.05        20.05         5.72         7.56 
TCGA-69-7974 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 
        6.05        13.41         4.24        19.43         8.42        26.30 
TCGA-73-4668 TCGA-73-4676 TCGA-73-A9RS TCGA-75-5125 TCGA-78-7147 TCGA-78-7148 
       15.35         9.24        11.18        66.64        19.27        20.58 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7163 TCGA-78-7220 
       19.50        38.50        64.90         9.57       238.29        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 
       31.20         8.02        26.01        10.55        77.59       110.50 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7701 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 
       93.11         5.88        31.13        32.78        35.24        37.74 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-A4D0 
       31.04        31.20        23.05        21.47        14.60         3.81 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 TCGA-93-7348 TCGA-93-A4JO 
       41.36        10.19        12.23         7.36        17.46         1.08 
TCGA-95-7039 TCGA-95-8494 TCGA-97-7553 TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 
       41.82         2.76        61.48        18.54         5.39        16.41 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
        1.45        21.57        18.08         1.91        18.58        15.65 
TCGA-MN-A4N4 TCGA-MP-A4T6 TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-O1-A52J 
       38.63        58.85        14.10        11.15        71.05        59.11 
TCGA-S2-AA1A 
       16.87 

$`AMP PEAK 15(11Q13.3) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       15.02        35.28        11.64        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 
       38.10        23.93        27.78        86.01        29.00        29.23 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
       11.08        46.72        16.04        17.16        11.64       156.66 
TCGA-49-AARN TCGA-50-5935 TCGA-55-6978 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       37.32        21.47         5.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 
       14.53        21.44         6.15        19.66        19.73        16.93 
TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       32.12        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-67-6217 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       20.19        13.87        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-7771 TCGA-93-A4JQ TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       85.32        16.18        17.29        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8192 
       18.18        17.92        20.19        20.52        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
       23.80        21.83         5.29        10.09        50.07         3.98 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4422 
       37.02         0.00        24.03        47.05        19.00        12.00 
TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 
       30.02        26.01        25.02        29.00        22.03         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-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 
       37.71         4.37        46.98        44.42        42.77         3.19 
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        33.73        26.56 
TCGA-44-5643 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6777 TCGA-44-7659 
       33.30        23.77        19.56        23.15        32.45        22.72 
TCGA-44-7667 TCGA-44-7672 TCGA-44-8120 TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       36.07        23.64         8.55        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4506 
       76.21        28.11        28.57        12.66        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV 
        8.81        29.46        55.89        53.29        55.33        22.26 
TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       73.12        28.90         8.55       123.58       221.33       164.12 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 
       49.28         8.22         9.27        14.27         8.45        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 
       60.72        57.53        42.35         3.91        25.55        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
       30.54        35.21        42.51        40.73        15.25        53.65 
TCGA-55-6980 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       69.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 
       70.26        28.67        20.02        27.09        32.71         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7913 
       23.15        25.41        18.64        11.28        17.65        18.44 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       29.72        15.19        23.08        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 
       15.42        17.56        15.72        14.47        20.28        19.96 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 
       26.01        17.62        12.33        20.71        21.40         0.92 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       39.98        42.38        14.60        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 
       67.96        72.30        13.61        40.96        29.92        81.80 
TCGA-64-1680 TCGA-64-5778 TCGA-64-5781 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       37.02        42.90        51.25        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
       14.73         4.64         6.64         6.12        22.68        13.61 
TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        5.42         4.41        13.51        14.01        13.45        26.73 
TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 TCGA-75-5146 
       23.38         4.31        30.31         1.25        50.33        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
      163.10        27.16         5.69       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7167 
      119.51        32.09         5.88        22.92       104.19        88.14 
TCGA-78-7537 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-83-5908 TCGA-86-6562 
       53.33        39.35       232.18        39.75        27.09        12.36 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 
       34.39        38.04        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        22.82        32.65        11.61        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        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 
       24.23        13.64        26.47        10.62         1.97         2.60 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
       27.68         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
       22.45        23.61        19.00        18.67        12.39        27.29 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7938 
       19.89        42.25        64.60        63.52        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 
       15.91        18.67        18.12        15.39        14.30        21.60 
TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       20.58        21.44        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       34.85        36.76        21.63        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       14.30        14.53         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       37.35        86.04         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       24.36        19.13        73.91        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       47.08         0.49         0.43        19.82        20.28 

  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                          0.36                           0.00 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                        238.29                         232.18 
  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE 
                         19.99                          22.45 
[1] "0.4 - 238.3 (20.0)" "0.0 - 232.2 (22.4)"
[1] "hr=" "1.2"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 15(11Q13.3) MUTATED         0       41       46        0        18
  AMP PEAK 15(11Q13.3) WILD-TYPE       5       92       93        1        32
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 15(11Q13.3) MUTATED          27         24          4       10
  AMP PEAK 15(11Q13.3) WILD-TYPE        45         48          7       15
D15V3, multiclass
            clus
vv           AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                             41                             92
  STAGE IB                             46                             93
  STAGE II                              0                              1
  STAGE IIA                            18                             32
  STAGE IIB                            27                             45
  STAGE IIIA                           24                             48
  STAGE IIIB                            4                              7
  STAGE IV                             10                             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 15(11Q13.3) MUTATED    50 100  16   5
  AMP PEAK 15(11Q13.3) WILD-TYPE 121 178  30  14
D15V4, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  T1                           50                            121
  T2                          100                            178
  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 15(11Q13.3) MUTATED   111  29    28
  AMP PEAK 15(11Q13.3) WILD-TYPE 222  67    48
D15V5, multiclass
       clus
vv      AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  N0                             111                            222
  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"
D15V6, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED   111  10
  AMP PEAK 15(11Q13.3) WILD-TYPE 238  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED    111   10
  AMP PEAK 15(11Q13.3) WILD-TYPE  238   15
   clus
vv  AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  0                          111                            238
  1                           10                             15
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED    92  80
  AMP PEAK 15(11Q13.3) WILD-TYPE 184 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED     92   80
  AMP PEAK 15(11Q13.3) WILD-TYPE  184  160
        clus
vv       AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  FEMALE                           92                            184
  MALE                             80                            160
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED   135  17
  AMP PEAK 15(11Q13.3) WILD-TYPE 275  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED    135   17
  AMP PEAK 15(11Q13.3) WILD-TYPE  275   43
     clus
vv    AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  NO                           135                            275
  YES                           17                             43
[1] 2 2
[1] FALSE
D15V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                            4
  AMP PEAK 15(11Q13.3) WILD-TYPE                         14
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 15(11Q13.3) MUTATED                                  33
  AMP PEAK 15(11Q13.3) WILD-TYPE                                74
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 15(11Q13.3) MUTATED                                                  121
  AMP PEAK 15(11Q13.3) WILD-TYPE                                                200
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 15(11Q13.3) MUTATED                                            2
  AMP PEAK 15(11Q13.3) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 15(11Q13.3) MUTATED                                               4
  AMP PEAK 15(11Q13.3) WILD-TYPE                                            15
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                                1
  AMP PEAK 15(11Q13.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                                    2
  AMP PEAK 15(11Q13.3) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                              0
  AMP PEAK 15(11Q13.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                               3
  AMP PEAK 15(11Q13.3) WILD-TYPE                            20
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                                 1
  AMP PEAK 15(11Q13.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                                               1
  AMP PEAK 15(11Q13.3) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 15(11Q13.3) MUTATED                              0
  AMP PEAK 15(11Q13.3) WILD-TYPE                           10
D15V10, multiclass
                                                    clus
vv                                                   AMP PEAK 15(11Q13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          121
  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                                                 3
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK 15(11Q13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              74
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            200
  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                                                  20
  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"
D15V11, continuous
D15V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(11Q13.3) MUTATED   115   5   1  10
  AMP PEAK 15(11Q13.3) WILD-TYPE 229   8   3  16
D15V13, multiclass
    clus
vv   AMP PEAK 15(11Q13.3) MUTATED AMP PEAK 15(11Q13.3) WILD-TYPE
  R0                          115                            229
  R1                            5                              8
  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
  AMP PEAK 15(11Q13.3) MUTATED                                  1     4
  AMP PEAK 15(11Q13.3) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(11Q13.3) MUTATED                          22   126
  AMP PEAK 15(11Q13.3) WILD-TYPE                        30   264
D15V14, multiclass
                                  clus
vv                                 AMP PEAK 15(11Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                     126
                                  clus
vv                                 AMP PEAK 15(11Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    30
  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"
D15V15, binary
                                cls
clus                               0   1
  AMP PEAK 15(11Q13.3) MUTATED     3 128
  AMP PEAK 15(11Q13.3) WILD-TYPE   4 256
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(11Q13.3) MUTATED      3  128
  AMP PEAK 15(11Q13.3) WILD-TYPE    4  256
                        clus
vv                       AMP PEAK 15(11Q13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          128
                        clus
vv                       AMP PEAK 15(11Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            256
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(12P12.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(12P12.1) MUTATED   104  71
  AMP PEAK 16(12P12.1) WILD-TYPE 219 110
  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                           175                            329 
  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                            71                            110 
$`AMP PEAK 16(12P12.1) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 TCGA-44-7661 
       19.96         8.02         9.01        15.02        15.02        18.31 
TCGA-44-7670 TCGA-49-6742 TCGA-49-6745 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       29.00        16.04        17.16        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7726 TCGA-55-A4DF TCGA-73-4662 
       48.62         5.79         7.99        21.44        20.19        82.68 
TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 TCGA-97-A4M7 TCGA-L9-A443 TCGA-MN-A4N1 
       13.71        16.18         6.12        20.68         6.35        27.19 
TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4415 
       10.09         3.98        45.01        37.02         0.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4432 TCGA-05-4433 TCGA-05-5428 TCGA-35-4122 
       14.96        29.98        25.02        24.00        22.03         7.40 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 TCGA-44-2657 TCGA-44-2668 
        8.68        97.74        49.05        44.61        44.42        25.02 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       33.30        28.37        16.44        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-4488 
       18.87        23.64        15.98        15.32         9.44        28.57 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAR9 TCGA-49-AARO 
        8.81        29.46        29.75        22.26         8.55       123.58 
TCGA-49-AARQ TCGA-50-5045 TCGA-50-5072 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 
      221.33        71.47         8.22        14.27        48.46        57.53 
TCGA-50-6592 TCGA-50-6673 TCGA-50-8459 TCGA-55-1594 TCGA-55-1596 TCGA-55-6712 
       25.55         0.72        36.79        38.73        67.89         5.62 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6981 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 
       46.03        69.34        45.34        24.99        40.54        70.26 
TCGA-55-7283 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 
       20.02        22.03        23.15        25.41        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       17.65        18.44        29.23        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8208 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       23.64        22.16        15.72        14.47        13.74        20.28 
TCGA-55-8615 TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-62-8398 TCGA-62-8402 
       14.66         3.25         0.92        15.81        14.60        49.25 
TCGA-62-A46O TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 TCGA-64-1681 
       47.80        13.61        39.25        40.96        39.09        38.37 
TCGA-64-5775 TCGA-67-3774 TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 
        2.04        12.66         7.56         6.05        13.41        13.51 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 
        4.24        19.43        26.30        15.35         4.31        30.31 
TCGA-75-5125 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7154 
       66.64       100.57        27.16         5.69        20.58        19.50 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 TCGA-78-8655 
       38.50        64.90         9.57        88.14        26.53        77.59 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 
       27.09        12.36         5.88        31.13        38.04        32.78 
TCGA-86-7954 TCGA-86-8278 TCGA-86-8280 TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 
       19.89        31.04        23.05        30.84        28.34         3.81 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 
       10.62        41.36         2.60        27.68         7.36         1.18 
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-99-8028 TCGA-99-8032 TCGA-99-8033 
       25.48        15.39        20.58        36.76         1.45        21.57 
TCGA-L9-A5IP TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T7 
        1.91        38.63         2.76        86.14        49.35         5.49 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A55R 
       29.46        11.05        14.10        19.13        71.05        19.82 
TCGA-S2-AA1A 
       16.87 

$`AMP PEAK 16(12P12.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4427 TCGA-38-4629 TCGA-38-4630 
       14.01         9.96        20.05        26.01        28.41        35.28 
TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 
       11.64        14.73        26.30        43.53        38.10        42.08 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F 
       23.93        27.78        86.01        29.23         9.37        11.08 
TCGA-49-4501 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-55-6979 
       46.72        11.64       156.66        37.32        40.60         7.79 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       16.01        23.18        14.53         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       17.98        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 TCGA-67-6217 
       16.93        22.65        20.58        19.59        20.65        13.87 
TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       52.60        39.09         8.48        50.24        10.55        85.32 
TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 
        1.45        17.29        16.54         2.86        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA 
       24.30        23.80        10.09        21.83         5.29        31.23 
TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4422 
        2.43        50.07        24.03        47.05        19.00        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-5423 TCGA-05-5425 
       30.02        21.99        26.01        25.02         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-A44F TCGA-44-2656 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 
        4.37        46.98        44.94        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        33.73        26.56        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-7659 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47G TCGA-44-A4SS 
       61.28        22.72        12.66         8.55        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       13.45        76.21        28.11        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 
       32.84        55.89        53.29        55.33        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       62.24        28.90        40.41       164.12         9.86        20.52 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 
      101.72        15.72        60.16        47.41        49.28         9.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 
       78.67         8.45        15.12        60.72        53.16        42.35 
TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 
        3.91        11.05        12.16         6.21        10.13        36.99 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
       27.25        34.29        30.54        13.94        35.21        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
       14.30        80.52        42.51        40.73        15.25        53.65 
TCGA-55-6975 TCGA-55-6982 TCGA-55-6983 TCGA-55-6986 TCGA-55-7281 TCGA-55-7570 
        3.88        32.71        92.81       107.21        28.67        27.09 
TCGA-55-7574 TCGA-55-7727 TCGA-55-7903 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
       32.71         3.91        18.64        19.82        29.72        15.19 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 
       15.65        29.19        15.42        17.56         0.36        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 
       19.96        26.01        17.10        17.62         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
       20.71        21.40        19.99        17.95         4.57        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       42.38        88.64        19.53        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
       72.30        29.92        56.81        81.80        37.02        87.98 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       42.90        28.41        51.25        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       18.84        14.04        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-8253 
        6.12        22.68        13.61         5.42         4.41        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 TCGA-73-4659 TCGA-73-4676 TCGA-73-4677 
       13.45        26.73         8.42        23.38         9.24         1.25 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        11.18        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
       36.66       108.66       163.10        19.27       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 
       39.95       119.51        32.09         5.88        22.92       104.19 
TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
      238.29        31.20         8.02        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 TCGA-86-7711 
       10.55       232.18        39.75       110.50        93.11        34.39 
TCGA-86-7714 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       20.55        35.24        37.74         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        22.82        32.65        31.20        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 
       11.61        13.91        27.58         0.62        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 
       24.23        13.64        26.47         1.97        10.19        12.23 
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        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       23.61        19.00        41.82        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       61.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 
       18.12        16.41        14.30        21.60        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-AA5R TCGA-J2-A4AD 
       20.84        18.67        24.56        34.85        21.63        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV 
       35.47        32.48        19.00        14.30        14.53        18.58 
TCGA-L9-A8F4 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 
       15.65        58.45        37.35        86.04        58.85        41.59 
TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       24.36        11.15        73.91        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
       47.08         0.49         0.43        20.28        59.11 

  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                          0.00                           0.13 
  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                        221.33                         238.29 
  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE 
                         20.58                          22.26 
[1] "0.0 - 221.3 (20.6)" "0.1 - 238.3 (22.3)"
[1] "hr=" "1.4"
D16V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 16(12P12.1) MUTATED         4       42       42        0        20
  AMP PEAK 16(12P12.1) WILD-TYPE       1       91       97        1        30
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 16(12P12.1) MUTATED          23         31          2       12
  AMP PEAK 16(12P12.1) WILD-TYPE        49         41          9       13
D16V3, multiclass
            clus
vv           AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                             42                             91
  STAGE IB                             42                             97
  STAGE II                              0                              1
  STAGE IIA                            20                             30
  STAGE IIB                            23                             49
  STAGE IIIA                           31                             41
  STAGE IIIB                            2                              9
  STAGE IV                             12                             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 16(12P12.1) MUTATED    51 102  19   5
  AMP PEAK 16(12P12.1) WILD-TYPE 120 176  27  14
D16V4, multiclass
    clus
vv   AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE
  T1                           51                            120
  T2                          102                            176
  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 16(12P12.1) MUTATED   111  34    29
  AMP PEAK 16(12P12.1) WILD-TYPE 222  62    47
D16V5, multiclass
       clus
vv      AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE
  N0                             111                            222
  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"
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(12P12.1) MUTATED   114  12
  AMP PEAK 16(12P12.1) WILD-TYPE 235  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(12P12.1) MUTATED    114   12
  AMP PEAK 16(12P12.1) WILD-TYPE  235   13
   clus
vv  AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE
  0                          114                            235
  1                           12                             13
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(12P12.1) MUTATED    93  85
  AMP PEAK 16(12P12.1) WILD-TYPE 183 155
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(12P12.1) MUTATED     93   85
  AMP PEAK 16(12P12.1) WILD-TYPE  183  155
        clus
vv       AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE
  FEMALE                           93                            183
  MALE                             85                            155
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(12P12.1) MUTATED   143  20
  AMP PEAK 16(12P12.1) WILD-TYPE 267  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(12P12.1) MUTATED    143   20
  AMP PEAK 16(12P12.1) WILD-TYPE  267   40
     clus
vv    AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE
  NO                           143                            267
  YES                           20                             40
[1] 2 2
[1] FALSE
D16V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 16(12P12.1) MUTATED                            6
  AMP PEAK 16(12P12.1) WILD-TYPE                         12
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 16(12P12.1) MUTATED                                  30
  AMP PEAK 16(12P12.1) WILD-TYPE                                77
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 16(12P12.1) MUTATED                                                  122
  AMP PEAK 16(12P12.1) WILD-TYPE                                                199
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 16(12P12.1) MUTATED                                            1
  AMP PEAK 16(12P12.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 16(12P12.1) MUTATED                                               8
  AMP PEAK 16(12P12.1) WILD-TYPE                                            11
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 16(12P12.1) MUTATED                                1
  AMP PEAK 16(12P12.1) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 16(12P12.1) MUTATED                                    1
  AMP PEAK 16(12P12.1) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 16(12P12.1) MUTATED                              0
  AMP PEAK 16(12P12.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 16(12P12.1) MUTATED                               4
  AMP PEAK 16(12P12.1) WILD-TYPE                            19
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 16(12P12.1) MUTATED                                 0
  AMP PEAK 16(12P12.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 16(12P12.1) MUTATED                                               1
  AMP PEAK 16(12P12.1) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 16(12P12.1) MUTATED                              4
  AMP PEAK 16(12P12.1) WILD-TYPE                            6
D16V10, multiclass
                                                    clus
vv                                                   AMP PEAK 16(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 16(12P12.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            199
  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"
D16V11, continuous
D16V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(12P12.1) MUTATED   120   5   4   8
  AMP PEAK 16(12P12.1) WILD-TYPE 224   8   0  18
D16V13, multiclass
    clus
vv   AMP PEAK 16(12P12.1) MUTATED AMP PEAK 16(12P12.1) WILD-TYPE
  R0                          120                            224
  R1                            5                              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 16(12P12.1) MUTATED                                  1     3
  AMP PEAK 16(12P12.1) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(12P12.1) MUTATED                          19   130
  AMP PEAK 16(12P12.1) WILD-TYPE                        33   260
D16V14, multiclass
                                  clus
vv                                 AMP PEAK 16(12P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  19
  WHITE                                                     130
                                  clus
vv                                 AMP PEAK 16(12P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    33
  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"
D16V15, binary
                                cls
clus                               0   1
  AMP PEAK 16(12P12.1) MUTATED     2 129
  AMP PEAK 16(12P12.1) WILD-TYPE   5 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(12P12.1) MUTATED      2  129
  AMP PEAK 16(12P12.1) WILD-TYPE    5  255
                        clus
vv                       AMP PEAK 16(12P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          129
                        clus
vv                       AMP PEAK 16(12P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            255
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(12Q14.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(12Q14.1) MUTATED    98  67
  AMP PEAK 17(12Q14.1) WILD-TYPE 225 114
  AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE 
                           165                            339 
  AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE 
                            67                            114 
$`AMP PEAK 17(12Q14.1) MUTATED`
TCGA-05-4402 TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 TCGA-38-4631 TCGA-44-7670 
        8.02         9.01        15.02        15.02        11.64        29.00 
TCGA-44-8119 TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 TCGA-50-6597 TCGA-55-1595 
        9.37        16.04        17.16       156.66        41.69        48.62 
TCGA-55-6978 TCGA-55-7284 TCGA-55-7726 TCGA-55-A4DF TCGA-91-6836 TCGA-91-7771 
        5.79         7.99        21.44        20.19        13.71        16.18 
TCGA-93-8067 TCGA-97-A4M7 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MP-A4TD TCGA-05-4389 
        6.12        20.68         6.35        27.19        10.09        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4430 
       37.02         0.00         2.99        14.96        29.98        25.02 
TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 TCGA-35-4122 TCGA-35-5375 TCGA-38-4628 
       25.02         4.96        29.00         7.40         8.68        49.05 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2668 TCGA-44-3918 TCGA-44-5644 TCGA-44-6778 
       46.98        44.42        25.02        34.06        28.37        61.28 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 
       16.44        19.46        36.07        18.87        23.64        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6767 
       15.32         9.44         8.81        29.46        55.89        22.26 
TCGA-49-AAQV TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-50-5045 TCGA-50-5051 
       22.26         8.55        40.41       123.58        71.47        15.72 
TCGA-50-5055 TCGA-50-5072 TCGA-50-5931 TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 
       60.16         8.22        14.27        57.53        53.16        25.55 
TCGA-50-6673 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 TCGA-55-6712 
        0.72        34.29        13.94        38.73        67.89         5.62 
TCGA-55-6971 TCGA-55-6980 TCGA-55-6982 TCGA-55-6987 TCGA-55-7728 TCGA-55-7815 
       46.03        69.34        32.71        70.26        23.15        25.41 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8089 TCGA-55-8096 TCGA-55-8208 
       11.28        34.19        29.23        23.08        23.64        22.16 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 TCGA-55-A490 
       15.72        14.47        13.74        20.28        14.66         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46V 
        0.92        15.81        14.60        49.25        47.80        72.30 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 
       39.25        40.96        39.09        38.37         2.04        28.41 
TCGA-67-3774 TCGA-69-7760 TCGA-69-7973 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K 
       12.66         6.64         7.56        13.51         4.24        19.43 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-A9RS TCGA-75-5125 TCGA-75-7027 
       26.30         4.31        30.31        11.18        66.64       100.57 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 
       27.16         5.69        20.58         9.57        88.14        26.53 
TCGA-78-7536 TCGA-78-8655 TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 
        8.02        77.59        12.36        31.13        38.04        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 
       19.89        35.24        31.04        31.20        21.47        14.60 
TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6840 TCGA-91-6848 
       11.61        30.84         3.81        10.62        12.23         7.36 
TCGA-91-6849 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 TCGA-95-A4VP TCGA-97-8176 
        1.15        18.67        12.39         2.76        19.89        15.39 
TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M6 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A5IP 
       16.41        20.58        18.67         1.45        21.57         1.91 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T6 
       15.65        38.63         2.76        86.14        49.35        58.85 
TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI 
        5.49        29.46        14.10        19.13        71.05         0.13 
TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        59.11        16.87 

$`AMP PEAK 17(12Q14.1) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4427 TCGA-38-4629 
       19.96        14.01         9.96        20.05        26.01        28.41 
TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 
       35.28        14.73        26.30        43.53        38.10        42.08 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-A47F 
       23.93        27.78        86.01        18.31        29.23        11.08 
TCGA-49-4501 TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 
       46.72        11.64        37.32        40.60        21.47        23.05 
TCGA-55-6979 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 
        7.79        16.01        23.18        14.53         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
       19.73        17.98        16.93        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 
       13.68        16.93        22.65        20.58        19.59        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       10.55        85.32         1.45        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 
       20.52        17.75        24.30        23.80        10.09        21.83 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4250 TCGA-05-4397 
        5.29        31.23         2.43        50.07         3.98        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       47.05        19.00        12.00        30.02        21.99        26.01 
TCGA-05-4433 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 
       24.00        22.03         9.04         2.04         0.46         5.98 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2659 
       97.74       120.79        37.71        44.61         4.37        44.94 
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        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       26.56        33.30        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7662 TCGA-44-8117 
       21.63        23.18        32.45        22.72         7.17        12.66 
TCGA-44-8120 TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 
        8.55        11.54        13.64        13.45        76.21        28.11 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 
       28.57        12.66        35.54        14.07        32.84        29.75 
TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARQ 
       53.29        55.33        73.12        62.24        28.90       221.33 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 
      164.12         9.86        20.52       101.72        47.41        49.28 
TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        9.27        78.67         8.45        15.12        48.46        60.72 
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-55-5899 
       36.99        36.79        27.25        30.54        35.21        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
       14.30        80.52        42.51        40.73        15.25        53.65 
TCGA-55-6975 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
        3.88        45.34        92.81        24.99        40.54       107.21 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       28.67        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 
       18.64        17.65        18.44        19.82        29.72        15.19 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 
        5.06        17.79        15.65        29.19        15.42        17.56 
TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
        0.36        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A4DG TCGA-55-A57B 
        1.58        12.33        20.71        21.40        19.99        17.95 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R 
        4.57        39.98        42.38        88.64        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 
       54.35        67.96        13.61        29.92        56.81        81.80 
TCGA-64-1680 TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       37.02        87.98        42.90        51.25        28.47        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        18.84        14.04        14.73         5.72         4.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
        6.12        22.68        13.61         5.42         6.05         4.41 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 TCGA-73-4659 
       13.41        14.01        13.45        26.73         8.42        23.38 
TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5146 TCGA-75-5147 
       15.35         9.24         1.25        50.33        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7147 
       85.15        49.84        36.66       108.66       163.10        19.27 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        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        22.92       104.19       238.29 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
       31.20        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 
       39.75       110.50        93.11        27.09         5.88        34.39 
TCGA-86-7714 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       20.55        37.74         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8280 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
       22.82        32.65        23.05        13.91        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46        24.23        13.64        26.47 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-8496 
       41.36         1.97        10.19         2.60        27.68        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 
        1.08        19.00        41.82        27.29        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 
       18.67         5.39        18.12        14.30        21.60        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R 
       19.76        20.84        24.56        34.85        36.76        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W 
       18.08        35.47        32.48        19.00        14.30        14.53 
TCGA-L9-A7SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TF 
       18.58        58.45        37.35        86.04        41.59        11.05 
TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       24.36        11.15        73.91        74.33         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A7XG 
        0.49         0.43        20.28 

  AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE 
                          0.00                           0.36 
  AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE 
                        156.66                         238.29 
  AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE 
                         20.19                          22.45 
[1] "0.0 - 156.7 (20.2)" "0.4 - 238.3 (22.4)"
[1] "hr=" "1.4"
D17V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 17(12Q14.1) MUTATED         3       38       40        1        18
  AMP PEAK 17(12Q14.1) WILD-TYPE       2       95       99        0        32
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 17(12Q14.1) MUTATED          25         28          3       11
  AMP PEAK 17(12Q14.1) WILD-TYPE        47         44          8       14
D17V3, multiclass
            clus
vv           AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             38                             95
  STAGE IB                             40                             99
  STAGE II                              1                              0
  STAGE IIA                            18                             32
  STAGE IIB                            25                             47
  STAGE IIIA                           28                             44
  STAGE IIIB                            3                              8
  STAGE IV                             11                             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 17(12Q14.1) MUTATED    48  96  18   6
  AMP PEAK 17(12Q14.1) WILD-TYPE 123 182  28  13
D17V4, multiclass
    clus
vv   AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE
  T1                           48                            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 17(12Q14.1) MUTATED   105  34    27
  AMP PEAK 17(12Q14.1) WILD-TYPE 228  62    49
D17V5, multiclass
       clus
vv      AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE
  N0                             105                            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"
D17V6, binary
                                cls
clus                               0   1
  AMP PEAK 17(12Q14.1) MUTATED   113  11
  AMP PEAK 17(12Q14.1) WILD-TYPE 236  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(12Q14.1) MUTATED    113   11
  AMP PEAK 17(12Q14.1) WILD-TYPE  236   14
   clus
vv  AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE
  0                          113                            236
  1                           11                             14
[1] 2 2
[1] FALSE
D17V7, binary
                                cls
clus                               0   1
  AMP PEAK 17(12Q14.1) MUTATED    85  84
  AMP PEAK 17(12Q14.1) WILD-TYPE 191 156
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(12Q14.1) MUTATED     85   84
  AMP PEAK 17(12Q14.1) WILD-TYPE  191  156
        clus
vv       AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE
  FEMALE                           85                            191
  MALE                             84                            156
[1] 2 2
[1] FALSE
D17V8, binary
                                cls
clus                               0   1
  AMP PEAK 17(12Q14.1) MUTATED   135  19
  AMP PEAK 17(12Q14.1) WILD-TYPE 275  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(12Q14.1) MUTATED    135   19
  AMP PEAK 17(12Q14.1) WILD-TYPE  275   41
     clus
vv    AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE
  NO                           135                            275
  YES                           19                             41
[1] 2 2
[1] FALSE
D17V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 17(12Q14.1) MUTATED                            5
  AMP PEAK 17(12Q14.1) WILD-TYPE                         13
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 17(12Q14.1) MUTATED                                  32
  AMP PEAK 17(12Q14.1) WILD-TYPE                                75
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 17(12Q14.1) MUTATED                                                  115
  AMP PEAK 17(12Q14.1) WILD-TYPE                                                206
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 17(12Q14.1) MUTATED                                            1
  AMP PEAK 17(12Q14.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 17(12Q14.1) MUTATED                                               5
  AMP PEAK 17(12Q14.1) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 17(12Q14.1) MUTATED                                1
  AMP PEAK 17(12Q14.1) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 17(12Q14.1) MUTATED                                    0
  AMP PEAK 17(12Q14.1) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(12Q14.1) MUTATED                              0
  AMP PEAK 17(12Q14.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 17(12Q14.1) MUTATED                               5
  AMP PEAK 17(12Q14.1) WILD-TYPE                            18
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 17(12Q14.1) MUTATED                                 0
  AMP PEAK 17(12Q14.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 17(12Q14.1) MUTATED                                               2
  AMP PEAK 17(12Q14.1) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 17(12Q14.1) MUTATED                              3
  AMP PEAK 17(12Q14.1) WILD-TYPE                            7
D17V10, multiclass
                                                    clus
vv                                                   AMP PEAK 17(12Q14.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          115
  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 17(12Q14.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              75
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            206
  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"
D17V11, continuous
D17V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 17(12Q14.1) MUTATED   115   4   3   7
  AMP PEAK 17(12Q14.1) WILD-TYPE 229   9   1  19
D17V13, multiclass
    clus
vv   AMP PEAK 17(12Q14.1) MUTATED AMP PEAK 17(12Q14.1) WILD-TYPE
  R0                          115                            229
  R1                            4                              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 17(12Q14.1) MUTATED                                  0     3
  AMP PEAK 17(12Q14.1) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(12Q14.1) MUTATED                          20   121
  AMP PEAK 17(12Q14.1) WILD-TYPE                        32   269
D17V14, multiclass
                                  clus
vv                                 AMP PEAK 17(12Q14.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     121
                                  clus
vv                                 AMP PEAK 17(12Q14.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    32
  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"
D17V15, binary
                                cls
clus                               0   1
  AMP PEAK 17(12Q14.1) MUTATED     3 118
  AMP PEAK 17(12Q14.1) WILD-TYPE   4 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(12Q14.1) MUTATED      3  118
  AMP PEAK 17(12Q14.1) WILD-TYPE    4  266
                        clus
vv                       AMP PEAK 17(12Q14.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          118
                        clus
vv                       AMP PEAK 17(12Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            266
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(12Q15) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 18(12Q15) MUTATED    95  69
  AMP PEAK 18(12Q15) WILD-TYPE 228 112
  AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE 
                         164                          340 
  AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE 
                          69                          112 
$`AMP PEAK 18(12Q15) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 TCGA-38-4631 
       19.96         8.02         9.01        15.02        15.02        11.64 
TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 
       29.00         9.37        46.72        16.04        17.16       156.66 
TCGA-49-AARN TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7726 
       37.32        41.69        48.62         5.79         7.99        21.44 
TCGA-55-8090 TCGA-55-A491 TCGA-55-A4DF TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 
       19.66        20.58        20.19        13.71        16.18         6.12 
TCGA-95-7947 TCGA-97-A4M7 TCGA-L9-A443 TCGA-MP-A4TD TCGA-05-4389 TCGA-05-4390 
       15.68        20.68         6.35        10.09        45.01        37.02 
TCGA-05-4395 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4430 TCGA-05-4432 
        0.00         2.99        14.96        29.98        25.02        25.02 
TCGA-05-4433 TCGA-05-5425 TCGA-35-4122 TCGA-35-5375 TCGA-38-4628 TCGA-44-2656 
       24.00        29.00         7.40         8.68        49.05        46.98 
TCGA-44-5644 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       28.37        61.28        16.44        19.46        36.07        18.87 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-49-4488 TCGA-49-4507 TCGA-49-4510 
       15.98        15.32         9.44        28.57         8.81        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR9 TCGA-49-AARE 
       29.75        55.89        55.33        22.26         8.55        40.41 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5931 
       71.47       101.72        15.72        60.16         8.22        14.27 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 TCGA-50-6673 TCGA-53-7624 TCGA-53-7813 
       57.53        53.16        25.55         0.72        34.29        13.94 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6712 TCGA-55-6971 TCGA-55-6982 TCGA-55-6984 
       38.73        67.89         5.62        46.03        32.71        24.99 
TCGA-55-6987 TCGA-55-7728 TCGA-55-7815 TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 
       70.26        23.15        25.41        34.19        29.23        29.72 
TCGA-55-8089 TCGA-55-8208 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       23.08        22.16        15.72        14.47        13.74        20.28 
TCGA-55-8615 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-62-8398 
       14.66        20.71         3.25         0.92        15.81        14.60 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1678 
       49.25        47.80        72.30        39.25        40.96        39.09 
TCGA-64-1681 TCGA-64-5779 TCGA-67-3774 TCGA-69-7760 TCGA-69-7973 TCGA-69-7980 
       38.37        28.41        12.66         6.64         7.56        13.51 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4666 TCGA-73-4675 TCGA-73-A9RS TCGA-75-5125 
        4.24        19.43        26.30        30.31        11.18        66.64 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7161 
      100.57       163.10        27.16         5.69        20.58         9.57 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-8655 TCGA-86-6562 TCGA-86-6851 
       88.14        26.53         8.02        77.59        12.36         5.88 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-8074 TCGA-86-8278 TCGA-86-8279 
       31.13        38.04        32.78         0.79        31.04        31.20 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 
       21.47        14.60        11.61        30.84         3.81        10.62 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-95-7567 TCGA-95-7944 
       10.19        12.23         7.36         1.18        18.67        12.39 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-8176 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M6 
        2.76        19.89        15.39        16.41        20.58        18.67 
TCGA-99-8032 TCGA-99-8033 TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4SW 
        1.45        21.57         1.91        15.65        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TI TCGA-NJ-A4YI 
       49.35        58.85         5.49        29.46        14.10         0.13 
TCGA-NJ-A55R TCGA-S2-AA1A 
       19.82        16.87 

$`AMP PEAK 18(12Q15) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4427 TCGA-38-4629 TCGA-38-4630 
       14.01         9.96        20.05        26.01        28.41        35.28 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       14.73        26.30        43.53        38.10        42.08        23.93 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-A47F TCGA-49-6761 
       27.78        86.01        18.31        29.23        11.08        11.64 
TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 TCGA-55-6979 TCGA-55-7573 TCGA-55-7724 
       40.60        21.47        23.05         7.79        16.01        23.18 
TCGA-55-7725 TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
       14.53         6.15        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 
       32.12        18.15        13.68        16.93        22.65        19.59 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.65        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 
       50.24        10.55        85.32         1.45        17.29        16.54 
TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
        2.86        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 
       20.52        17.75        24.30        23.80        10.09        21.83 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4250 
       27.19         5.29        31.23         2.43        50.07         3.98 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
       24.03        47.05        19.00        12.00        30.02        21.99 
TCGA-05-4426 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-38-4632 TCGA-38-A44F 
        5.98        97.74       120.79        37.71        44.61         4.37 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        44.94        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        33.73        26.56        33.30 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-7659 TCGA-44-7662 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       32.45        22.72         7.17        23.64        12.66         8.55 
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-49-6767 TCGA-49-AAR2 
       35.54        14.07        32.84        53.29        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       62.24        28.90       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 
       20.52        47.41        49.28         9.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 
       15.12        48.46        60.72        42.35         3.91        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       12.16         6.21        10.13        36.99        36.79        27.25 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 
       30.54        35.21        30.58        14.30        80.52        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       40.73        15.25        53.65         3.88        69.34        45.34 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
       92.81        40.54       107.21        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
       32.71        22.03         3.91        18.64        11.28        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
       18.44        19.82        15.19         5.06        17.79        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 
       15.65        29.19        15.42        17.56         0.36        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 
       19.96        26.01        17.10        17.62         1.58        12.33 
TCGA-55-A48Z TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       21.40        19.99        17.95         4.57        39.98        42.38 
TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y 
       88.64        19.53        56.71        54.35        67.96        13.61 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 
       29.92        56.81        81.80        37.02        87.98         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        20.05        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
       14.04        14.73         5.72         4.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
       13.61         5.42         6.05         4.41        13.41        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 
       13.45        26.73         8.42        23.38        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        9.24         1.25        50.33        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 
       49.84        36.66       108.66        19.27       129.53        21.90 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       39.95       119.51        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7537 
       64.90        22.92       104.19       238.29        31.20        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8662 
       26.01        39.35        10.55       232.18        39.75       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
       93.11        27.09        34.39        20.55        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 
       37.74         4.08         4.57        24.33        22.82        32.65 
TCGA-86-8280 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       23.05        13.91        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
       29.46        24.23        13.64        26.47        41.36         1.97 
TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
        2.60        27.68         1.15        16.60        14.27        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       27.29        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 
       14.30        21.60        21.44        19.76        20.84        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       34.85        36.76        21.63        18.08        35.47        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 
       19.00        14.30        14.53        18.58        38.63         2.76 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ 
       37.35        86.04        41.59        11.05        24.36        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        73.91        71.05        74.33         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
        0.49         0.43        20.28        59.11 

  AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE 
                        0.00                         0.36 
  AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE 
                      163.10                       238.29 
  AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE 
                      20.235                       22.550 
[1] "0.0 - 163.1 (20.2)" "0.4 - 238.3 (22.5)"
[1] "hr=" "1.4"
D18V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 18(12Q15) MUTATED         3       38       40        1        20
  AMP PEAK 18(12Q15) WILD-TYPE       2       95       99        0        30
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 18(12Q15) MUTATED          24         28          3       10
  AMP PEAK 18(12Q15) WILD-TYPE        48         44          8       15
D18V3, multiclass
            clus
vv           AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE
  STAGE I                             3                            2
  STAGE IA                           38                           95
  STAGE IB                           40                           99
  STAGE II                            1                            0
  STAGE IIA                          20                           30
  STAGE IIB                          24                           48
  STAGE IIIA                         28                           44
  STAGE IIIB                          3                            8
  STAGE IV                           10                           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 18(12Q15) MUTATED    49  97  17   5
  AMP PEAK 18(12Q15) WILD-TYPE 122 181  29  14
D18V4, multiclass
    clus
vv   AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE
  T1                         49                          122
  T2                         97                          181
  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 18(12Q15) MUTATED   104  35    28
  AMP PEAK 18(12Q15) WILD-TYPE 229  61    48
D18V5, multiclass
       clus
vv      AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE
  N0                           104                          229
  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"
D18V6, binary
                              cls
clus                             0   1
  AMP PEAK 18(12Q15) MUTATED   114  10
  AMP PEAK 18(12Q15) WILD-TYPE 235  15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(12Q15) MUTATED    114   10
  AMP PEAK 18(12Q15) WILD-TYPE  235   15
   clus
vv  AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE
  0                        114                          235
  1                         10                           15
[1] 2 2
[1] FALSE
D18V7, binary
                              cls
clus                             0   1
  AMP PEAK 18(12Q15) MUTATED    84  85
  AMP PEAK 18(12Q15) WILD-TYPE 192 155
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(12Q15) MUTATED     84   85
  AMP PEAK 18(12Q15) WILD-TYPE  192  155
        clus
vv       AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE
  FEMALE                         84                          192
  MALE                           85                          155
[1] 2 2
[1] FALSE
D18V8, binary
                              cls
clus                             0   1
  AMP PEAK 18(12Q15) MUTATED   136  19
  AMP PEAK 18(12Q15) WILD-TYPE 274  41
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(12Q15) MUTATED    136   19
  AMP PEAK 18(12Q15) WILD-TYPE  274   41
     clus
vv    AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE
  NO                         136                          274
  YES                         19                           41
[1] 2 2
[1] FALSE
D18V9, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 18(12Q15) MUTATED                            5
  AMP PEAK 18(12Q15) WILD-TYPE                         13
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 18(12Q15) MUTATED                                  35
  AMP PEAK 18(12Q15) WILD-TYPE                                72
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 18(12Q15) MUTATED                                                  113
  AMP PEAK 18(12Q15) WILD-TYPE                                                208
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 18(12Q15) MUTATED                                            1
  AMP PEAK 18(12Q15) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 18(12Q15) MUTATED                                               4
  AMP PEAK 18(12Q15) WILD-TYPE                                            15
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 18(12Q15) MUTATED                                1
  AMP PEAK 18(12Q15) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 18(12Q15) MUTATED                                    0
  AMP PEAK 18(12Q15) WILD-TYPE                                  3
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 18(12Q15) MUTATED                              0
  AMP PEAK 18(12Q15) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 18(12Q15) MUTATED                               5
  AMP PEAK 18(12Q15) WILD-TYPE                            18
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 18(12Q15) MUTATED                                 0
  AMP PEAK 18(12Q15) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 18(12Q15) MUTATED                                               2
  AMP PEAK 18(12Q15) WILD-TYPE                                             3
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 18(12Q15) MUTATED                              3
  AMP PEAK 18(12Q15) WILD-TYPE                            7
D18V10, multiclass
                                                    clus
vv                                                   AMP PEAK 18(12Q15) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          35
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        113
  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 18(12Q15) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            72
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          208
  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"
D18V11, continuous
D18V12, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 18(12Q15) MUTATED   115   5   3   6
  AMP PEAK 18(12Q15) WILD-TYPE 229   8   1  20
D18V13, multiclass
    clus
vv   AMP PEAK 18(12Q15) MUTATED AMP PEAK 18(12Q15) WILD-TYPE
  R0                        115                          229
  R1                          5                            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 18(12Q15) MUTATED                                  0     3
  AMP PEAK 18(12Q15) WILD-TYPE                                1     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(12Q15) MUTATED                          17   123
  AMP PEAK 18(12Q15) WILD-TYPE                        35   267
D18V14, multiclass
                                  clus
vv                                 AMP PEAK 18(12Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                17
  WHITE                                                   123
                                  clus
vv                                 AMP PEAK 18(12Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  35
  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"
D18V15, binary
                              cls
clus                             0   1
  AMP PEAK 18(12Q15) MUTATED     3 116
  AMP PEAK 18(12Q15) WILD-TYPE   4 268
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(12Q15) MUTATED      3  116
  AMP PEAK 18(12Q15) WILD-TYPE    4  268
                        clus
vv                       AMP PEAK 18(12Q15) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        116
                        clus
vv                       AMP PEAK 18(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          268
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(13Q33.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(13Q33.3) MUTATED    43  31
  AMP PEAK 19(13Q33.3) WILD-TYPE 280 150
  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                            74                            430 
  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                            31                            150 
$`AMP PEAK 19(13Q33.3) MUTATED`
TCGA-05-4382 TCGA-38-4629 TCGA-38-4631 TCGA-44-2655 TCGA-44-7670 TCGA-44-7671 
       19.96        28.41        11.64        43.53        29.00        29.23 
TCGA-49-4501 TCGA-49-6742 TCGA-55-7726 TCGA-55-8205 TCGA-55-8511 TCGA-55-A492 
       46.72        16.04        21.44        19.69        18.15        19.59 
TCGA-L9-A444 TCGA-05-4249 TCGA-05-4397 TCGA-05-5428 TCGA-44-2659 TCGA-44-7660 
       10.09        50.07        24.03        22.03        44.94        19.46 
TCGA-49-6743 TCGA-50-5045 TCGA-50-5930 TCGA-50-5941 TCGA-50-6591 TCGA-50-6673 
       53.29        71.47         9.27        48.46         3.91         0.72 
TCGA-53-7624 TCGA-53-7626 TCGA-55-5899 TCGA-55-6968 TCGA-55-7281 TCGA-55-7907 
       34.29        30.54        30.58        42.51        28.67        11.28 
TCGA-55-7910 TCGA-55-8089 TCGA-55-8094 TCGA-55-8507 TCGA-55-8508 TCGA-55-8620 
       34.19        23.08        17.79        13.74        20.28        12.33 
TCGA-55-A48Z TCGA-55-A490 TCGA-62-8394 TCGA-62-8402 TCGA-62-A46U TCGA-62-A470 
       21.40         3.25         4.57        49.25        67.96        39.25 
TCGA-64-1680 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-69-7979 TCGA-69-7980 
       37.02        20.05        18.84         5.72        13.41        13.51 
TCGA-69-8253 TCGA-73-4677 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7149 
       14.01         1.25        36.66       100.57       163.10       129.53 
TCGA-78-7155 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-86-6562 TCGA-86-6851 
       38.50        88.14        26.53        53.33        12.36         5.88 
TCGA-86-7955 TCGA-86-8074 TCGA-86-8075 TCGA-91-6847 TCGA-95-7567 TCGA-97-7546 
       35.24         0.79        22.82        27.68        18.67        42.25 
TCGA-97-7547 TCGA-97-7938 TCGA-97-8177 TCGA-J2-A4AE TCGA-MN-A4N4 TCGA-MP-A4SW 
       64.60         0.59        16.41        35.47        38.63        58.45 
TCGA-MP-A4T7 TCGA-NJ-A4YG 
        5.49        74.33 

$`AMP PEAK 19(13Q33.3) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       14.01         9.96         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-44-2661 
       15.02        15.02        35.28        14.73        26.30        38.10 
TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-8119 
       42.08        23.93        27.78        86.01        18.31         9.37 
TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       11.08        17.16        11.64       156.66        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       21.47        41.69        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 
        7.99        16.01        23.18        14.53         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 
       19.73        17.98        16.93        32.12        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       22.65        20.58        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       82.68        39.09         8.48        50.24        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       13.71        16.18         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 
       10.09         3.98        45.01        37.02         0.00        47.05 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       19.00         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       21.99        26.01        25.02        25.02        24.00         4.96 
TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
       29.00         9.04         2.04         0.46         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 
        8.68        97.74       120.79        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        4.37        46.98        44.42        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        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        7.17        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        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-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 
       32.84         8.81        29.46        29.75        55.89        55.33 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26        22.26        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       40.41       123.58       221.33       164.12         9.86        20.52 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
      101.72        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 
       14.27        78.67         8.45        15.12        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       53.16        42.35        25.55        11.05        12.16         6.21 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ 
       10.13        36.99        36.79        27.25        13.94        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       38.73        67.89        14.30        80.52         5.62        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       20.02        27.09        32.71        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 
       25.41        18.64        17.65        18.44        19.82        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       29.72        15.19         5.06        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-A48Y TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B 
        1.58        20.71         0.92        15.81        19.99        17.95 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P 
       39.98        42.38        14.60        88.64        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 
       56.71        54.35        72.30        13.61        40.96        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       56.81        39.09        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 
       42.90        28.41        51.25        28.47        20.05        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       12.66        14.73         4.64         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-8254 
       13.61         5.42         7.56         6.05         4.41        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 
        4.24        26.73        19.43         8.42        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS 
       15.35         4.31        30.31         9.24        50.33        11.18 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 
       66.64        77.85        43.82        85.15        49.84       108.66 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        19.27        20.58        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 
      119.51        19.50        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
        9.57       104.19       238.29        31.20         8.02        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       93.11        27.09        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       32.78        19.89        37.74         4.08         4.57        24.33 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       32.65        31.04        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       11.61        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       26.50        29.46         3.81        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
        7.36         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       22.45        17.46        23.61         1.08        19.00        41.82 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 
       12.39        27.29         2.76        19.89        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       25.48        18.54        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 
       15.39        14.30        21.60        20.58        21.44        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
       21.57        21.63        18.08        32.48        19.00        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.53         1.91        18.58        15.65         2.76        86.14 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TE 
       49.35        37.35        86.04        58.85        41.59        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       11.05        24.36        14.10        11.15        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05         0.13         1.64        47.08         0.49         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                          0.59                           0.00 
  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                        163.10                         238.29 
  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE 
                        23.555                         21.470 
[1] "0.6 - 163.1 (23.6)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.1"
D19V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 19(13Q33.3) MUTATED         2       12       22        0        13
  AMP PEAK 19(13Q33.3) WILD-TYPE       3      121      117        1        37
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 19(13Q33.3) MUTATED           6          7          3        8
  AMP PEAK 19(13Q33.3) WILD-TYPE        66         65          8       17
D19V3, multiclass
            clus
vv           AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             12                            121
  STAGE IB                             22                            117
  STAGE II                              0                              1
  STAGE IIA                            13                             37
  STAGE IIB                             6                             66
  STAGE IIIA                            7                             65
  STAGE IIIB                            3                              8
  STAGE IV                              8                             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 19(13Q33.3) MUTATED    26  46   2   2
  AMP PEAK 19(13Q33.3) WILD-TYPE 145 232  44  17
D19V4, multiclass
    clus
vv   AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  T1                           26                            145
  T2                           46                            232
  T3                            2                             44
  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
  AMP PEAK 19(13Q33.3) MUTATED    48  18    10
  AMP PEAK 19(13Q33.3) WILD-TYPE 285  78    66
D19V5, multiclass
       clus
vv      AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  N0                              48                            285
  N1                              18                             78
  N2+N3                           10                             66
[1] 3 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(13Q33.3) MUTATED    50   8
  AMP PEAK 19(13Q33.3) WILD-TYPE 299  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q33.3) MUTATED     50    8
  AMP PEAK 19(13Q33.3) WILD-TYPE  299   17
   clus
vv  AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  0                           50                            299
  1                            8                             17
[1] 2 2
[1] FALSE
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q33.3) MUTATED    45  31
  AMP PEAK 19(13Q33.3) WILD-TYPE 231 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q33.3) MUTATED     45   31
  AMP PEAK 19(13Q33.3) WILD-TYPE  231  209
        clus
vv       AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  FEMALE                           45                            231
  MALE                             31                            209
[1] 2 2
[1] FALSE
D19V8, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q33.3) MUTATED    57  14
  AMP PEAK 19(13Q33.3) WILD-TYPE 353  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q33.3) MUTATED     57   14
  AMP PEAK 19(13Q33.3) WILD-TYPE  353   46
     clus
vv    AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  NO                            57                            353
  YES                           14                             46
[1] 2 2
[1] FALSE
D19V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 19(13Q33.3) MUTATED                            3
  AMP PEAK 19(13Q33.3) WILD-TYPE                         15
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 19(13Q33.3) MUTATED                                  17
  AMP PEAK 19(13Q33.3) WILD-TYPE                                90
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 19(13Q33.3) MUTATED                                                   48
  AMP PEAK 19(13Q33.3) WILD-TYPE                                                273
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 19(13Q33.3) MUTATED                                            0
  AMP PEAK 19(13Q33.3) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 19(13Q33.3) MUTATED                                               2
  AMP PEAK 19(13Q33.3) WILD-TYPE                                            17
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 19(13Q33.3) MUTATED                                1
  AMP PEAK 19(13Q33.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 19(13Q33.3) MUTATED                                    0
  AMP PEAK 19(13Q33.3) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 19(13Q33.3) MUTATED                              0
  AMP PEAK 19(13Q33.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 19(13Q33.3) MUTATED                               3
  AMP PEAK 19(13Q33.3) WILD-TYPE                            20
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 19(13Q33.3) MUTATED                                 0
  AMP PEAK 19(13Q33.3) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 19(13Q33.3) MUTATED                                               0
  AMP PEAK 19(13Q33.3) WILD-TYPE                                             5
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 19(13Q33.3) MUTATED                              2
  AMP PEAK 19(13Q33.3) WILD-TYPE                            8
D19V10, multiclass
                                                    clus
vv                                                   AMP PEAK 19(13Q33.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           48
  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                                                 3
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 0
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   AMP PEAK 19(13Q33.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              90
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            273
  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                                                  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"
D19V11, continuous
D19V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(13Q33.3) MUTATED    55   0   1   1
  AMP PEAK 19(13Q33.3) WILD-TYPE 289  13   3  25
D19V13, multiclass
    clus
vv   AMP PEAK 19(13Q33.3) MUTATED AMP PEAK 19(13Q33.3) WILD-TYPE
  R0                           55                            289
  R1                            0                             13
  R2                            1                              3
  RX                            1                             25
[1] 4 2
[1] 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(13Q33.3) MUTATED                                  0     0
  AMP PEAK 19(13Q33.3) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(13Q33.3) MUTATED                           6    60
  AMP PEAK 19(13Q33.3) WILD-TYPE                        46   330
D19V14, multiclass
                                  clus
vv                                 AMP PEAK 19(13Q33.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      60
                                  clus
vv                                 AMP PEAK 19(13Q33.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  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"
D19V15, binary
                                cls
clus                               0   1
  AMP PEAK 19(13Q33.3) MUTATED     2  53
  AMP PEAK 19(13Q33.3) WILD-TYPE   5 331
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(13Q33.3) MUTATED      2   53
  AMP PEAK 19(13Q33.3) WILD-TYPE    5  331
                        clus
vv                       AMP PEAK 19(13Q33.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           53
                        clus
vv                       AMP PEAK 19(13Q33.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            331
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(14Q13.3) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(14Q13.3) MUTATED   154  76
  AMP PEAK 20(14Q13.3) WILD-TYPE 169 105
  AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE 
                           230                            274 
  AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE 
                            76                            105 
$`AMP PEAK 20(14Q13.3) MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 TCGA-38-4629 TCGA-38-4630 TCGA-44-6147 
        8.02        20.05        26.01        28.41        35.28        27.78 
TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 TCGA-49-6761 TCGA-49-AAR0 TCGA-50-5935 
       29.00         9.37        46.72        11.64       156.66        21.47 
TCGA-55-1595 TCGA-55-7724 TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       48.62        23.18         6.15        19.73        17.98        16.93 
TCGA-55-8207 TCGA-55-8511 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       32.12        18.15        20.19        20.65        13.87        52.60 
TCGA-73-4662 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       82.68        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-97-A4LX TCGA-97-A4M3 TCGA-J2-8192 
        6.12        17.29         2.86        20.19        17.75        24.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-05-4389 TCGA-05-4390 
        6.35        10.09        27.19         5.29        45.01        37.02 
TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4424 TCGA-05-4432 TCGA-05-5423 
       47.05         2.99        14.96        30.02        25.02         4.96 
TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 
        2.04         5.98         8.68        37.71        49.05        44.61 
TCGA-44-2659 TCGA-44-2668 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-4112 
       44.94        25.02        38.24        38.89        34.06        26.56 
TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       21.63        61.28        16.44        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       36.07        18.87        23.64        15.98        15.32         9.44 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4512 
       13.45        76.21        28.11        28.57        12.66        29.75 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V 
       22.26        22.26        28.90       123.58       221.33         9.86 
TCGA-50-5045 TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       71.47        78.67        48.46        53.16        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        36.99        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       35.21        38.73        30.58        14.30        80.52         5.62 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 TCGA-55-6981 TCGA-55-6983 TCGA-55-7281 
       15.25        46.03         3.88        45.34        92.81        28.67 
TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 
        3.91        25.41        18.64        11.28        34.19        18.44 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8096 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 
       29.23        29.72        23.64        29.19        17.56        15.72 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.36        13.74        17.72        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG 
        1.58        20.71        21.40         3.25         0.92        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8402 TCGA-62-A46U TCGA-64-1676 TCGA-64-1678 
       17.95         4.57        49.25        67.96        56.81        39.09 
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        20.05        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-69-7760 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 
       18.84        14.04         6.64        22.68         7.56         6.05 
TCGA-69-7979 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4676 
       13.41        19.43         8.42        23.38        26.30         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5147 TCGA-75-6212 TCGA-75-7025 
        1.25        50.33        11.18        43.82        49.84       108.66 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7155 TCGA-78-7159 
       27.16         5.69        20.58       129.53        38.50        64.90 
TCGA-78-7161 TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 TCGA-78-8662 TCGA-80-5608 
        9.57         8.02        26.01       232.18       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 
       27.09        12.36        31.13        38.04        32.78        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
       37.74         4.08         0.79        31.04        31.20        23.05 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 TCGA-91-6828 
       21.47        11.61        30.84        28.34         3.81        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       41.36        10.19         2.60        12.23        27.68         7.36 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7567 
       16.60        14.27         1.18        23.61        19.00        18.67 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 
        2.76        19.89        42.25        25.48        18.54        18.67 
TCGA-97-8179 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8032 
       14.30        21.44        19.76        18.67        24.56         1.45 
TCGA-J2-A4AG TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 
       32.48        38.63        86.14        49.35        86.04        58.85 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YP 
       41.59        29.46        11.05        19.13        71.05         1.64 
TCGA-NJ-A55R TCGA-O1-A52J 
       19.82        59.11 

$`AMP PEAK 20(14Q13.3) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 
       19.96        14.01         9.96         9.01        15.02        15.02 
TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 
       11.64        14.73        26.30        43.53        38.10        42.08 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-A47F TCGA-49-6742 
       23.93        86.01        18.31        29.23        11.08        16.04 
TCGA-49-6745 TCGA-49-AARN TCGA-50-5932 TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 
       17.16        37.32        40.60        41.69        23.05         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 
        7.79         7.99        16.01        14.53        21.44        19.66 
TCGA-55-8205 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       19.69        13.68        16.93        22.65        20.58        19.59 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 
       39.09         8.48        50.24        16.54        15.68        15.65 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8194 
       21.40        18.18        17.92        20.52        20.68        23.80 
TCGA-L9-A743 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
       21.83        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 
        0.00        24.03        19.00        29.98        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       26.01        25.02        24.00        29.00        22.03         9.04 
TCGA-35-3615 TCGA-35-4122 TCGA-38-4625 TCGA-38-4626 TCGA-38-A44F TCGA-44-2656 
        0.46         7.40        97.74       120.79         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3919 TCGA-44-5643 
       44.42        42.77         3.19        37.15        33.73        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 
       28.37        28.01        23.77        19.56        23.15        23.18 
TCGA-44-6777 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47G TCGA-44-A4SS TCGA-49-4494 
       32.45        12.66         8.55        11.54        13.64        35.54 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 
       14.07        32.84         8.81        29.46        55.89        53.29 
TCGA-49-6744 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARR 
       55.33        73.12        62.24         8.55        40.41       164.12 
TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
        8.22         9.27        14.27         8.45        15.12        60.72 
TCGA-50-5944 TCGA-50-6592 TCGA-50-6593 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
       57.53        25.55        11.05        36.79        27.25        34.29 
TCGA-53-7626 TCGA-55-1596 TCGA-55-6968 TCGA-55-6969 TCGA-55-6972 TCGA-55-6980 
       30.54        67.89        42.51        40.73        53.65        69.34 
TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 
       32.71        24.99        40.54       107.21        70.26        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 TCGA-55-7911 TCGA-55-7994 
       27.09        32.71        22.03        23.15        17.65        19.82 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8208 
       15.19        23.08         5.06        17.79        15.65        22.16 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8620 
       15.42        14.47        20.28        19.96        26.01        12.33 
TCGA-55-A494 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O 
       15.81        39.98        42.38        14.60        88.64        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        54.35        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 
       40.96        29.92        81.80        37.02        38.37        42.90 
TCGA-64-5781 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 
       51.25        12.66        14.73         5.72         4.64         6.12 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
       13.61         5.42         4.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-75-5125 
        4.24        26.73        15.35         4.31        30.31        66.64 
TCGA-75-5146 TCGA-75-6206 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7147 
       77.85        85.15        36.66       100.57       163.10        19.27 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95       119.51        19.50        32.09         5.88 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
       22.92       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-86-6851 
       53.33        39.35        10.55        39.75        77.59         5.88 
TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
       34.39        20.55        19.89         4.57        24.33        22.82 
TCGA-86-8076 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
       32.65        14.60        13.91        27.58         0.62        26.50 
TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6849 
       29.46        24.23        13.64        26.47         1.97         1.15 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7944 
       19.82        22.45        17.46         1.08        41.82        12.39 
TCGA-95-8039 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 
       27.29        64.60        63.52        61.48         0.59        15.91 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 
        5.39        18.12        15.39        16.41        21.60        20.58 
TCGA-97-A4M5 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD 
       20.84        34.85        36.76        21.57        21.63        18.08 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV 
       35.47        19.00        14.30        14.53         1.91        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TH 
       15.65         2.76        58.45        37.35         5.49        24.36 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ 
       14.10        11.15        73.91        74.33         0.13        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.49         0.43        20.28        16.87 

  AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE 
                          0.36                           0.00 
  AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE 
                        232.18                         238.29 
  AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE 
                        21.420                         21.945 
[1] "0.4 - 232.2 (21.4)" "0.0 - 238.3 (21.9)"
[1] "hr=" "1.1"
D20V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 20(14Q13.3) MUTATED         2       61       60        1        28
  AMP PEAK 20(14Q13.3) WILD-TYPE       3       72       79        0        22
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 20(14Q13.3) MUTATED          30         30          7       10
  AMP PEAK 20(14Q13.3) WILD-TYPE        42         42          4       15
D20V3, multiclass
            clus
vv           AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             61                             72
  STAGE IB                             60                             79
  STAGE II                              1                              0
  STAGE IIA                            28                             22
  STAGE IIB                            30                             42
  STAGE IIIA                           30                             42
  STAGE IIIB                            7                              4
  STAGE IV                             10                             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 20(14Q13.3) MUTATED    78 131  14   9
  AMP PEAK 20(14Q13.3) WILD-TYPE  93 147  32  10
D20V4, multiclass
    clus
vv   AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE
  T1                           78                             93
  T2                          131                            147
  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
  AMP PEAK 20(14Q13.3) MUTATED   151  42    35
  AMP PEAK 20(14Q13.3) WILD-TYPE 182  54    41
D20V5, multiclass
       clus
vv      AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE
  N0                             151                            182
  N1                              42                             54
  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"
D20V6, binary
                                cls
clus                               0   1
  AMP PEAK 20(14Q13.3) MUTATED   147  10
  AMP PEAK 20(14Q13.3) WILD-TYPE 202  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(14Q13.3) MUTATED    147   10
  AMP PEAK 20(14Q13.3) WILD-TYPE  202   15
   clus
vv  AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE
  0                          147                            202
  1                           10                             15
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(14Q13.3) MUTATED   128 105
  AMP PEAK 20(14Q13.3) WILD-TYPE 148 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(14Q13.3) MUTATED    128  105
  AMP PEAK 20(14Q13.3) WILD-TYPE  148  135
        clus
vv       AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE
  FEMALE                          128                            148
  MALE                            105                            135
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(14Q13.3) MUTATED   188  28
  AMP PEAK 20(14Q13.3) WILD-TYPE 222  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(14Q13.3) MUTATED    188   28
  AMP PEAK 20(14Q13.3) WILD-TYPE  222   32
     clus
vv    AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE
  NO                           188                            222
  YES                           28                             32
[1] 2 2
[1] FALSE
D20V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 20(14Q13.3) MUTATED                           10
  AMP PEAK 20(14Q13.3) WILD-TYPE                          8
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 20(14Q13.3) MUTATED                                  42
  AMP PEAK 20(14Q13.3) WILD-TYPE                                65
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 20(14Q13.3) MUTATED                                                  159
  AMP PEAK 20(14Q13.3) WILD-TYPE                                                162
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 20(14Q13.3) MUTATED                                            1
  AMP PEAK 20(14Q13.3) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 20(14Q13.3) MUTATED                                               6
  AMP PEAK 20(14Q13.3) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 20(14Q13.3) MUTATED                                1
  AMP PEAK 20(14Q13.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 20(14Q13.3) MUTATED                                    2
  AMP PEAK 20(14Q13.3) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(14Q13.3) MUTATED                              0
  AMP PEAK 20(14Q13.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 20(14Q13.3) MUTATED                               9
  AMP PEAK 20(14Q13.3) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 20(14Q13.3) MUTATED                                 0
  AMP PEAK 20(14Q13.3) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 20(14Q13.3) MUTATED                                               2
  AMP PEAK 20(14Q13.3) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 20(14Q13.3) MUTATED                              1
  AMP PEAK 20(14Q13.3) WILD-TYPE                            9
D20V10, multiclass
                                                    clus
vv                                                   AMP PEAK 20(14Q13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          159
  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 20(14Q13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            162
  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"
D20V11, continuous
D20V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(14Q13.3) MUTATED   152   7   1  12
  AMP PEAK 20(14Q13.3) WILD-TYPE 192   6   3  14
D20V13, multiclass
    clus
vv   AMP PEAK 20(14Q13.3) MUTATED AMP PEAK 20(14Q13.3) WILD-TYPE
  R0                          152                            192
  R1                            7                              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 20(14Q13.3) MUTATED                                  0     5
  AMP PEAK 20(14Q13.3) WILD-TYPE                                1     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(14Q13.3) MUTATED                          23   178
  AMP PEAK 20(14Q13.3) WILD-TYPE                        29   212
D20V14, multiclass
                                  clus
vv                                 AMP PEAK 20(14Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     178
                                  clus
vv                                 AMP PEAK 20(14Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    29
  WHITE                                                       212
[1] 4 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(14Q13.3) MUTATED     2 180
  AMP PEAK 20(14Q13.3) WILD-TYPE   5 204
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(14Q13.3) MUTATED      2  180
  AMP PEAK 20(14Q13.3) WILD-TYPE    5  204
                        clus
vv                       AMP PEAK 20(14Q13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          180
                        clus
vv                       AMP PEAK 20(14Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            204
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(16P11.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(16P11.2) MUTATED   101  61
  AMP PEAK 21(16P11.2) WILD-TYPE 222 120
  AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE 
                           162                            342 
  AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE 
                            61                            120 
$`AMP PEAK 21(16P11.2) MUTATED`
TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-44-2662 TCGA-44-6147 TCGA-44-7670 
       28.41        11.64        14.73        42.08        27.78        29.00 
TCGA-49-AAR0 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-7284 TCGA-55-7573 
      156.66        21.47        41.69        23.05         7.99        16.01 
TCGA-55-7726 TCGA-55-8091 TCGA-67-6217 TCGA-73-4658 TCGA-95-7562 TCGA-95-7947 
       21.44        19.73        13.87        52.60         2.86        15.68 
TCGA-95-A4VK TCGA-97-A4M7 TCGA-L9-A443 TCGA-05-4249 TCGA-05-4390 TCGA-05-4395 
       21.40        20.68         6.35        50.07        37.02         0.00 
TCGA-05-4420 TCGA-05-5423 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
       29.98         4.96         7.40         8.68        97.74        37.71 
TCGA-38-4628 TCGA-44-2659 TCGA-44-2665 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       49.05        44.94        42.77        33.73        26.56        28.37 
TCGA-44-5645 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7662 
       28.01        23.18        32.45        61.28        16.44         7.17 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 
       15.32         9.44        13.45        28.57        12.66        14.07 
TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 TCGA-49-AARE TCGA-49-AARO TCGA-4B-A93V 
        8.81        29.75        55.33        40.41       123.58         9.86 
TCGA-50-5933 TCGA-50-5941 TCGA-50-6593 TCGA-50-6673 TCGA-50-8457 TCGA-50-8460 
       78.67        48.46        11.05         0.72        36.99        27.25 
TCGA-55-1594 TCGA-55-6712 TCGA-55-6980 TCGA-55-7281 TCGA-55-7907 TCGA-55-7910 
       38.73         5.62        69.34        28.67        11.28        34.19 
TCGA-55-7913 TCGA-55-7995 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       18.44        29.23         5.06        23.64        15.65        29.19 
TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
        0.36        17.72        19.96        12.33        21.40         3.25 
TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8398 TCGA-62-A46S TCGA-62-A46V 
        0.92        19.99        17.95        14.60        54.35        72.30 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-67-3770 TCGA-67-3772 
       56.81        81.80        37.02        38.37        20.05        18.84 
TCGA-67-6215 TCGA-69-7760 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 
        5.72         6.64        13.61         7.56         4.41        13.51 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4668 TCGA-73-4675 TCGA-73-A9RS TCGA-75-5125 
       19.43         8.42        15.35        30.31        11.18        66.64 
TCGA-75-6206 TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 TCGA-78-7146 TCGA-78-7149 
       85.15        36.66       108.66        27.16         5.69       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 
       21.90        39.95        19.50        32.09        64.90         9.57 
TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-86-7701 
      238.29        31.20         8.02        10.55       232.18        31.13 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8278 TCGA-86-8279 
       38.04        32.78        35.24         4.08        31.04        31.20 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8673 
       23.05        14.60        11.61        13.91        30.84        28.34 
TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6840 TCGA-91-8499 TCGA-93-7348 TCGA-93-A4JN 
       29.46         3.81        12.23         1.18        17.46        23.61 
TCGA-93-A4JP TCGA-97-7546 TCGA-97-7547 TCGA-97-7937 TCGA-97-7941 TCGA-97-8177 
       19.00        42.25        64.60        18.54        15.91        16.41 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD 
       14.30        20.58        19.76        34.85        21.57        18.08 
TCGA-J2-A4AG TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T6 
       32.48         1.91        15.65        38.63        58.45        58.85 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       71.05        74.33         1.64        19.82        59.11        16.87 

$`AMP PEAK 21(16P11.2) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 
       26.01        15.02        15.02        35.28        26.30        43.53 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 
       38.10        23.93        86.01        18.31        29.23         9.37 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN 
       11.08        46.72        16.04        17.16        11.64        37.32 
TCGA-50-5932 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7724 TCGA-55-7725 
       40.60        48.62         5.79         7.79        23.18        14.53 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
        6.15        19.66        17.98        16.93        19.69        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       18.15        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-64-1677 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       20.19        20.65        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       17.29        16.54        15.65        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 
       20.52        17.75        24.30        23.80        10.09        21.83 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 
       27.19         5.29        31.23         2.43        10.09         3.98 
TCGA-05-4389 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
       45.01        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       12.00        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       24.00        29.00        22.03         9.04         2.04         0.46 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
        5.98       120.79        44.61         4.37        46.98        44.42 
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-44-5643 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-7659 
       33.30        23.77        19.56        23.15        21.63        22.72 
TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       19.46        36.07        18.87        23.64        12.66         8.55 
TCGA-44-A479 TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 
       15.98        11.54        13.64        76.21        28.11        35.54 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV 
       32.84        29.46        55.89        53.29        22.26        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARQ TCGA-49-AARR 
       73.12        62.24        28.90         8.55       221.33       164.12 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 
       49.28         8.22         9.27        14.27         8.45        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       60.72        57.53        53.16        42.35         3.91        25.55 
TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 
       12.16         6.21        10.13        36.79        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       13.94        35.21        67.89        30.58        14.30        80.52 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 
       70.26        20.02        27.09        32.71        22.03         3.91 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7994 TCGA-55-8085 
       23.15        25.41        18.64        17.65        19.82        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       15.19        23.08        17.79        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8513 TCGA-55-8514 
       15.72        14.47        13.74        20.28        26.01        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A494 TCGA-62-8394 
       17.62        14.66         1.58        20.71        15.81         4.57 
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-A46U TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       56.71        67.96        13.61        39.25        40.96        29.92 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       39.09        87.98         2.04        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6216 
       28.47        20.05        14.04        12.66        14.73         4.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 
        6.12        22.68         5.42         6.05        13.41        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 
       13.45         4.24        26.73        23.38        26.30         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 
        9.24         1.25        50.33        77.85        43.82        49.84 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7147 TCGA-78-7148 TCGA-78-7153 TCGA-78-7155 
      100.57       163.10        19.27        20.58       119.51        38.50 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 
        5.88        22.92       104.19        88.14        26.53        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       26.01        39.35        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 
       27.09        12.36         5.88        34.39        20.55        19.89 
TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 
       37.74         4.57        24.33         0.79        22.82        32.65 
TCGA-86-8358 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 
       21.47        27.58         0.62        26.50        24.23        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-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
       27.68         7.36         1.15        16.60        14.27        19.82 
TCGA-93-7347 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
       22.45         1.08        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
        2.76        19.89        63.52        61.48        25.48         0.59 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8547 TCGA-97-A4M0 
       18.67         5.39        18.12        15.39        21.60        21.44 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R 
       20.84        18.67        24.56        36.76         1.45        21.63 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N5 
       35.47        19.00        14.30        14.53        18.58         2.76 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
       86.14        49.35        37.35        86.04         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
       29.46        11.05        24.36        14.10        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A7XG 
       73.91         0.13        47.08         0.49         0.43        20.28 

  AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE 
                          0.00                           0.13 
  AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE 
                        238.29                         221.33 
  AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE 
                         21.52                          21.63 
[1] "0.0 - 238.3 (21.5)" "0.1 - 221.3 (21.6)"
[1] "hr=" "1"  
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 21(16P11.2) MUTATED         3       51       41        0        15
  AMP PEAK 21(16P11.2) WILD-TYPE       2       82       98        1        35
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 21(16P11.2) MUTATED          20         22          4       11
  AMP PEAK 21(16P11.2) WILD-TYPE        52         50          7       14
D21V3, multiclass
            clus
vv           AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             51                             82
  STAGE IB                             41                             98
  STAGE II                              0                              1
  STAGE IIA                            15                             35
  STAGE IIB                            20                             52
  STAGE IIIA                           22                             50
  STAGE IIIB                            4                              7
  STAGE IV                             11                             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 21(16P11.2) MUTATED    63  81  16   5
  AMP PEAK 21(16P11.2) WILD-TYPE 108 197  30  14
D21V4, multiclass
    clus
vv   AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE
  T1                           63                            108
  T2                           81                            197
  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 21(16P11.2) MUTATED   107  28    26
  AMP PEAK 21(16P11.2) WILD-TYPE 226  68    50
D21V5, multiclass
       clus
vv      AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE
  N0                             107                            226
  N1                              28                             68
  N2+N3                           26                             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                                cls
clus                               0   1
  AMP PEAK 21(16P11.2) MUTATED   110  11
  AMP PEAK 21(16P11.2) WILD-TYPE 239  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(16P11.2) MUTATED    110   11
  AMP PEAK 21(16P11.2) WILD-TYPE  239   14
   clus
vv  AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE
  0                          110                            239
  1                           11                             14
[1] 2 2
[1] FALSE
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(16P11.2) MUTATED    94  73
  AMP PEAK 21(16P11.2) WILD-TYPE 182 167
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(16P11.2) MUTATED     94   73
  AMP PEAK 21(16P11.2) WILD-TYPE  182  167
        clus
vv       AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE
  FEMALE                           94                            182
  MALE                             73                            167
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(16P11.2) MUTATED   133  21
  AMP PEAK 21(16P11.2) WILD-TYPE 277  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(16P11.2) MUTATED    133   21
  AMP PEAK 21(16P11.2) WILD-TYPE  277   39
     clus
vv    AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE
  NO                           133                            277
  YES                           21                             39
[1] 2 2
[1] FALSE
D21V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 21(16P11.2) MUTATED                            4
  AMP PEAK 21(16P11.2) WILD-TYPE                         14
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 21(16P11.2) MUTATED                                  30
  AMP PEAK 21(16P11.2) WILD-TYPE                                77
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 21(16P11.2) MUTATED                                                  113
  AMP PEAK 21(16P11.2) WILD-TYPE                                                208
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 21(16P11.2) MUTATED                                            2
  AMP PEAK 21(16P11.2) WILD-TYPE                                          3
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 21(16P11.2) MUTATED                                               6
  AMP PEAK 21(16P11.2) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 21(16P11.2) MUTATED                                0
  AMP PEAK 21(16P11.2) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 21(16P11.2) MUTATED                                    2
  AMP PEAK 21(16P11.2) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(16P11.2) MUTATED                              0
  AMP PEAK 21(16P11.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 21(16P11.2) MUTATED                               9
  AMP PEAK 21(16P11.2) WILD-TYPE                            14
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 21(16P11.2) MUTATED                                 0
  AMP PEAK 21(16P11.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 21(16P11.2) MUTATED                                               1
  AMP PEAK 21(16P11.2) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 21(16P11.2) MUTATED                              0
  AMP PEAK 21(16P11.2) WILD-TYPE                           10
D21V10, multiclass
                                                    clus
vv                                                   AMP PEAK 21(16P11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          113
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 6
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 9
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 1
  MUCINOUS (COLLOID) CARCINOMA                                                  0
                                                    clus
vv                                                   AMP PEAK 21(16P11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            208
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  14
  LUNG SIGNET RING ADENOCARCINOMA                                                 1
  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"
D21V11, continuous
D21V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(16P11.2) MUTATED   115   6   1  11
  AMP PEAK 21(16P11.2) WILD-TYPE 229   7   3  15
D21V13, multiclass
    clus
vv   AMP PEAK 21(16P11.2) MUTATED AMP PEAK 21(16P11.2) WILD-TYPE
  R0                          115                            229
  R1                            6                              7
  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
  AMP PEAK 21(16P11.2) MUTATED                                  1     3
  AMP PEAK 21(16P11.2) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(16P11.2) MUTATED                          18   130
  AMP PEAK 21(16P11.2) WILD-TYPE                        34   260
D21V14, multiclass
                                  clus
vv                                 AMP PEAK 21(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     130
                                  clus
vv                                 AMP PEAK 21(16P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    34
  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"
D21V15, binary
                                cls
clus                               0   1
  AMP PEAK 21(16P11.2) MUTATED     2 126
  AMP PEAK 21(16P11.2) WILD-TYPE   5 258
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(16P11.2) MUTATED      2  126
  AMP PEAK 21(16P11.2) WILD-TYPE    5  258
                        clus
vv                       AMP PEAK 21(16P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          126
                        clus
vv                       AMP PEAK 21(16P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            258
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(17Q12) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 22(17Q12) MUTATED   139  83
  AMP PEAK 22(17Q12) WILD-TYPE 184  98
  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                         222                          282 
  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                          83                           98 
$`AMP PEAK 22(17Q12) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 TCGA-38-4630 
       19.96         8.02         9.01        26.01        28.41        35.28 
TCGA-38-4631 TCGA-44-2662 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 
       11.64        42.08        18.31        29.00         9.37        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 
       16.04        17.16        21.47        41.69        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-A491 
        5.79         7.79        19.69        32.12        18.15        20.58 
TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       20.65        52.60        82.68        50.24        10.55        85.32 
TCGA-91-6836 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VN 
       13.71         6.12        17.29        16.54        15.68        18.18 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TD 
        6.35        10.09        21.83        27.19         5.29        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 
       50.07         3.98        45.01         0.00        47.05         2.99 
TCGA-05-4417 TCGA-05-4424 TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-5715 
       14.96        30.02        21.99        25.02        25.02         2.04 
TCGA-35-4122 TCGA-38-4628 TCGA-38-4632 TCGA-44-3396 TCGA-44-3917 TCGA-44-3919 
        7.40        49.05        44.61        37.15        38.89        33.73 
TCGA-44-6144 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7660 
       23.77        23.15        23.18        32.45        61.28        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-8120 TCGA-44-A47B TCGA-44-A4SS TCGA-49-4490 
        7.17        36.07         8.55         9.44        13.64        12.66 
TCGA-49-4505 TCGA-49-4507 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR4 TCGA-49-AARO 
       14.07         8.81        53.29        55.33        28.90       123.58 
TCGA-49-AARQ TCGA-50-5049 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 
      221.33       101.72         9.27        14.27        78.67        48.46 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       57.53        53.16         3.91        25.55        11.05        12.16 
TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
       13.94        38.73        67.89        30.58        80.52         5.62 
TCGA-55-6981 TCGA-55-6982 TCGA-55-7281 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 
       45.34        32.71        28.67        22.03         3.91        25.41 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       18.64        11.28        17.65        19.82        29.23        29.72 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 
       23.08         5.06        17.79        22.16        15.72        13.74 
TCGA-55-8510 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
       17.72        17.10         1.58        12.33        21.40         3.25 
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-A46R TCGA-62-A46S TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 
       56.71        54.35        13.61        39.25        40.96        56.81 
TCGA-64-1680 TCGA-64-5774 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 
       37.02        87.98        20.05        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         4.41        13.51 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
       19.43         8.42        26.30        15.35        30.31         9.24 
TCGA-73-7499 TCGA-75-5125 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       50.33        66.64       163.10        27.16         5.69        19.27 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 
      129.53        19.50        32.09        64.90         9.57        88.14 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 TCGA-78-8662 TCGA-86-6562 
       26.53         8.02        26.01       232.18       110.50        12.36 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
        5.88        34.39        38.04        32.78        19.89        35.24 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 
        4.08         0.79        22.82        31.20        21.47        11.61 
TCGA-86-8668 TCGA-86-8669 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6835 
       13.91        30.84         3.81        13.64        10.62         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-93-7348 TCGA-93-A4JP TCGA-95-7039 
       12.23        27.68         7.36        17.46        19.00        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7553 TCGA-97-7554 
       18.67        12.39        27.29         2.76        61.48        25.48 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M6 
       18.12        16.41        14.30        21.60        20.58        18.67 
TCGA-99-8025 TCGA-99-8032 TCGA-J2-A4AD TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       34.85         1.45        18.08        18.58        15.65        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 
        2.76        86.14        49.35        86.04        58.85        41.59 
TCGA-MP-A4TE TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A7XG TCGA-O1-A52J 
       29.46        19.13        71.05        74.33        20.28        59.11 

$`AMP PEAK 22(17Q12) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4434 TCGA-05-5420 TCGA-38-6178 
       14.01         9.96        20.05        15.02        15.02        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 
       26.30        43.53        38.10        23.93        27.78        86.01 
TCGA-44-7671 TCGA-44-A47F TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       29.23        11.08        11.64       156.66        37.32        40.60 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.99        16.01        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8619 TCGA-55-8621 
       19.66        19.73        17.98        16.93        13.68        16.93 
TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-7498 TCGA-78-7166 
       22.65        19.59        20.19        13.87        39.09         8.48 
TCGA-91-7771 TCGA-91-A4BC TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 
       16.18         1.45         2.86        15.65        21.40        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4390 TCGA-05-4397 TCGA-05-4403 TCGA-05-4420 
       31.23         2.43        37.02        24.03        19.00        29.98 
TCGA-05-4422 TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       12.00        26.01        24.00         4.96        29.00        22.03 
TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        9.04         0.46         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 
       37.71         4.37        46.98        44.42        44.94        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 
        3.19        25.02        38.24        34.06        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6774 TCGA-44-6779 TCGA-44-7659 
       28.37        28.01        19.56        21.63        16.44        22.72 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G 
       18.87        23.64        12.66        15.98        15.32        11.54 
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-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 
       29.46        29.75        55.89        22.26        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       62.24         8.55        40.41       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       71.47        15.72        60.16        47.41        49.28         8.22 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 TCGA-50-6595 TCGA-50-6673 
        8.45        15.12        60.72        42.35         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       35.21        14.30        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       53.65         3.88        69.34        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7728 
      107.21        70.26        20.02        27.09        32.71        23.15 
TCGA-55-7910 TCGA-55-7913 TCGA-55-8087 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       34.19        18.44        15.19        23.64        15.65        29.19 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 
       15.42        17.56        14.47         0.36        20.28        19.96 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48Y TCGA-55-A493 TCGA-62-8395 
       26.01        17.62        14.66        20.71         0.92        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        81.80        38.37         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       28.41        51.25        28.47        14.04        12.66        14.73 
TCGA-67-6216 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 TCGA-69-8253 
        4.64        22.68        13.61         5.42        13.41        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-A9RS TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
       11.18        77.85        43.82        85.15        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
      108.66       100.57        20.58        21.90        39.95       119.51 
TCGA-78-7155 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 
       38.50         5.88        22.92       104.19       238.29        31.20 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 
       53.33        39.35        10.55        39.75        77.59        93.11 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       27.09        31.13        20.55        37.74         4.57        24.33 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8671 TCGA-86-8672 
       32.65        31.04        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 
       28.34        26.50        29.46        24.23        26.47        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 
        1.97        10.19         1.15        16.60        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-A4VP TCGA-97-7546 
       19.82        22.45        23.61         1.08        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       64.60        63.52        18.54         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8176 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 
        5.39        15.39        21.44        19.76        20.84        24.56 
TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       36.76        21.57        21.63        35.47        32.48        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-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YI 
       11.05        24.36        14.10        11.15        73.91         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        1.64        47.08         0.49         0.43        19.82        16.87 

  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                        0.00                         0.13 
  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                      232.18                       238.29 
  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE 
                      20.165                       22.665 
[1] "0.0 - 232.2 (20.2)" "0.1 - 238.3 (22.7)"
[1] "hr=" "1.1"
D22V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 22(17Q12) MUTATED         3       53       62        0        25
  AMP PEAK 22(17Q12) WILD-TYPE       2       80       77        1        25
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 22(17Q12) MUTATED          27         35          8       13
  AMP PEAK 22(17Q12) WILD-TYPE        45         37          3       12
D22V3, multiclass
            clus
vv           AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  STAGE I                             3                            2
  STAGE IA                           53                           80
  STAGE IB                           62                           77
  STAGE II                            0                            1
  STAGE IIA                          25                           25
  STAGE IIB                          27                           45
  STAGE IIIA                         35                           37
  STAGE IIIB                          8                            3
  STAGE IV                           13                           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 22(17Q12) MUTATED    66 132  18  10
  AMP PEAK 22(17Q12) WILD-TYPE 105 146  28   9
D22V4, multiclass
    clus
vv   AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  T1                         66                          105
  T2                        132                          146
  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 22(17Q12) MUTATED   140  44    39
  AMP PEAK 22(17Q12) WILD-TYPE 193  52    37
D22V5, multiclass
       clus
vv      AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  N0                           140                          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"
D22V6, binary
                              cls
clus                             0   1
  AMP PEAK 22(17Q12) MUTATED   157  13
  AMP PEAK 22(17Q12) WILD-TYPE 192  12
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(17Q12) MUTATED    157   13
  AMP PEAK 22(17Q12) WILD-TYPE  192   12
   clus
vv  AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  0                        157                          192
  1                         13                           12
[1] 2 2
[1] FALSE
D22V7, binary
                              cls
clus                             0   1
  AMP PEAK 22(17Q12) MUTATED   117 110
  AMP PEAK 22(17Q12) WILD-TYPE 159 130
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(17Q12) MUTATED    117  110
  AMP PEAK 22(17Q12) WILD-TYPE  159  130
        clus
vv       AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  FEMALE                        117                          159
  MALE                          110                          130
[1] 2 2
[1] FALSE
D22V8, binary
                              cls
clus                             0   1
  AMP PEAK 22(17Q12) MUTATED   180  30
  AMP PEAK 22(17Q12) WILD-TYPE 230  30
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(17Q12) MUTATED    180   30
  AMP PEAK 22(17Q12) WILD-TYPE  230   30
     clus
vv    AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  NO                         180                          230
  YES                         30                           30
[1] 2 2
[1] FALSE
D22V9, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 22(17Q12) MUTATED                            7
  AMP PEAK 22(17Q12) WILD-TYPE                         11
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 22(17Q12) MUTATED                                  49
  AMP PEAK 22(17Q12) WILD-TYPE                                58
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 22(17Q12) MUTATED                                                  148
  AMP PEAK 22(17Q12) WILD-TYPE                                                173
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 22(17Q12) MUTATED                                            1
  AMP PEAK 22(17Q12) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 22(17Q12) MUTATED                                               5
  AMP PEAK 22(17Q12) WILD-TYPE                                            14
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 22(17Q12) MUTATED                                2
  AMP PEAK 22(17Q12) WILD-TYPE                              0
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 22(17Q12) MUTATED                                    1
  AMP PEAK 22(17Q12) WILD-TYPE                                  2
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 22(17Q12) MUTATED                              1
  AMP PEAK 22(17Q12) WILD-TYPE                            1
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 22(17Q12) MUTATED                               8
  AMP PEAK 22(17Q12) WILD-TYPE                            15
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 22(17Q12) MUTATED                                 0
  AMP PEAK 22(17Q12) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 22(17Q12) MUTATED                                               4
  AMP PEAK 22(17Q12) WILD-TYPE                                             1
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 22(17Q12) MUTATED                              1
  AMP PEAK 22(17Q12) WILD-TYPE                            9
D22V10, multiclass
                                                    clus
vv                                                   AMP PEAK 22(17Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          49
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        148
  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 22(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"
D22V11, continuous
D22V12, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 22(17Q12) MUTATED   148   6   2  17
  AMP PEAK 22(17Q12) WILD-TYPE 196   7   2   9
D22V13, multiclass
    clus
vv   AMP PEAK 22(17Q12) MUTATED AMP PEAK 22(17Q12) WILD-TYPE
  R0                        148                          196
  R1                          6                            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 22(17Q12) MUTATED                                  1     5
  AMP PEAK 22(17Q12) WILD-TYPE                                0     2
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(17Q12) MUTATED                          19   171
  AMP PEAK 22(17Q12) WILD-TYPE                        33   219
D22V14, multiclass
                                  clus
vv                                 AMP PEAK 22(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     5
  BLACK OR AFRICAN AMERICAN                                19
  WHITE                                                   171
                                  clus
vv                                 AMP PEAK 22(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  33
  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"
D22V15, binary
                              cls
clus                             0   1
  AMP PEAK 22(17Q12) MUTATED     3 162
  AMP PEAK 22(17Q12) WILD-TYPE   4 222
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 22(17Q12) MUTATED      3  162
  AMP PEAK 22(17Q12) WILD-TYPE    4  222
                        clus
vv                       AMP PEAK 22(17Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        162
                        clus
vv                       AMP PEAK 22(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          222
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(17Q23.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(17Q23.1) MUTATED   150  93
  AMP PEAK 23(17Q23.1) WILD-TYPE 173  88
  AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE 
                           243                            261 
  AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE 
                            93                             88 
$`AMP PEAK 23(17Q23.1) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 TCGA-38-4631 
       19.96         8.02         9.01        26.01        28.41        11.64 
TCGA-44-2662 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 
       42.08        18.31        29.00         9.37        46.72        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16        11.64        37.32        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-8205 TCGA-55-8207 TCGA-55-A491 
       48.62         5.79         7.79        19.69        32.12        20.58 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-78-7633 TCGA-78-8660 
       20.65        13.87        52.60        82.68        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-A4VK 
       85.32        13.71         6.12        17.29        16.54        21.40 
TCGA-95-A4VN TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 
       18.18         6.35        10.09        21.83        27.19         5.29 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 
       10.09        50.07         3.98        45.01         0.00        24.03 
TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 
       47.05         2.99        14.96        29.98        30.02        21.99 
TCGA-05-4430 TCGA-05-4432 TCGA-35-4122 TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 
       25.02        25.02         7.40        49.05        44.61        46.98 
TCGA-44-2657 TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 TCGA-44-3919 TCGA-44-6144 
       44.42        25.02        37.15        34.06        33.73        23.77 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 
       23.15        23.18        32.45        16.44        19.46         7.17 
TCGA-44-7667 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       36.07        12.66         8.55        15.98        15.32         9.44 
TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR4 
       12.66        14.07         8.81        53.29        55.33        28.90 
TCGA-49-AARO TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 
      123.58        49.28         9.27        14.27        78.67        48.46 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       57.53        53.16         3.91        25.55        11.05        12.16 
TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
       34.29        13.94        38.73        30.58        80.52         5.62 
TCGA-55-6971 TCGA-55-6981 TCGA-55-6982 TCGA-55-7281 TCGA-55-7283 TCGA-55-7576 
       46.03        45.34        32.71        28.67        20.02        22.03 
TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 
        3.91        25.41        18.64        11.28        17.65        19.82 
TCGA-55-7995 TCGA-55-8089 TCGA-55-8094 TCGA-55-8208 TCGA-55-8302 TCGA-55-8506 
       29.23        23.08        17.79        22.16        15.72         0.36 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z 
       13.74        17.72        17.10         1.58        12.33        21.40 
TCGA-55-A490 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 
        3.25        15.81        19.99        17.95         4.57        14.60 
TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y 
       49.25        47.80        56.71        54.35        67.96        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1680 TCGA-64-5774 TCGA-64-5815 
       39.25        40.96        56.81        37.02        87.98        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-6215 TCGA-69-7760 TCGA-69-7764 
       20.05        20.05        18.84         5.72         6.64        13.61 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 
        7.56         6.05         4.41        13.51         4.24         8.42 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-7499 TCGA-75-5125 
       26.30        15.35        30.31         9.24        50.33        66.64 
TCGA-75-6214 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
       36.66       163.10        27.16         5.69        19.27       129.53 
TCGA-78-7154 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 
       19.50        64.90         9.57        88.14        26.53        26.01 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 
       10.55       232.18        77.59       110.50        12.36         5.88 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 
       34.39        38.04        32.78        35.24         4.08         4.57 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
        0.79        22.82        31.20        21.47        11.61        13.91 
TCGA-86-8669 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 
       30.84         0.62        28.34        29.46         3.81        13.64 
TCGA-91-6828 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-93-7348 TCGA-93-A4JO 
       10.62         2.60        27.68         7.36        17.46         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
       19.00        41.82        18.67        12.39        27.29         2.76 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       61.48        25.48        18.54        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-8025 
       14.30        21.60        20.58        19.76        18.67        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV 
       36.76         1.45        21.57        18.08        19.00        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 
       15.65        38.63         2.76        86.14        49.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A4YI 
       58.85        41.59        29.46        19.13        74.33         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A7XG TCGA-O1-A52J 
       47.08        20.28        59.11 

$`AMP PEAK 23(17Q23.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 
       14.01         9.96        20.05        15.02        15.02        35.28 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 
       14.73        26.30        43.53        38.10        23.93        27.78 
TCGA-44-6776 TCGA-44-7671 TCGA-44-A47F TCGA-49-AAR0 TCGA-50-5932 TCGA-55-7284 
       86.01        29.23        11.08       156.66        40.60         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       19.73        17.98        16.93        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-73-7498 TCGA-78-7166 TCGA-91-7771 
       22.65        19.59        20.19        39.09         8.48        16.18 
TCGA-91-A4BC TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-97-8172 TCGA-97-A4LX 
        1.45         2.86        15.68        15.65        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-MP-A4TA 
       20.52        17.75        20.68        24.30        23.80        31.23 
TCGA-MP-A4TC TCGA-05-4390 TCGA-05-4403 TCGA-05-4422 TCGA-05-4426 TCGA-05-4433 
        2.43        37.02        19.00        12.00        26.01        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
        4.96        29.00        22.03         9.04         2.04         0.46 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F 
        5.98         8.68        97.74       120.79        37.71         4.37 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-3398 TCGA-44-3917 TCGA-44-4112 
       44.94        42.77         3.19        38.24        38.89        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6774 TCGA-44-6778 
       33.30        28.37        28.01        19.56        21.63        61.28 
TCGA-44-7659 TCGA-44-7669 TCGA-44-7672 TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       22.72        18.87        23.64        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 
       76.21        28.11        28.57        35.54        32.84        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       29.75        55.89        22.26        22.26        73.12        62.24 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
        8.55        40.41       221.33       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       101.72        15.72        60.16        47.41         8.22 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6590 TCGA-50-6595 TCGA-50-6673 
        8.45        15.12        60.72        42.35         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ 
       10.13        36.99        36.79        27.25        30.54        35.21 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
       67.89        14.30        42.51        40.73        15.25        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
        3.88        69.34        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7570 TCGA-55-7574 TCGA-55-7728 TCGA-55-7910 TCGA-55-7913 
       70.26        27.09        32.71        23.15        34.19        18.44 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       29.72        15.19         5.06        23.64        15.65        29.19 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
       15.42        17.56        14.47        20.28        19.96        26.01 
TCGA-55-8614 TCGA-55-8615 TCGA-55-A48Y TCGA-55-A493 TCGA-62-8395 TCGA-62-8397 
       17.62        14.66        20.71         0.92        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        81.80 
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-67-4679 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 
       12.66        14.73         4.64         6.12        22.68         5.42 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 
       13.41        14.01        13.45        26.73        19.43        23.38 
TCGA-73-4670 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 
        4.31         1.25        11.18        77.85        43.82        85.15 
TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
       49.84       108.66       100.57        20.58        21.90        39.95 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 
      119.51        38.50        32.09         5.88        22.92       104.19 
TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8648 
      238.29        31.20         8.02        53.33        39.35        39.75 
TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
       93.11        27.09        31.13        20.55        19.89        37.74 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8671 
       24.33        32.65        31.04        23.05        14.60        27.58 
TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       26.50        24.23        26.47        41.36         1.97        10.19 
TCGA-91-6840 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
       12.23         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-A4JN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       22.45        23.61        19.89        42.25        64.60        63.52 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-A4M0 TCGA-97-A4M5 
        0.59        15.91        18.67         5.39        21.44        20.84 
TCGA-99-7458 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W 
       24.56        21.63        35.47        32.48        14.30        14.53 
TCGA-L9-A5IP TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TH 
        1.91        58.45        37.35         5.49        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YP TCGA-NJ-A55A 
       14.10        11.15        73.91        71.05         1.64         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        0.43        19.82        16.87 

  AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE 
                          0.00                           0.43 
  AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE 
                        232.18                         238.29 
  AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE 
                         20.58                          22.68 
[1] "0.0 - 232.2 (20.6)" "0.4 - 238.3 (22.7)"
[1] "hr=" "1.2"
D23V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 23(17Q23.1) MUTATED         3       56       69        0        26
  AMP PEAK 23(17Q23.1) WILD-TYPE       2       77       70        1        24
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 23(17Q23.1) MUTATED          31         41          8       14
  AMP PEAK 23(17Q23.1) WILD-TYPE        41         31          3       11
D23V3, multiclass
            clus
vv           AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             56                             77
  STAGE IB                             69                             70
  STAGE II                              0                              1
  STAGE IIA                            26                             24
  STAGE IIB                            31                             41
  STAGE IIIA                           41                             31
  STAGE IIIB                            8                              3
  STAGE IV                             14                             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
  AMP PEAK 23(17Q23.1) MUTATED    72 145  20  10
  AMP PEAK 23(17Q23.1) WILD-TYPE  99 133  26   9
D23V4, multiclass
    clus
vv   AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE
  T1                           72                             99
  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 23(17Q23.1) MUTATED   151  49    43
  AMP PEAK 23(17Q23.1) WILD-TYPE 182  47    33
D23V5, multiclass
       clus
vv      AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE
  N0                             151                            182
  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"
D23V6, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q23.1) MUTATED   172  14
  AMP PEAK 23(17Q23.1) WILD-TYPE 177  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q23.1) MUTATED    172   14
  AMP PEAK 23(17Q23.1) WILD-TYPE  177   11
   clus
vv  AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE
  0                          172                            177
  1                           14                             11
[1] 2 2
[1] FALSE
D23V7, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q23.1) MUTATED   135 114
  AMP PEAK 23(17Q23.1) WILD-TYPE 141 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q23.1) MUTATED    135  114
  AMP PEAK 23(17Q23.1) WILD-TYPE  141  126
        clus
vv       AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE
  FEMALE                          135                            141
  MALE                            114                            126
[1] 2 2
[1] FALSE
D23V8, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q23.1) MUTATED   198  31
  AMP PEAK 23(17Q23.1) WILD-TYPE 212  29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q23.1) MUTATED    198   31
  AMP PEAK 23(17Q23.1) WILD-TYPE  212   29
     clus
vv    AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE
  NO                           198                            212
  YES                           31                             29
[1] 2 2
[1] FALSE
D23V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 23(17Q23.1) MUTATED                            7
  AMP PEAK 23(17Q23.1) WILD-TYPE                         11
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 23(17Q23.1) MUTATED                                  54
  AMP PEAK 23(17Q23.1) WILD-TYPE                                53
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 23(17Q23.1) MUTATED                                                  162
  AMP PEAK 23(17Q23.1) WILD-TYPE                                                159
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 23(17Q23.1) MUTATED                                            1
  AMP PEAK 23(17Q23.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 23(17Q23.1) MUTATED                                               6
  AMP PEAK 23(17Q23.1) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 23(17Q23.1) MUTATED                                2
  AMP PEAK 23(17Q23.1) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 23(17Q23.1) MUTATED                                    2
  AMP PEAK 23(17Q23.1) WILD-TYPE                                  1
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 23(17Q23.1) MUTATED                              1
  AMP PEAK 23(17Q23.1) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 23(17Q23.1) MUTATED                               8
  AMP PEAK 23(17Q23.1) WILD-TYPE                            15
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 23(17Q23.1) MUTATED                                 0
  AMP PEAK 23(17Q23.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 23(17Q23.1) MUTATED                                               5
  AMP PEAK 23(17Q23.1) WILD-TYPE                                             0
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 23(17Q23.1) MUTATED                              1
  AMP PEAK 23(17Q23.1) WILD-TYPE                            9
D23V10, multiclass
                                                    clus
vv                                                   AMP PEAK 23(17Q23.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          162
  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 23(17Q23.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            159
  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"
D23V11, continuous
D23V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 23(17Q23.1) MUTATED   164   5   2  20
  AMP PEAK 23(17Q23.1) WILD-TYPE 180   8   2   6
D23V13, multiclass
    clus
vv   AMP PEAK 23(17Q23.1) MUTATED AMP PEAK 23(17Q23.1) WILD-TYPE
  R0                          164                            180
  R1                            5                              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 23(17Q23.1) MUTATED                                  1     5
  AMP PEAK 23(17Q23.1) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(17Q23.1) MUTATED                          18   190
  AMP PEAK 23(17Q23.1) WILD-TYPE                        34   200
D23V14, multiclass
                                  clus
vv                                 AMP PEAK 23(17Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     190
                                  clus
vv                                 AMP PEAK 23(17Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       200
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V15, binary
                                cls
clus                               0   1
  AMP PEAK 23(17Q23.1) MUTATED     5 177
  AMP PEAK 23(17Q23.1) WILD-TYPE   2 207
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(17Q23.1) MUTATED      5  177
  AMP PEAK 23(17Q23.1) WILD-TYPE    2  207
                        clus
vv                       AMP PEAK 23(17Q23.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          177
                        clus
vv                       AMP PEAK 23(17Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            207
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(18Q11.2) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 24(18Q11.2) MUTATED    67  34
  AMP PEAK 24(18Q11.2) WILD-TYPE 256 147
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                           101                            403 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                            34                            147 
$`AMP PEAK 24(18Q11.2) MUTATED`
TCGA-05-4396 TCGA-38-4631 TCGA-44-6146 TCGA-44-7670 TCGA-44-8119 TCGA-49-6745 
        9.96        11.64        23.93        29.00         9.37        17.16 
TCGA-49-6761 TCGA-55-1592 TCGA-55-1595 TCGA-55-8511 TCGA-55-A4DF TCGA-64-1677 
       11.64        23.05        48.62        18.15        20.19        20.65 
TCGA-73-4662 TCGA-95-7562 TCGA-MP-A4TD TCGA-05-4390 TCGA-05-4415 TCGA-05-4420 
       82.68         2.86        10.09        37.02         2.99        29.98 
TCGA-05-4424 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-38-4632 TCGA-44-2659 
       30.02        24.00        29.00        22.03        44.61        44.94 
TCGA-44-3917 TCGA-44-5644 TCGA-44-6144 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 
       38.89        28.37        23.77        61.28        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-A47A TCGA-49-4514 TCGA-49-6743 
       36.07        18.87        23.64        15.32        55.89        53.29 
TCGA-49-AAR2 TCGA-4B-A93V TCGA-50-5068 TCGA-50-5931 TCGA-50-6673 TCGA-53-7813 
       73.12         9.86        49.28        14.27         0.72        13.94 
TCGA-55-6642 TCGA-55-6970 TCGA-55-6980 TCGA-55-7728 TCGA-55-7907 TCGA-55-8089 
       80.52        15.25        69.34        23.15        11.28        23.08 
TCGA-55-8096 TCGA-55-8508 TCGA-55-8615 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8398 
       23.64        20.28        14.66        15.81        19.99        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-64-1676 TCGA-64-1678 TCGA-64-5779 TCGA-69-7764 
       88.64        49.25        56.81        39.09        28.41        13.61 
TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8453 TCGA-73-4668 
        7.56        13.41        13.51        14.01        26.73        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-75-6214 TCGA-78-7148 TCGA-78-7150 TCGA-78-7155 
       30.31         9.24        36.66        20.58        21.90        38.50 
TCGA-78-7167 TCGA-78-7542 TCGA-78-8655 TCGA-78-8662 TCGA-86-7713 TCGA-86-7955 
       88.14        10.55        77.59       110.50        38.04        35.24 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8358 TCGA-86-8359 
        4.08        24.33         0.79        22.82        21.47        14.60 
TCGA-86-8585 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 TCGA-91-8499 
       11.61         3.81        41.36        10.19        12.23         1.18 
TCGA-93-A4JN TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-8175 TCGA-97-8179 
       23.61        42.25        64.60        25.48        18.12        14.30 
TCGA-97-8552 TCGA-L9-A7SV TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       20.58        18.58        19.82        20.28        16.87 

$`AMP PEAK 24(18Q11.2) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         8.02        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        28.41        35.28        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       43.53        38.10        42.08        27.78        86.01        18.31 
TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 TCGA-49-AAR0 TCGA-49-AARN 
       29.23        11.08        46.72        16.04       156.66        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       40.60        21.47        41.69         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 
       19.73        17.98        16.93        19.69        32.12        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 TCGA-73-4658 
       16.93        22.65        20.58        19.59        13.87        52.60 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 
       16.18         1.45         6.12        17.29        16.54        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.65        21.40        18.18        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       17.75        20.68        24.30        23.80         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4249 
       21.83        27.19         5.29        31.23         2.43        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
        3.98        45.01         0.00        24.03        47.05        19.00 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       14.96        12.00        21.99        26.01        25.02        25.02 
TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
        4.96         9.04         2.04         0.46         7.40         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F 
        8.68        97.74       120.79        37.71        49.05         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       46.98        44.42        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        33.73        26.56        33.30        28.01 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 
       19.56        23.15        21.63        23.18        32.45        16.44 
TCGA-44-7659 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G 
       22.72        12.66         8.55        15.98         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-49-4505 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-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       55.33        22.26        22.26        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 
       40.41       123.58       221.33       164.12        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 
      101.72        15.72        60.16        47.41         8.22         9.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       53.16        42.35         3.91        25.55        11.05        12.16 
TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        6.21        10.13        36.99        36.79        27.25        34.29 
TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
       30.54        35.21        38.73        67.89        30.58        14.30 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        5.62        42.51        40.73        46.03        53.65         3.88 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       70.26        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
        3.91        25.41        18.64        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8094 
       19.82        29.23        29.72        15.19         5.06        17.79 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.65        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
       14.47         0.36        13.74        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.10        17.62         1.58        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        3.25         0.92        17.95         4.57        39.98        42.38 
TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       47.80        19.53        56.71        54.35        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 
       13.61        39.25        40.96        29.92        81.80        37.02 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 
       38.37        87.98         2.04        42.90        51.25        28.47 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       20.05        20.05        18.84        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 
        5.72         4.64         6.64         6.12        22.68         5.42 
TCGA-69-7974 TCGA-69-7978 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
        6.05         4.41        13.45         4.24        19.43         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS 
       23.38        26.30         4.31         1.25        50.33        11.18 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 
       66.64        77.85        43.82        85.15        49.84       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
      100.57       163.10        27.16         5.69        19.27       129.53 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.95       119.51        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 
       22.92         9.57       104.19       238.29        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 
        8.02        53.33        26.01        39.35       232.18        39.75 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 
       20.55        32.78        19.89        37.74         4.57        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       31.04        31.20        23.05        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        28.34        26.50        29.46        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 
       26.47        10.62         1.97         2.60        27.68         7.36 
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        22.45        17.46 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
        2.76        19.89        63.52        61.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       15.91        18.67         5.39        15.39        16.41        21.60 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         1.45        21.57        21.63        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 
       32.48        19.00        14.30        14.53         1.91        15.65 
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-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       86.04        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
       24.36        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 
       74.33         0.13         1.64        47.08         0.49         0.43 
TCGA-O1-A52J 
       59.11 

  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                          0.72                           0.00 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                        110.50                         238.29 
  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE 
                         21.47                          21.63 
[1] "0.7 - 110.5 (21.5)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1"  
D24V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 24(18Q11.2) MUTATED         3       21       34        0        13
  AMP PEAK 24(18Q11.2) WILD-TYPE       2      112      105        1        37
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 24(18Q11.2) MUTATED          11         16          3        3
  AMP PEAK 24(18Q11.2) WILD-TYPE        61         56          8       22
D24V3, multiclass
            clus
vv           AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             21                            112
  STAGE IB                             34                            105
  STAGE II                              0                              1
  STAGE IIA                            13                             37
  STAGE IIB                            11                             61
  STAGE IIIA                           16                             56
  STAGE IIIB                            3                              8
  STAGE IV                              3                             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
  AMP PEAK 24(18Q11.2) MUTATED    31  62   8   4
  AMP PEAK 24(18Q11.2) WILD-TYPE 140 216  38  15
D24V4, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  T1                           31                            140
  T2                           62                            216
  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
  AMP PEAK 24(18Q11.2) MUTATED    69  21    15
  AMP PEAK 24(18Q11.2) WILD-TYPE 264  75    61
D24V5, multiclass
       clus
vv      AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  N0                              69                            264
  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"
D24V6, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED    70   3
  AMP PEAK 24(18Q11.2) WILD-TYPE 279  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED     70    3
  AMP PEAK 24(18Q11.2) WILD-TYPE  279   22
   clus
vv  AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  0                           70                            279
  1                            3                             22
[1] 2 2
[1] FALSE
D24V7, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED    49  56
  AMP PEAK 24(18Q11.2) WILD-TYPE 227 184
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED     49   56
  AMP PEAK 24(18Q11.2) WILD-TYPE  227  184
        clus
vv       AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  FEMALE                           49                            227
  MALE                             56                            184
[1] 2 2
[1] FALSE
D24V8, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED    88  10
  AMP PEAK 24(18Q11.2) WILD-TYPE 322  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED     88   10
  AMP PEAK 24(18Q11.2) WILD-TYPE  322   50
     clus
vv    AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  NO                            88                            322
  YES                           10                             50
[1] 2 2
[1] FALSE
D24V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                            6
  AMP PEAK 24(18Q11.2) WILD-TYPE                         12
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 24(18Q11.2) MUTATED                                  17
  AMP PEAK 24(18Q11.2) WILD-TYPE                                90
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 24(18Q11.2) MUTATED                                                   61
  AMP PEAK 24(18Q11.2) WILD-TYPE                                                260
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 24(18Q11.2) MUTATED                                            1
  AMP PEAK 24(18Q11.2) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 24(18Q11.2) MUTATED                                               5
  AMP PEAK 24(18Q11.2) WILD-TYPE                                            14
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                                2
  AMP PEAK 24(18Q11.2) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                                    1
  AMP PEAK 24(18Q11.2) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                              1
  AMP PEAK 24(18Q11.2) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                               6
  AMP PEAK 24(18Q11.2) WILD-TYPE                            17
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                                 0
  AMP PEAK 24(18Q11.2) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                                               2
  AMP PEAK 24(18Q11.2) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 24(18Q11.2) MUTATED                              3
  AMP PEAK 24(18Q11.2) WILD-TYPE                            7
D24V10, multiclass
                                                    clus
vv                                                   AMP PEAK 24(18Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           61
  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                                                 6
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   AMP PEAK 24(18Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              90
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            260
  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                                                  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"
D24V11, continuous
D24V12, continuous
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 24(18Q11.2) MUTATED    66   2   0   7
  AMP PEAK 24(18Q11.2) WILD-TYPE 278  11   4  19
D24V13, multiclass
    clus
vv   AMP PEAK 24(18Q11.2) MUTATED AMP PEAK 24(18Q11.2) WILD-TYPE
  R0                           66                            278
  R1                            2                             11
  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 24(18Q11.2) MUTATED                                  1     1
  AMP PEAK 24(18Q11.2) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(18Q11.2) MUTATED                          11    77
  AMP PEAK 24(18Q11.2) WILD-TYPE                        41   313
D24V14, multiclass
                                  clus
vv                                 AMP PEAK 24(18Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      77
                                  clus
vv                                 AMP PEAK 24(18Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       313
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V15, binary
                                cls
clus                               0   1
  AMP PEAK 24(18Q11.2) MUTATED     1  75
  AMP PEAK 24(18Q11.2) WILD-TYPE   6 309
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 24(18Q11.2) MUTATED      1   75
  AMP PEAK 24(18Q11.2) WILD-TYPE    6  309
                        clus
vv                       AMP PEAK 24(18Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           75
                        clus
vv                       AMP PEAK 24(18Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            309
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(19Q12) MUTATION ANALYSIS
D25V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 25(19Q12) MUTATED    87  48
  AMP PEAK 25(19Q12) WILD-TYPE 236 133
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                         135                          369 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                          48                          133 
$`AMP PEAK 25(19Q12) MUTATED`
TCGA-05-4418 TCGA-38-4630 TCGA-38-4631 TCGA-44-2662 TCGA-44-6147 TCGA-44-6776 
        9.01        35.28        11.64        42.08        27.78        86.01 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 TCGA-50-6597 TCGA-55-6978 
       29.23         9.37        11.08        16.04        41.69         5.79 
TCGA-55-6979 TCGA-55-A491 TCGA-55-A4DF TCGA-95-7043 TCGA-95-A4VK TCGA-97-8172 
        7.79        20.58        20.19        16.54        21.40        17.92 
TCGA-L9-A443 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4415 
        6.35         3.98        45.01        37.02        47.05         2.99 
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-38-4632 TCGA-44-3917 TCGA-44-5644 TCGA-44-6144 
        8.68        49.05        44.61        38.89        28.37        23.77 
TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SS 
       19.46        36.07        18.87        15.32         9.44        13.64 
TCGA-49-4487 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR4 TCGA-49-AARE 
       28.11        53.29        55.33        22.26        28.90        40.41 
TCGA-50-5049 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5936 TCGA-50-5946 
      101.72        47.41         8.22         9.27         8.45        53.16 
TCGA-50-6591 TCGA-50-6594 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
        3.91        12.16        34.29        13.94        35.21        38.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-7907 TCGA-55-7913 TCGA-55-7995 
       15.25        46.03        53.65        11.28        18.44        29.23 
TCGA-55-8085 TCGA-55-8092 TCGA-55-8301 TCGA-55-8302 TCGA-55-8507 TCGA-55-8614 
       29.72         5.06        17.56        15.72        13.74        17.62 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A493 TCGA-62-8394 TCGA-62-8399 
       14.66        12.33        21.40         0.92         4.57        88.64 
TCGA-62-A46O TCGA-62-A46S TCGA-64-1678 TCGA-64-1679 TCGA-64-5778 TCGA-64-5779 
       47.80        54.35        39.09        81.80        42.90        28.41 
TCGA-64-5781 TCGA-69-7760 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 
       51.25         6.64        22.68        13.61         7.56         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8453 TCGA-69-A59K TCGA-73-4675 
       13.41        13.51        14.01        26.73        19.43        30.31 
TCGA-75-5147 TCGA-78-7148 TCGA-78-7150 TCGA-78-7154 TCGA-80-5608 TCGA-86-7713 
       43.82        20.58        21.90        19.50        93.11        38.04 
TCGA-86-7953 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8358 
       32.78         4.08        24.33         0.79        22.82        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8673 TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 
       14.60        11.61        28.34        29.46        41.36         1.97 
TCGA-91-6840 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-97-7554 
       12.23        23.61        19.00        18.67        12.39        25.48 
TCGA-97-7937 TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-99-8025 TCGA-99-8033 
       18.54         5.39        18.12        14.30        34.85        21.57 
TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TH 
        1.91        15.65        38.63        86.04         5.49        24.36 
TCGA-MP-A4TJ TCGA-NJ-A55O TCGA-S2-AA1A 
       11.15         0.43        16.87 

$`AMP PEAK 25(19Q12) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 
       19.96        14.01         9.96         8.02        20.05        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       15.02        15.02        28.41        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-6146 TCGA-44-7661 TCGA-44-7670 TCGA-49-4501 TCGA-49-6745 
       38.10        23.93        18.31        29.00        46.72        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 
       11.64       156.66        37.32        40.60        21.47        23.05 
TCGA-55-1595 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
       48.62         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        6.15        19.66        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 
       32.12        18.15        13.68        16.93        22.65        19.59 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.65        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VN 
        6.12        17.29         2.86        15.68        15.65        18.18 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       10.09        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 TCGA-05-4417 
       10.09        50.07         0.00        24.03        19.00        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 
       29.98        12.00        21.99        26.01        25.02        24.00 
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-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 
       37.71         4.37        46.98        44.42        44.94        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        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 
       26.56        33.30        28.01        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 
       23.18        32.45        61.28        16.44        22.72         7.17 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47G TCGA-44-A4SU 
       23.64        12.66         8.55        15.98        11.54        13.45 
TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       76.21        28.57        12.66        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6767 TCGA-49-AAR2 
        8.81        29.46        29.75        55.89        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       62.24         8.55       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5931 
       20.52        71.47        15.72        60.16        49.28        14.27 
TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
       78.67        15.12        48.46        60.72        57.53        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        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 
       36.79        27.25        30.54        67.89        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6975 TCGA-55-6980 
       80.52         5.62        42.51        40.73         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 
       45.34        32.71        92.81        24.99        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       70.26        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 
        3.91        23.15        25.41        18.64        34.19        17.65 
TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       19.82        15.19        23.08        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       29.19        22.16        15.42        14.47         0.36        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 TCGA-55-A48Y 
       17.72        19.96        26.01        17.10         1.58        20.71 
TCGA-55-A490 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 
        3.25        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-64-1680 
       13.61        39.25        40.96        29.92        56.81        37.02 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       38.37        87.98         2.04        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       18.84        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 
        6.12         5.42         6.05        13.45         4.24         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 
       23.38        26.30        15.35         4.31         9.24         1.25 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-6206 TCGA-75-6212 
       50.33        11.18        66.64        77.85        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 
       19.27       129.53        39.95       119.51        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       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        35.24        37.74         4.57        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
       31.20        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 
       26.50         3.81        24.23        13.64        26.47        10.62 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       10.19         2.60        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO 
       14.27         1.18        19.82        22.45        17.46         1.08 
TCGA-95-7039 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       41.82        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8176 
       63.52        61.48         0.59        15.91        18.67        15.39 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       16.41        21.60        20.58        21.44        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AD 
       18.67        24.56        36.76         1.45        21.63        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A7SV 
       35.47        32.48        19.00        14.30        14.53        18.58 
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-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       41.59        29.46        11.05        14.10        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       71.05        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       19.82        20.28        59.11 

  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                        0.43                         0.00 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                      101.72                       238.29 
  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE 
                       20.58                        22.16 
[1] "0.4 - 101.7 (20.6)" "0.0 - 238.3 (22.2)"
[1] "hr=" "1.2"
D25V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 25(19Q12) MUTATED         1       31       38        1        14
  AMP PEAK 25(19Q12) WILD-TYPE       4      102      101        0        36
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 25(19Q12) MUTATED          17         22          5        9
  AMP PEAK 25(19Q12) WILD-TYPE        55         50          6       16
D25V3, multiclass
            clus
vv           AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  STAGE I                             1                            4
  STAGE IA                           31                          102
  STAGE IB                           38                          101
  STAGE II                            1                            0
  STAGE IIA                          14                           36
  STAGE IIB                          17                           55
  STAGE IIIA                         22                           50
  STAGE IIIB                          5                            6
  STAGE IV                            9                           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 25(19Q12) MUTATED    42  75  16   4
  AMP PEAK 25(19Q12) WILD-TYPE 129 203  30  15
D25V4, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  T1                         42                          129
  T2                         75                          203
  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 25(19Q12) MUTATED    85  26    25
  AMP PEAK 25(19Q12) WILD-TYPE 248  70    51
D25V5, multiclass
       clus
vv      AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  N0                            85                          248
  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"
D25V6, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED    93   9
  AMP PEAK 25(19Q12) WILD-TYPE 256  16
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     93    9
  AMP PEAK 25(19Q12) WILD-TYPE  256   16
   clus
vv  AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  0                         93                          256
  1                          9                           16
[1] 2 2
[1] FALSE
D25V7, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED    65  74
  AMP PEAK 25(19Q12) WILD-TYPE 211 166
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED     65   74
  AMP PEAK 25(19Q12) WILD-TYPE  211  166
        clus
vv       AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  FEMALE                         65                          211
  MALE                           74                          166
[1] 2 2
[1] FALSE
D25V8, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED   112  16
  AMP PEAK 25(19Q12) WILD-TYPE 298  44
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED    112   16
  AMP PEAK 25(19Q12) WILD-TYPE  298   44
     clus
vv    AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  NO                         112                          298
  YES                         16                           44
[1] 2 2
[1] FALSE
D25V9, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 25(19Q12) MUTATED                            6
  AMP PEAK 25(19Q12) WILD-TYPE                         12
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 25(19Q12) MUTATED                                  30
  AMP PEAK 25(19Q12) WILD-TYPE                                77
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 25(19Q12) MUTATED                                                   78
  AMP PEAK 25(19Q12) WILD-TYPE                                                243
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 25(19Q12) MUTATED                                            1
  AMP PEAK 25(19Q12) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 25(19Q12) MUTATED                                               5
  AMP PEAK 25(19Q12) WILD-TYPE                                            14
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 25(19Q12) MUTATED                                1
  AMP PEAK 25(19Q12) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 25(19Q12) MUTATED                                    1
  AMP PEAK 25(19Q12) WILD-TYPE                                  2
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 25(19Q12) MUTATED                              0
  AMP PEAK 25(19Q12) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 25(19Q12) MUTATED                              10
  AMP PEAK 25(19Q12) WILD-TYPE                            13
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 25(19Q12) MUTATED                                 1
  AMP PEAK 25(19Q12) WILD-TYPE                               0
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 25(19Q12) MUTATED                                               2
  AMP PEAK 25(19Q12) WILD-TYPE                                             3
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 25(19Q12) MUTATED                              4
  AMP PEAK 25(19Q12) WILD-TYPE                            6
D25V10, multiclass
                                                    clus
vv                                                   AMP PEAK 25(19Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         78
  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 25(19Q12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          243
  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"
D25V11, continuous
D25V12, continuous
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 25(19Q12) MUTATED    86   4   1   8
  AMP PEAK 25(19Q12) WILD-TYPE 258   9   3  18
D25V13, multiclass
    clus
vv   AMP PEAK 25(19Q12) MUTATED AMP PEAK 25(19Q12) WILD-TYPE
  R0                         86                          258
  R1                          4                            9
  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 25(19Q12) MUTATED                                  0     2
  AMP PEAK 25(19Q12) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(19Q12) MUTATED                          15   104
  AMP PEAK 25(19Q12) WILD-TYPE                        37   286
D25V14, multiclass
                                  clus
vv                                 AMP PEAK 25(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                15
  WHITE                                                   104
                                  clus
vv                                 AMP PEAK 25(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  37
  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"
D25V15, binary
                              cls
clus                             0   1
  AMP PEAK 25(19Q12) MUTATED     2 107
  AMP PEAK 25(19Q12) WILD-TYPE   5 277
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(19Q12) MUTATED      2  107
  AMP PEAK 25(19Q12) WILD-TYPE    5  277
                        clus
vv                       AMP PEAK 25(19Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                        107
                        clus
vv                       AMP PEAK 25(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          277
[1] 2 2
[1] FALSE

Clustering(26) Variable = AMP PEAK 26(20P11.21) MUTATION ANALYSIS
D26V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 26(20P11.21) MUTATED   123  75
  AMP PEAK 26(20P11.21) WILD-TYPE 200 106
  AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE 
                            198                             306 
  AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE 
                             75                             106 
$`AMP PEAK 26(20P11.21) MUTATED`
TCGA-05-4402 TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-44-6147 
        8.02        15.02        35.28        11.64        14.73        27.78 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-AAR0 TCGA-49-AARN 
       29.23         9.37        11.08        46.72       156.66        37.32 
TCGA-50-5935 TCGA-55-1592 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 
       21.47        23.05         7.79         7.99        23.18        21.44 
TCGA-55-8205 TCGA-55-8207 TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 
       19.69        32.12        20.58        20.19        20.65        52.60 
TCGA-73-4662 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 
       82.68        10.55        85.32        13.71         1.45         6.12 
TCGA-MN-A4N1 TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4417 
       27.19        50.07         3.98        45.01        37.02        14.96 
TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 TCGA-05-5425 TCGA-35-5375 TCGA-38-4625 
       30.02        25.02        25.02        29.00         8.68        97.74 
TCGA-38-4627 TCGA-38-4632 TCGA-44-2657 TCGA-44-3917 TCGA-44-3919 TCGA-44-5644 
       37.71        44.61        44.42        38.89        33.73        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-7660 
       28.01        23.77        21.63        23.18        61.28        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47B 
        7.17        36.07        18.87        23.64        15.98         9.44 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 
       13.64        13.45        28.11        35.54        32.84        29.46 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
       55.33        22.26        22.26         8.55        40.41       123.58 
TCGA-4B-A93V TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 
        9.86        71.47       101.72        47.41        49.28        14.27 
TCGA-50-5941 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 
       48.46        53.16        42.35         3.91        25.55         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 
        0.72        10.13        13.94        35.21        67.89        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-7574 
       14.30        80.52        40.73        15.25        53.65        32.71 
TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 
       18.44        29.23        29.72        15.19         5.06        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8302 TCGA-55-8507 TCGA-55-8508 
       15.65        29.19        22.16        15.72        13.74        20.28 
TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-A48Z TCGA-55-A493 
       19.96        17.10        17.62        14.66        21.40         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P 
       15.81        19.99         4.57        88.64        49.25        19.53 
TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-67-3770 TCGA-67-3771 
       39.09        38.37        87.98         2.04        20.05        20.05 
TCGA-67-3772 TCGA-69-7764 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
       18.84        13.61         4.41        13.41        13.51        14.01 
TCGA-73-4668 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5146 
       15.35        30.31         1.25        50.33        11.18        77.85 
TCGA-75-6206 TCGA-75-7027 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 
       85.15       100.57        39.95        19.50        38.50        64.90 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
      238.29        88.14        26.53        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       26.01        10.55       232.18        27.09        12.36         5.88 
TCGA-86-7713 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8358 
       38.04        37.74         4.08        24.33        22.82        21.47 
TCGA-86-8585 TCGA-86-8669 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       11.61        30.84        41.36        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       27.68         1.18        23.61         1.08        19.00        41.82 
TCGA-95-8494 TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-8174 TCGA-97-8175 
        2.76        42.25        61.48        18.54         5.39        18.12 
TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
       14.30        20.58        19.76         1.91        18.58        15.65 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4T7 
       38.63         2.76        49.35        37.35        58.85         5.49 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-NJ-A4YP TCGA-NJ-A55R TCGA-S2-AA1A 
       29.46        11.05        11.15         1.64        19.82        16.87 

$`AMP PEAK 26(20P11.21) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 
       15.02        28.41        26.30        43.53        38.10        42.08 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-49-6742 TCGA-49-6745 
       23.93        86.01        18.31        29.00        16.04        17.16 
TCGA-49-6761 TCGA-50-5932 TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-7573 
       11.64        40.60        41.69        48.62         5.79        16.01 
TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       14.53         6.15        19.66        19.73        17.98        16.93 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-67-6217 
       18.15        13.68        16.93        22.65        19.59        13.87 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-91-7771 TCGA-93-A4JQ TCGA-95-7043 
       39.09         8.48        50.24        16.18        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
        2.86        15.68        15.65        21.40        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        10.09        21.83         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       10.09         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 
       29.98        12.00        21.99        26.01        24.00         4.96 
TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 
       22.03         9.04         2.04         0.46         7.40         5.98 
TCGA-38-4626 TCGA-38-4628 TCGA-38-A44F TCGA-44-2656 TCGA-44-2659 TCGA-44-2665 
      120.79        49.05         4.37        46.98        44.94        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-44-6145 TCGA-44-6148 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 
       33.30        19.56        23.15        32.45        16.44        22.72 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47G TCGA-49-4486 TCGA-49-4488 
       12.66         8.55        15.32        11.54        76.21        28.57 
TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       12.66        14.07         8.81        29.75        55.89        53.29 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 
       73.12        62.24        28.90       221.33       164.12        20.52 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 
       15.72        60.16         8.22         9.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 
       15.12        60.72        57.53        11.05        12.16        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-6712 
       36.79        27.25        34.29        30.54        38.73         5.62 
TCGA-55-6968 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       42.51        46.03         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       92.81        24.99        40.54       107.21        70.26        28.67 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       20.02        27.09        22.03         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-8089 
       18.64        11.28        34.19        17.65        19.82        23.08 
TCGA-55-8094 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 
       17.79        15.42        17.56        14.47         0.36        17.72 
TCGA-55-8513 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A57B 
       26.01         1.58        12.33        20.71         3.25        17.95 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S 
       39.98        42.38        14.60        47.80        56.71        54.35 
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-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       56.81        81.80        37.02        42.90        28.41        51.25 
TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       28.47        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        6.64         6.12        22.68         5.42         7.56         6.05 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
       13.45         4.24        26.73        19.43         8.42        23.38 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-75-5125 TCGA-75-5147 TCGA-75-6212 
       26.30         4.31         9.24        66.64        43.82        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       36.66       108.66       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 
       20.58       129.53        21.90       119.51        32.09         5.88 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 
       22.92         9.57       104.19        39.35        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
      110.50        93.11        31.13        34.39        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 
       19.89        35.24         4.57         0.79        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
       31.20        23.05        14.60        13.91        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
       28.34        26.50        29.46         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       26.47        10.62         1.97         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7567 TCGA-95-7944 
       14.27        19.82        22.45        17.46        18.67        12.39 
TCGA-95-8039 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7938 
       27.29        19.89        64.60        63.52        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M0 
       15.91        18.67        15.39        16.41        21.60        21.44 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.57        21.63        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T9 
       14.30        14.53        86.14        58.45        86.04        41.59 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
        0.13        47.08         0.49         0.43        20.28        59.11 

  AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE 
                           0.72                            0.00 
  AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE 
                         238.29                          221.33 
  AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE 
                         21.895                          21.585 
[1] "0.7 - 238.3 (21.9)" "0.0 - 221.3 (21.6)"
[1] "hr=" "1.1"
D26V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 26(20P11.21) MUTATED         3       54       66        1        20
  AMP PEAK 26(20P11.21) WILD-TYPE       2       79       73        0        30
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 26(20P11.21) MUTATED          22         19          3        9
  AMP PEAK 26(20P11.21) WILD-TYPE        50         53          8       16
D26V3, multiclass
            clus
vv           AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE
  STAGE I                                3                               2
  STAGE IA                              54                              79
  STAGE IB                              66                              73
  STAGE II                               1                               0
  STAGE IIA                             20                              30
  STAGE IIB                             22                              50
  STAGE IIIA                            19                              53
  STAGE IIIB                             3                               8
  STAGE IV                               9                              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 26(20P11.21) MUTATED    66 116  15   3
  AMP PEAK 26(20P11.21) WILD-TYPE 105 162  31  16
D26V4, multiclass
    clus
vv   AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE
  T1                            66                             105
  T2                           116                             162
  T3                            15                              31
  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
  AMP PEAK 26(20P11.21) MUTATED   143  33    19
  AMP PEAK 26(20P11.21) WILD-TYPE 190  63    57
D26V5, multiclass
       clus
vv      AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE
  N0                              143                             190
  N1                               33                              63
  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"
D26V6, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20P11.21) MUTATED   127   9
  AMP PEAK 26(20P11.21) WILD-TYPE 222  16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20P11.21) MUTATED    127    9
  AMP PEAK 26(20P11.21) WILD-TYPE  222   16
   clus
vv  AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE
  0                           127                             222
  1                             9                              16
[1] 2 2
[1] FALSE
D26V7, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20P11.21) MUTATED   104  97
  AMP PEAK 26(20P11.21) WILD-TYPE 172 143
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20P11.21) MUTATED    104   97
  AMP PEAK 26(20P11.21) WILD-TYPE  172  143
        clus
vv       AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE
  FEMALE                           104                             172
  MALE                              97                             143
[1] 2 2
[1] FALSE
D26V8, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20P11.21) MUTATED   161  25
  AMP PEAK 26(20P11.21) WILD-TYPE 249  35
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20P11.21) MUTATED    161   25
  AMP PEAK 26(20P11.21) WILD-TYPE  249   35
     clus
vv    AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE
  NO                            161                             249
  YES                            25                              35
[1] 2 2
[1] FALSE
D26V9, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 26(20P11.21) MUTATED                            7
  AMP PEAK 26(20P11.21) WILD-TYPE                         11
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 26(20P11.21) MUTATED                                  30
  AMP PEAK 26(20P11.21) WILD-TYPE                                77
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 26(20P11.21) MUTATED                                                  138
  AMP PEAK 26(20P11.21) WILD-TYPE                                                183
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 26(20P11.21) MUTATED                                            2
  AMP PEAK 26(20P11.21) WILD-TYPE                                          3
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 26(20P11.21) MUTATED                                               7
  AMP PEAK 26(20P11.21) WILD-TYPE                                            12
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 26(20P11.21) MUTATED                                0
  AMP PEAK 26(20P11.21) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 26(20P11.21) MUTATED                                    2
  AMP PEAK 26(20P11.21) WILD-TYPE                                  1
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 26(20P11.21) MUTATED                              0
  AMP PEAK 26(20P11.21) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 26(20P11.21) MUTATED                              10
  AMP PEAK 26(20P11.21) WILD-TYPE                            13
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 26(20P11.21) MUTATED                                 1
  AMP PEAK 26(20P11.21) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 26(20P11.21) MUTATED                                               3
  AMP PEAK 26(20P11.21) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 26(20P11.21) MUTATED                              1
  AMP PEAK 26(20P11.21) WILD-TYPE                            9
D26V10, multiclass
                                                    clus
vv                                                   AMP PEAK 26(20P11.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           138
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  7
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                                 10
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  3
  MUCINOUS (COLLOID) CARCINOMA                                                   1
                                                    clus
vv                                                   AMP PEAK 26(20P11.21) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             183
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   12
  LUNG CLEAR CELL ADENOCARCINOMA                                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               1
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  LUNG PAPILLARY ADENOCARCINOMA                                                   13
  LUNG SIGNET RING ADENOCARCINOMA                                                  0
  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"
D26V11, continuous
D26V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 26(20P11.21) MUTATED   130   7   2   9
  AMP PEAK 26(20P11.21) WILD-TYPE 214   6   2  17
D26V13, multiclass
    clus
vv   AMP PEAK 26(20P11.21) MUTATED AMP PEAK 26(20P11.21) WILD-TYPE
  R0                           130                             214
  R1                             7                               6
  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
  AMP PEAK 26(20P11.21) MUTATED                                  1     3
  AMP PEAK 26(20P11.21) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(20P11.21) MUTATED                          27   147
  AMP PEAK 26(20P11.21) WILD-TYPE                        25   243
D26V14, multiclass
                                  clus
vv                                 AMP PEAK 26(20P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      147
                                  clus
vv                                 AMP PEAK 26(20P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     25
  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"
D26V15, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20P11.21) MUTATED     2 153
  AMP PEAK 26(20P11.21) WILD-TYPE   5 231
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20P11.21) MUTATED      2  153
  AMP PEAK 26(20P11.21) WILD-TYPE    5  231
                        clus
vv                       AMP PEAK 26(20P11.21) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           153
                        clus
vv                       AMP PEAK 26(20P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             231
[1] 2 2
[1] FALSE

Clustering(27) Variable = AMP PEAK 27(20Q13.33) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 27(20Q13.33) MUTATED   158  87
  AMP PEAK 27(20Q13.33) WILD-TYPE 165  94
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                            245                             259 
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                             87                              94 
$`AMP PEAK 27(20Q13.33) MUTATED`
TCGA-05-4405 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-44-2662 TCGA-44-6147 
       20.05        28.41        11.64        14.73        42.08        27.78 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-AAR0 
       29.00        29.23         9.37        11.08        46.72       156.66 
TCGA-49-AARN TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 
       37.32        21.47        41.69        23.05         5.79         7.79 
TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 TCGA-55-8205 TCGA-55-8207 TCGA-55-A491 
        7.99        23.18        21.44        19.69        32.12        20.58 
TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-78-8660 TCGA-80-5611 
       20.19        20.65        52.60        82.68        10.55        85.32 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7043 TCGA-95-7562 
       13.71        16.18         1.45         6.12        16.54         2.86 
TCGA-95-7947 TCGA-97-A4M3 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-05-4250 TCGA-05-4389 
       15.68        17.75        10.09        27.19         3.98        45.01 
TCGA-05-4390 TCGA-05-4397 TCGA-05-4415 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       37.02        24.03         2.99        29.98        12.00        30.02 
TCGA-05-4432 TCGA-05-5423 TCGA-05-5428 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 
       25.02         4.96        22.03         8.68        97.74        37.71 
TCGA-38-4628 TCGA-44-2656 TCGA-44-2657 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 
       49.05        46.98        44.42        38.89        34.06        33.73 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 
       28.37        28.01        23.77        21.63        23.18        61.28 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       19.46         7.17        36.07        18.87        23.64        12.66 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A4SU TCGA-49-4487 TCGA-49-4494 
       15.98        15.32         9.44        13.45        28.11        35.54 
TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6767 TCGA-49-AAR2 
       32.84        29.46        29.75        55.89        22.26        73.12 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5045 
        8.55        40.41       123.58       221.33         9.86        71.47 
TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 
      101.72        47.41        49.28        14.27        78.67        48.46 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 
       57.53        53.16        42.35         3.91        25.55         6.21 
TCGA-50-6673 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
        0.72        13.94        35.21        38.73        67.89        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
       14.30        80.52         5.62        40.73        15.25        53.65 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       11.28        34.19        18.44        29.23        29.72        15.19 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8302 
        5.06        23.64        15.65        29.19        22.16        15.72 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8514 TCGA-55-8615 TCGA-55-8620 
       13.74        20.28        19.96        17.10        14.66        12.33 
TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 
       21.40         0.92        15.81        19.99         4.57        42.38 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46S TCGA-64-1676 TCGA-64-1678 
       88.64        49.25        19.53        54.35        56.81        39.09 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-67-3771 TCGA-67-3772 
       38.37        87.98        28.41        51.25        20.05        18.84 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
        5.72         4.64         6.12        22.68        13.61         7.56 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-71-6725 
        4.41        13.41        13.51        14.01         4.24         8.42 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 
       26.30        15.35         4.31        30.31         1.25        50.33 
TCGA-73-A9RS TCGA-75-5125 TCGA-75-6206 TCGA-75-6214 TCGA-78-7143 TCGA-78-7152 
       11.18        66.64        85.15        36.66       163.10        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7163 
      119.51        19.50        38.50        64.90         9.57       238.29 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7542 TCGA-78-8640 
       26.53        31.20         8.02        53.33        10.55       232.18 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7954 TCGA-86-7955 
       93.11        27.09        12.36         5.88        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 
       37.74         4.08        24.33        22.82        31.04        31.20 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-91-6828 TCGA-91-6829 
       23.05        14.60        11.61        30.84        10.62        41.36 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-8499 TCGA-93-A4JN TCGA-93-A4JO 
       10.19         2.60        27.68         1.18        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-8494 TCGA-97-7546 TCGA-97-7553 
       19.00        41.82        18.67         2.76        42.25        61.48 
TCGA-97-7937 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 
       18.54        18.12        16.41        14.30        20.58        19.76 
TCGA-99-8025 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
       34.85        35.47        19.00         1.91        18.58        15.65 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 
       38.63         2.76        86.14        49.35        37.35        58.85 
TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-NJ-A4YF 
        5.49        29.46        11.05        24.36        11.15        71.05 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
        1.64        47.08        19.82        59.11        16.87 

$`AMP PEAK 27(20Q13.33) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96         8.02         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       15.02        15.02        35.28        26.30        43.53        38.10 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 
       23.93        86.01        18.31        16.04        17.16        11.64 
TCGA-50-5932 TCGA-55-1595 TCGA-55-7573 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 
       40.60        48.62        16.01        14.53         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       19.73        17.98        16.93        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A492 TCGA-67-6217 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       22.65        19.59        13.87        39.09         8.48        50.24 
TCGA-93-A4JQ TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       17.29        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A743 
       20.52        20.68        24.30        23.80         6.35        21.83 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4395 
        5.29        31.23         2.43        10.09        50.07         0.00 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       47.05        19.00        14.96        21.99        26.01        25.02 
TCGA-05-4433 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
       24.00        29.00         9.04         2.04         0.46         7.40 
TCGA-35-4123 TCGA-38-4626 TCGA-38-4632 TCGA-38-A44F TCGA-44-2659 TCGA-44-2665 
        5.98       120.79        44.61         4.37        44.94        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 TCGA-44-5643 
        3.19        25.02        37.15        38.24        26.56        33.30 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-8120 
       19.56        23.15        32.45        16.44        22.72         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-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 
        8.81        53.29        55.33        22.26        62.24        28.90 
TCGA-49-AARR TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 
      164.12        20.52        15.72        60.16         8.22         9.27 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 TCGA-50-6593 TCGA-50-6594 TCGA-50-7109 
        8.45        15.12        60.72        11.05        12.16        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-6968 
       36.99        36.79        27.25        34.29        30.54        42.51 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       46.03         3.88        69.34        45.34        32.71        92.81 
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        28.67        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7994 TCGA-55-8089 TCGA-55-8094 TCGA-55-8299 
       18.64        17.65        19.82        23.08        17.79        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8513 TCGA-55-8614 
       17.56        14.47         0.36        17.72        26.01        17.62 
TCGA-55-8616 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A57B TCGA-62-8395 TCGA-62-8398 
        1.58        20.71         3.25        17.95        39.98        14.60 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       47.80        56.71        67.96        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5778 
       40.96        29.92        81.80        37.02         2.04        42.90 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-69-7760 
       28.47        20.05        14.04        12.66        14.73         6.64 
TCGA-69-7765 TCGA-69-7974 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 
        5.42         6.05        13.45        26.73        19.43        23.38 
TCGA-73-4676 TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 
        9.24        77.85        43.82        49.84       108.66       100.57 
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       129.53        21.90 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7167 TCGA-78-7539 
       32.09         5.88        22.92       104.19        88.14        26.01 
TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-7701 TCGA-86-7711 
       39.35        39.75        77.59       110.50        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 
       38.04        20.55        32.78         4.57         0.79        32.65 
TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       21.47        13.91        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 
       29.46         3.81        24.23        13.64        26.47         1.97 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
       12.23         7.36         1.15        16.60        14.27        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7547 
       22.45        17.46        12.39        27.29        19.89        64.60 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       63.52        25.48         0.59        15.91        18.67         5.39 
TCGA-97-8176 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       15.39        21.60        21.44        20.84        18.67        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AG 
       36.76         1.45        21.57        21.63        18.08        32.48 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TI 
       14.30        14.53        58.45        86.04        41.59        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A55A TCGA-NJ-A55O 
       19.13        73.91        74.33         0.13         0.49         0.43 
TCGA-NJ-A7XG 
       20.28 

  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                           0.72                            0.00 
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                         238.29                          164.12 
  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE 
                          22.82                           20.84 
[1] "0.7 - 238.3 (22.8)" "0.0 - 164.1 (20.8)"
[1] "hr=" "1.1"
D27V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 27(20Q13.33) MUTATED         5       68       78        0        25
  AMP PEAK 27(20Q13.33) WILD-TYPE       0       65       61        1        25
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 27(20Q13.33) MUTATED          31         25          5       10
  AMP PEAK 27(20Q13.33) WILD-TYPE        41         47          6       15
D27V3, multiclass
            clus
vv           AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  STAGE I                                5                               0
  STAGE IA                              68                              65
  STAGE IB                              78                              61
  STAGE II                               0                               1
  STAGE IIA                             25                              25
  STAGE IIB                             31                              41
  STAGE IIIA                            25                              47
  STAGE IIIB                             5                               6
  STAGE IV                              10                              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 27(20Q13.33) MUTATED    84 140  22   4
  AMP PEAK 27(20Q13.33) WILD-TYPE  87 138  24  15
D27V4, multiclass
    clus
vv   AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  T1                            84                              87
  T2                           140                             138
  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 27(20Q13.33) MUTATED   175  42    29
  AMP PEAK 27(20Q13.33) WILD-TYPE 158  54    47
D27V5, multiclass
       clus
vv      AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  N0                              175                             158
  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"
D27V6, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.33) MUTATED   166  10
  AMP PEAK 27(20Q13.33) WILD-TYPE 183  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.33) MUTATED    166   10
  AMP PEAK 27(20Q13.33) WILD-TYPE  183   15
   clus
vv  AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  0                           166                             183
  1                            10                              15
[1] 2 2
[1] FALSE
D27V7, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.33) MUTATED   135 116
  AMP PEAK 27(20Q13.33) WILD-TYPE 141 124
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.33) MUTATED    135  116
  AMP PEAK 27(20Q13.33) WILD-TYPE  141  124
        clus
vv       AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  FEMALE                           135                             141
  MALE                             116                             124
[1] 2 2
[1] FALSE
D27V8, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.33) MUTATED   203  30
  AMP PEAK 27(20Q13.33) WILD-TYPE 207  30
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.33) MUTATED    203   30
  AMP PEAK 27(20Q13.33) WILD-TYPE  207   30
     clus
vv    AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  NO                            203                             207
  YES                            30                              30
[1] 2 2
[1] FALSE
D27V9, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                           11
  AMP PEAK 27(20Q13.33) WILD-TYPE                          7
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 27(20Q13.33) MUTATED                                  42
  AMP PEAK 27(20Q13.33) WILD-TYPE                                65
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 27(20Q13.33) MUTATED                                                  167
  AMP PEAK 27(20Q13.33) WILD-TYPE                                                154
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 27(20Q13.33) MUTATED                                            2
  AMP PEAK 27(20Q13.33) WILD-TYPE                                          3
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 27(20Q13.33) MUTATED                                              10
  AMP PEAK 27(20Q13.33) WILD-TYPE                                             9
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                                0
  AMP PEAK 27(20Q13.33) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                                    2
  AMP PEAK 27(20Q13.33) WILD-TYPE                                  1
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                              0
  AMP PEAK 27(20Q13.33) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                              11
  AMP PEAK 27(20Q13.33) WILD-TYPE                            12
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                                 1
  AMP PEAK 27(20Q13.33) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                                               4
  AMP PEAK 27(20Q13.33) WILD-TYPE                                             1
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 27(20Q13.33) MUTATED                              1
  AMP PEAK 27(20Q13.33) WILD-TYPE                            9
D27V10, multiclass
                                                    clus
vv                                                   AMP PEAK 27(20Q13.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             42
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           167
  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 27(20Q13.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               65
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             154
  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"
D27V11, continuous
D27V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 27(20Q13.33) MUTATED   161   8   2  14
  AMP PEAK 27(20Q13.33) WILD-TYPE 183   5   2  12
D27V13, multiclass
    clus
vv   AMP PEAK 27(20Q13.33) MUTATED AMP PEAK 27(20Q13.33) WILD-TYPE
  R0                           161                             183
  R1                             8                               5
  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
  AMP PEAK 27(20Q13.33) MUTATED                                  1     4
  AMP PEAK 27(20Q13.33) WILD-TYPE                                0     3
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(20Q13.33) MUTATED                          31   186
  AMP PEAK 27(20Q13.33) WILD-TYPE                        21   204
D27V14, multiclass
                                  clus
vv                                 AMP PEAK 27(20Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      186
                                  clus
vv                                 AMP PEAK 27(20Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          3
  BLACK OR AFRICAN AMERICAN                                     21
  WHITE                                                        204
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V15, binary
                                 cls
clus                                0   1
  AMP PEAK 27(20Q13.33) MUTATED     4 192
  AMP PEAK 27(20Q13.33) WILD-TYPE   3 192
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 27(20Q13.33) MUTATED      4  192
  AMP PEAK 27(20Q13.33) WILD-TYPE    3  192
                        clus
vv                       AMP PEAK 27(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           192
                        clus
vv                       AMP PEAK 27(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             192
[1] 2 2
[1] FALSE

Clustering(28) Variable = AMP PEAK 28(22Q11.22) MUTATION ANALYSIS
D28V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 28(22Q11.22) MUTATED    50  35
  AMP PEAK 28(22Q11.22) WILD-TYPE 273 146
  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                             85                             419 
  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                             35                             146 
$`AMP PEAK 28(22Q11.22) MUTATED`
TCGA-44-6147 TCGA-44-7670 TCGA-44-A47F TCGA-49-6742 TCGA-55-1592 TCGA-55-7724 
       27.78        29.00        11.08        16.04        23.05        23.18 
TCGA-55-7726 TCGA-55-8091 TCGA-55-8204 TCGA-55-8511 TCGA-55-A491 TCGA-MP-A4TC 
       21.44        19.73        16.93        18.15        20.58         2.43 
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-44-3918 TCGA-44-3919 TCGA-44-5644 TCGA-44-6777 TCGA-44-6779 TCGA-44-7662 
       34.06        33.73        28.37        32.45        16.44         7.17 
TCGA-44-7669 TCGA-44-8117 TCGA-44-A47A TCGA-49-4488 TCGA-49-6743 TCGA-49-6767 
       18.87        12.66        15.32        28.57        53.29        22.26 
TCGA-49-AARE TCGA-50-5931 TCGA-50-5944 TCGA-50-5946 TCGA-50-6594 TCGA-50-6673 
       40.41        14.27        57.53        53.16        12.16         0.72 
TCGA-55-1596 TCGA-55-6712 TCGA-55-6981 TCGA-55-6982 TCGA-55-7574 TCGA-55-7907 
       67.89         5.62        45.34        32.71        32.71        11.28 
TCGA-55-8096 TCGA-55-8208 TCGA-55-8506 TCGA-55-8514 TCGA-55-8614 TCGA-55-A490 
       23.64        22.16         0.36        17.10        17.62         3.25 
TCGA-55-A57B TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-64-1679 
       17.95        42.38        14.60        49.25        47.80        81.80 
TCGA-67-3770 TCGA-67-3771 TCGA-69-7979 TCGA-69-8253 TCGA-73-4675 TCGA-75-6212 
       20.05        20.05        13.41        14.01        30.31        49.84 
TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7536 TCGA-78-8662 TCGA-86-6562 
       21.90        19.50        38.50         8.02       110.50        12.36 
TCGA-86-7713 TCGA-86-7955 TCGA-86-8055 TCGA-86-8280 TCGA-86-8358 TCGA-86-A4D0 
       38.04        35.24         4.08        23.05        21.47         3.81 
TCGA-91-6847 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 TCGA-97-7553 TCGA-97-8174 
       27.68        18.67        12.39         2.76        61.48         5.39 
TCGA-97-8552 TCGA-J2-A4AE TCGA-L9-A8F4 TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A5C7 
       20.58        35.47        15.65        58.45         5.49        73.91 
TCGA-NJ-A4YF 
       71.05 

$`AMP PEAK 28(22Q11.22) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       26.01        15.02        15.02        28.41        35.28        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       14.73        26.30        43.53        38.10        42.08        23.93 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 TCGA-49-6745 
       86.01        18.31        29.23         9.37        46.72        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       11.64       156.66        37.32        40.60        21.47        41.69 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 
       48.62         5.79         7.79         7.99        16.01        14.53 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 
        6.15        19.66        17.98        19.69        32.12        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       16.93        22.65        19.59        20.19        20.65        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       85.32        13.71        16.18         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 
       23.80         6.35        10.09        21.83        27.19         5.29 
TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
       31.23        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
        0.00        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-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
        4.96        29.00         9.04         2.04         0.46         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 
        5.98         8.68       120.79        37.71        49.05        44.61 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       46.98        44.42        44.94        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3917 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 
       37.15        38.89        26.56        33.30        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-7659 
       19.56        23.15        21.63        23.18        61.28        22.72 
TCGA-44-7660 TCGA-44-7667 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B 
       19.46        36.07        23.64         8.55        15.98         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-49-4494 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-49-6744 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.89        55.33        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
        8.55       123.58       221.33       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       101.72        15.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        8.22         9.27        78.67         8.45        15.12        48.46 
TCGA-50-5942 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 
       60.72        42.35         3.91        25.55        11.05         6.21 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       13.94        35.21        38.73        30.58        14.30        80.52 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       69.34        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       28.67        20.02        27.09        22.03         3.91        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       25.41        18.64        34.19        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       15.65        29.19        15.42        17.56        15.72        14.47 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 
       13.74        20.28        17.72        19.96        26.01        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 
        1.58        12.33        20.71        21.40         0.92        15.81 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R 
       19.99         4.57        39.98        88.64        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
       54.35        67.96        72.30        13.61        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       29.92        56.81        39.09        37.02        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
        2.04        42.90        28.41        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         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-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K 
        4.41        13.51        13.45         4.24        26.73        19.43 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 
        8.42        23.38        26.30        15.35         4.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        1.25        50.33        11.18        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       85.15        36.66       108.66       100.57       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       129.53        39.95       119.51 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
      238.29        88.14        26.53        31.20        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 
       39.35        10.55       232.18        39.75        77.59        93.11 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
       27.09         5.88        31.13        34.39        20.55        32.78 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       19.89        37.74         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       32.65        31.04        31.20        14.60        11.61        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        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
       24.23        13.64        26.47        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       10.19         2.60        12.23         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 
        1.08        19.00        41.82        27.29        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        25.48        18.54         0.59        15.91 
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-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       21.44        19.76        20.84        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AG 
       36.76         1.45        21.57        21.63        18.08        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N4 
       19.00        14.30        14.53         1.91        18.58        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-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       41.59        29.46        11.05        24.36        14.10        11.15 
TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       19.13        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.43        19.82        20.28        59.11        16.87 

  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                           0.36                            0.00 
  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                         110.50                          238.29 
  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE 
                           21.9                            21.6 
[1] "0.4 - 110.5 (21.9)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1.2"
D28V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 28(22Q11.22) MUTATED         2       19       29        0        15
  AMP PEAK 28(22Q11.22) WILD-TYPE       3      114      110        1        35
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 28(22Q11.22) MUTATED          11         12          1        1
  AMP PEAK 28(22Q11.22) WILD-TYPE        61         60         10       24
D28V3, multiclass
            clus
vv           AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  STAGE I                                2                               3
  STAGE IA                              19                             114
  STAGE IB                              29                             110
  STAGE II                               0                               1
  STAGE IIA                             15                              35
  STAGE IIB                             11                              61
  STAGE IIIA                            12                              60
  STAGE IIIB                             1                              10
  STAGE IV                               1                              24
[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 28(22Q11.22) MUTATED    28  55   6   1
  AMP PEAK 28(22Q11.22) WILD-TYPE 143 223  40  18
D28V4, multiclass
    clus
vv   AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  T1                            28                             143
  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 28(22Q11.22) MUTATED    57  19    12
  AMP PEAK 28(22Q11.22) WILD-TYPE 276  77    64
D28V5, multiclass
       clus
vv      AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  N0                               57                             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"
D28V6, binary
                                 cls
clus                                0   1
  AMP PEAK 28(22Q11.22) MUTATED    58   1
  AMP PEAK 28(22Q11.22) WILD-TYPE 291  24
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(22Q11.22) MUTATED     58    1
  AMP PEAK 28(22Q11.22) WILD-TYPE  291   24
   clus
vv  AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  0                            58                             291
  1                             1                              24
[1] 2 2
[1] FALSE
D28V7, binary
                                 cls
clus                                0   1
  AMP PEAK 28(22Q11.22) MUTATED    55  35
  AMP PEAK 28(22Q11.22) WILD-TYPE 221 205
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(22Q11.22) MUTATED     55   35
  AMP PEAK 28(22Q11.22) WILD-TYPE  221  205
        clus
vv       AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  FEMALE                            55                             221
  MALE                              35                             205
[1] 2 2
[1] FALSE
D28V8, binary
                                 cls
clus                                0   1
  AMP PEAK 28(22Q11.22) MUTATED    74   9
  AMP PEAK 28(22Q11.22) WILD-TYPE 336  51
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(22Q11.22) MUTATED     74    9
  AMP PEAK 28(22Q11.22) WILD-TYPE  336   51
     clus
vv    AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  NO                             74                             336
  YES                             9                              51
[1] 2 2
[1] FALSE
D28V9, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                            2
  AMP PEAK 28(22Q11.22) WILD-TYPE                         16
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 28(22Q11.22) MUTATED                                  13
  AMP PEAK 28(22Q11.22) WILD-TYPE                                94
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 28(22Q11.22) MUTATED                                                   68
  AMP PEAK 28(22Q11.22) WILD-TYPE                                                253
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 28(22Q11.22) MUTATED                                            0
  AMP PEAK 28(22Q11.22) WILD-TYPE                                          5
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 28(22Q11.22) MUTATED                                               3
  AMP PEAK 28(22Q11.22) WILD-TYPE                                            16
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                                1
  AMP PEAK 28(22Q11.22) WILD-TYPE                              1
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                                    1
  AMP PEAK 28(22Q11.22) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                              0
  AMP PEAK 28(22Q11.22) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                               1
  AMP PEAK 28(22Q11.22) WILD-TYPE                            22
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                                 0
  AMP PEAK 28(22Q11.22) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                                               0
  AMP PEAK 28(22Q11.22) WILD-TYPE                                             5
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 28(22Q11.22) MUTATED                              1
  AMP PEAK 28(22Q11.22) WILD-TYPE                            9
D28V10, multiclass
                                                    clus
vv                                                   AMP PEAK 28(22Q11.22) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             13
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            68
  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 28(22Q11.22) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      16
  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"
D28V11, continuous
D28V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 28(22Q11.22) MUTATED    62   2   0   3
  AMP PEAK 28(22Q11.22) WILD-TYPE 282  11   4  23
D28V13, multiclass
    clus
vv   AMP PEAK 28(22Q11.22) MUTATED AMP PEAK 28(22Q11.22) WILD-TYPE
  R0                            62                             282
  R1                             2                              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 28(22Q11.22) MUTATED                                  0     1
  AMP PEAK 28(22Q11.22) WILD-TYPE                                1     6
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 28(22Q11.22) MUTATED                           9    69
  AMP PEAK 28(22Q11.22) WILD-TYPE                        43   321
D28V14, multiclass
                                  clus
vv                                 AMP PEAK 28(22Q11.22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                       69
                                  clus
vv                                 AMP PEAK 28(22Q11.22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     43
  WHITE                                                        321
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V15, binary
                                 cls
clus                                0   1
  AMP PEAK 28(22Q11.22) MUTATED     1  64
  AMP PEAK 28(22Q11.22) WILD-TYPE   6 320
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 28(22Q11.22) MUTATED      1   64
  AMP PEAK 28(22Q11.22) WILD-TYPE    6  320
                        clus
vv                       AMP PEAK 28(22Q11.22) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            64
                        clus
vv                       AMP PEAK 28(22Q11.22) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             320
[1] 2 2
[1] FALSE

Clustering(29) Variable = AMP PEAK 29(XQ28) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 29(XQ28) MUTATED    95  58
  AMP PEAK 29(XQ28) WILD-TYPE 228 123
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                        153                         351 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                         58                         123 
$`AMP PEAK 29(XQ28) MUTATED`
TCGA-05-4382 TCGA-05-4405 TCGA-05-4434 TCGA-38-4629 TCGA-38-4631 TCGA-38-7271 
       19.96        20.05        15.02        28.41        11.64        26.30 
TCGA-44-7661 TCGA-49-6761 TCGA-55-1592 TCGA-55-1595 TCGA-55-7726 TCGA-55-8090 
       18.31        11.64        23.05        48.62        21.44        19.66 
TCGA-55-8203 TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-78-7166 TCGA-91-7771 
       17.98        20.58        20.19        20.65         8.48        16.18 
TCGA-93-A4JQ TCGA-95-7043 TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M7 TCGA-L9-A444 
       17.29        16.54        17.92        20.19        20.68        10.09 
TCGA-MN-A4N1 TCGA-05-4390 TCGA-05-4397 TCGA-05-4425 TCGA-05-4426 TCGA-05-4432 
       27.19        37.02        24.03        21.99        26.01        25.02 
TCGA-05-5423 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-44-2659 
        4.96        22.03         7.40         5.98         8.68        44.94 
TCGA-44-3917 TCGA-44-3918 TCGA-44-5644 TCGA-44-5645 TCGA-44-6778 TCGA-44-6779 
       38.89        34.06        28.37        28.01        61.28        16.44 
TCGA-44-7662 TCGA-44-7669 TCGA-44-8117 TCGA-44-A47A TCGA-44-A4SU TCGA-49-4488 
        7.17        18.87        12.66        15.32        13.45        28.57 
TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 TCGA-49-6767 
       35.54        14.07         8.81        29.75        55.33        22.26 
TCGA-49-AAR3 TCGA-49-AARO TCGA-49-AARQ TCGA-4B-A93V TCGA-50-5045 TCGA-50-5933 
       62.24       123.58       221.33         9.86        71.47        78.67 
TCGA-50-5941 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
       48.46        53.16         3.91        25.55        11.05        12.16 
TCGA-50-7109 TCGA-53-7624 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       10.13        34.29        67.89        30.58        14.30        80.52 
TCGA-55-6712 TCGA-55-6970 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7576 
        5.62        15.25        40.54        70.26        28.67        22.03 
TCGA-55-7907 TCGA-55-7994 TCGA-55-8092 TCGA-55-8096 TCGA-55-A48Z TCGA-55-A494 
       11.28        19.82         5.06        23.64        21.40        15.81 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8399 TCGA-62-A46U TCGA-64-1676 TCGA-64-1678 
       19.99        17.95        88.64        67.96        56.81        39.09 
TCGA-64-1680 TCGA-64-5815 TCGA-67-3772 TCGA-67-4679 TCGA-67-6215 TCGA-69-7764 
       37.02        28.47        18.84        14.73         5.72        13.61 
TCGA-69-7979 TCGA-71-6725 TCGA-73-4666 TCGA-73-4670 TCGA-73-4676 TCGA-73-7499 
       13.41         8.42        26.30         4.31         9.24        50.33 
TCGA-75-5125 TCGA-75-6206 TCGA-75-6214 TCGA-75-7025 TCGA-78-7146 TCGA-78-7147 
       66.64        85.15        36.66       108.66         5.69        19.27 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7155 TCGA-78-7161 TCGA-78-7163 TCGA-78-7220 
      129.53        19.50        38.50         9.57       238.29        26.53 
TCGA-78-7535 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 
       31.20        10.55       232.18        77.59        27.09        12.36 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8280 TCGA-86-8358 
       35.24        37.74         4.08        22.82        23.05        21.47 
TCGA-86-8359 TCGA-86-8673 TCGA-86-A4P7 TCGA-91-6829 TCGA-91-8496 TCGA-91-8499 
       14.60        28.34        13.64        41.36        16.60         1.18 
TCGA-93-A4JO TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 
        1.08        18.67        27.29         2.76        25.48        18.54 
TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M6 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N4 
       14.30        21.60        18.67         1.91        18.58        38.63 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        2.76        58.45        86.04        11.05        14.10        19.13 
TCGA-NJ-A55A TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.49        20.28        16.87 

$`AMP PEAK 29(XQ28) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 TCGA-05-5420 
       14.01         9.96         8.02         9.01        26.01        15.02 
TCGA-38-4630 TCGA-38-6178 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       35.28        14.73        43.53        38.10        42.08        23.93 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F 
       27.78        86.01        29.00        29.23         9.37        11.08 
TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       46.72        16.04        17.16       156.66        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       21.47        41.69         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 
       23.18        14.53         6.15        19.73        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 
       32.12        18.15        13.68        16.93        22.65        19.59 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7633 TCGA-78-8660 
       13.87        52.60        82.68        39.09        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7562 TCGA-95-7947 
       85.32        13.71         1.45         6.12         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 
       15.65        21.40        18.18        20.52        17.75        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
       23.80         6.35        21.83         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4395 TCGA-05-4398 
       10.09        50.07         3.98        45.01         0.00        47.05 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       19.00         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       25.02        24.00        29.00         9.04         2.04         0.46 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F 
       97.74       120.79        37.71        49.05        44.61         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       46.98        44.42        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-6144 TCGA-44-6145 
       38.24        33.73        26.56        33.30        23.77        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 
       23.15        21.63        23.18        32.45        22.72        19.46 
TCGA-44-7667 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47G 
       36.07        23.64         8.55        15.98         9.44        11.54 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4506 TCGA-49-4510 
       13.64        76.21        28.11        12.66        32.84        29.46 
TCGA-49-4514 TCGA-49-6743 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 
       55.89        53.29        22.26        73.12        28.90         8.55 
TCGA-49-AARE TCGA-49-AARR TCGA-50-5044 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
       40.41       164.12        20.52       101.72        15.72        60.16 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 
       47.41        49.28         8.22         9.27        14.27         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6595 TCGA-50-6673 
       15.12        60.72        57.53        42.35         6.21         0.72 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.99        36.79        27.25        30.54        13.94        35.21 
TCGA-55-1594 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       38.73        42.51        40.73        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 
       69.34        45.34        32.71        92.81        24.99       107.21 
TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       20.02        27.09        32.71         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 
       18.64        34.19        17.65        18.44        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       15.19        23.08        17.79        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 
       14.66         1.58        12.33        20.71         3.25         0.92 
TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O 
        4.57        39.98        42.38        14.60        49.25        47.80 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       19.53        56.71        54.35        72.30        13.61        39.25 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 
       40.96        29.92        81.80        38.37        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 
       42.90        28.41        51.25        20.05        20.05        14.04 
TCGA-67-3774 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 
       12.66         4.64         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         4.41        13.51        14.01        13.45 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 
        4.24        26.73        19.43        23.38        15.35        30.31 
TCGA-73-4677 TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 TCGA-75-7027 
        1.25        11.18        77.85        43.82        49.84       100.57 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
      163.10        27.16        20.58        21.90        39.95       119.51 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7167 
       32.09         5.88        64.90        22.92       104.19        88.14 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8648 TCGA-78-8662 
        8.02        53.33        26.01        39.35        39.75       110.50 
TCGA-80-5608 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       93.11         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 
       32.78        19.89         4.57        24.33         0.79        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       31.04        31.20        11.61        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        26.50        29.46         3.81        24.23        26.47 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 
       10.62         1.97        10.19         2.60        12.23        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
        7.36         1.15        14.27        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-A4VP TCGA-97-7546 
       23.61        19.00        41.82        12.39        19.89        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       64.60        63.52        61.48         0.59        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M0 
        5.39        18.12        15.39        16.41        20.58        21.44 
TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       19.76        20.84        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.57        21.63        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 
       14.30        14.53        15.65        86.14        49.35        37.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TJ 
       58.85         5.49        41.59        29.46        24.36        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                       0.49                        0.00 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                     238.29                      164.12 
  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE 
                      20.58                       22.45 
[1] "0.5 - 238.3 (20.6)" "0.0 - 164.1 (22.4)"
[1] "hr=" "1.1"
D29V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  AMP PEAK 29(XQ28) MUTATED         1       41       42        0        15
  AMP PEAK 29(XQ28) WILD-TYPE       4       92       97        1        35
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  AMP PEAK 29(XQ28) MUTATED          24         20          3        9
  AMP PEAK 29(XQ28) WILD-TYPE        48         52          8       16
D29V3, multiclass
            clus
vv           AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  STAGE I                            1                           4
  STAGE IA                          41                          92
  STAGE IB                          42                          97
  STAGE II                           0                           1
  STAGE IIA                         15                          35
  STAGE IIB                         24                          48
  STAGE IIIA                        20                          52
  STAGE IIIB                         3                           8
  STAGE IV                           9                          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 29(XQ28) MUTATED    49  93  13   4
  AMP PEAK 29(XQ28) WILD-TYPE 122 185  33  15
D29V4, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  T1                        49                         122
  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 29(XQ28) MUTATED    97  36    23
  AMP PEAK 29(XQ28) WILD-TYPE 236  60    53
D29V5, multiclass
       clus
vv      AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  N0                           97                         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"
D29V6, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED   105   9
  AMP PEAK 29(XQ28) WILD-TYPE 244  16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED    105    9
  AMP PEAK 29(XQ28) WILD-TYPE  244   16
   clus
vv  AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  0                       105                         244
  1                         9                          16
[1] 2 2
[1] FALSE
D29V7, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED    81  78
  AMP PEAK 29(XQ28) WILD-TYPE 195 162
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED     81   78
  AMP PEAK 29(XQ28) WILD-TYPE  195  162
        clus
vv       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  FEMALE                        81                         195
  MALE                          78                         162
[1] 2 2
[1] FALSE
D29V8, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED   123  17
  AMP PEAK 29(XQ28) WILD-TYPE 287  43
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED    123   17
  AMP PEAK 29(XQ28) WILD-TYPE  287   43
     clus
vv    AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  NO                        123                         287
  YES                        17                          43
[1] 2 2
[1] FALSE
D29V9, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                            6
  AMP PEAK 29(XQ28) WILD-TYPE                         12
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  AMP PEAK 29(XQ28) MUTATED                                  33
  AMP PEAK 29(XQ28) WILD-TYPE                                74
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  AMP PEAK 29(XQ28) MUTATED                                                  107
  AMP PEAK 29(XQ28) WILD-TYPE                                                214
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  AMP PEAK 29(XQ28) MUTATED                                            2
  AMP PEAK 29(XQ28) WILD-TYPE                                          3
                             vv
clus                          LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  AMP PEAK 29(XQ28) MUTATED                                               4
  AMP PEAK 29(XQ28) WILD-TYPE                                            15
                             vv
clus                          LUNG CLEAR CELL ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                                1
  AMP PEAK 29(XQ28) WILD-TYPE                              1
                             vv
clus                          LUNG MICROPAPILLARY ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                                    1
  AMP PEAK 29(XQ28) WILD-TYPE                                  2
                             vv
clus                          LUNG MUCINOUS ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                              0
  AMP PEAK 29(XQ28) WILD-TYPE                            2
                             vv
clus                          LUNG PAPILLARY ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                               5
  AMP PEAK 29(XQ28) WILD-TYPE                            18
                             vv
clus                          LUNG SIGNET RING ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                                 0
  AMP PEAK 29(XQ28) WILD-TYPE                               1
                             vv
clus                          LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  AMP PEAK 29(XQ28) MUTATED                                               0
  AMP PEAK 29(XQ28) WILD-TYPE                                             5
                             vv
clus                          MUCINOUS (COLLOID) CARCINOMA
  AMP PEAK 29(XQ28) MUTATED                              0
  AMP PEAK 29(XQ28) WILD-TYPE                           10
D29V10, multiclass
                                                    clus
vv                                                   AMP PEAK 29(XQ28) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       107
  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 29(XQ28) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                  12
  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"
D29V11, continuous
D29V12, continuous
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 29(XQ28) MUTATED   108   6   1   6
  AMP PEAK 29(XQ28) WILD-TYPE 236   7   3  20
D29V13, multiclass
    clus
vv   AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  R0                       108                         236
  R1                         6                           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 29(XQ28) MUTATED                                  0     3
  AMP PEAK 29(XQ28) WILD-TYPE                                1     4
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 29(XQ28) MUTATED                          16   117
  AMP PEAK 29(XQ28) WILD-TYPE                        36   273
D29V14, multiclass
                                  clus
vv                                 AMP PEAK 29(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               16
  WHITE                                                  117
                                  clus
vv                                 AMP PEAK 29(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"
D29V15, binary
                             cls
clus                            0   1
  AMP PEAK 29(XQ28) MUTATED     1 110
  AMP PEAK 29(XQ28) WILD-TYPE   6 274
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 29(XQ28) MUTATED      1  110
  AMP PEAK 29(XQ28) WILD-TYPE    6  274
                        clus
vv                       AMP PEAK 29(XQ28) MUTATED AMP PEAK 29(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             1                           6
  NOT HISPANIC OR LATINO                       110                         274
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  1(1P36.13) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.13) MUTATED    75  45
  DEL PEAK  1(1P36.13) WILD-TYPE 248 136
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                           120                            384 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                            45                            136 
$`DEL PEAK  1(1P36.13) MUTATED`
TCGA-05-4396 TCGA-05-4434 TCGA-05-5420 TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 
        9.96        15.02        15.02        11.08        17.16        11.64 
TCGA-50-5932 TCGA-50-5935 TCGA-55-1595 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 
       40.60        21.47        48.62         6.15        19.66        17.98 
TCGA-55-8205 TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 TCGA-80-5611 TCGA-91-7771 
       19.69        20.58        19.59        20.65        85.32        16.18 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-A4VN TCGA-97-8172 TCGA-L9-A743 TCGA-MP-A4TC 
       17.29        16.54        18.18        17.92        21.83         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 
       10.09        50.07         3.98        45.01        37.02        47.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4424 TCGA-05-4425 TCGA-05-5425 TCGA-05-5429 
        2.99        14.96        30.02        21.99        29.00         9.04 
TCGA-35-3615 TCGA-38-4625 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 
        0.46        97.74         3.19        25.02        38.89        34.06 
TCGA-44-5643 TCGA-44-6144 TCGA-44-6779 TCGA-44-7660 TCGA-44-A479 TCGA-49-4488 
       33.30        23.77        16.44        19.46        15.98        28.57 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-6767 TCGA-49-AARE TCGA-50-5051 
       35.54        32.84         8.81        22.26        40.41        15.72 
TCGA-50-5936 TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-55-1596 TCGA-55-5899 
        8.45        12.16         6.21        10.13        67.89        30.58 
TCGA-55-6986 TCGA-55-7283 TCGA-55-7911 TCGA-55-7913 TCGA-55-8507 TCGA-55-8508 
      107.21        20.02        17.65        18.44        13.74        20.28 
TCGA-55-8615 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A494 TCGA-62-8398 TCGA-62-A46S 
       14.66        20.71        21.40        15.81        14.60        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-5774 TCGA-64-5778 TCGA-64-5815 
       67.96        72.30        29.92        87.98        42.90        28.47 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7978 TCGA-73-4659 
        6.64         6.12        22.68         7.56         4.41        23.38 
TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-A9RS TCGA-75-7027 
       26.30         4.31        30.31         1.25        11.18       100.57 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7153 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 
        5.69        20.58       119.51        19.50        64.90        22.92 
TCGA-78-7536 TCGA-78-8655 TCGA-80-5608 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
        8.02        77.59        93.11        12.36         5.88        31.13 
TCGA-86-7713 TCGA-86-8054 TCGA-86-8358 TCGA-86-8669 TCGA-86-A4JF TCGA-91-6828 
       38.04        37.74        21.47        30.84        24.23        10.62 
TCGA-91-6830 TCGA-91-8499 TCGA-95-7944 TCGA-95-A4VP TCGA-97-8176 TCGA-97-A4M5 
        1.97         1.18        12.39        19.89        15.39        20.84 
TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TJ TCGA-NJ-A4YQ TCGA-NJ-A7XG TCGA-O1-A52J 
        5.49        29.46        11.15        47.08        20.28        59.11 

$`DEL PEAK  1(1P36.13) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         8.02        20.05         9.01        26.01 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       28.41        35.28        11.64        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       38.10        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-AAR0 
       29.00        29.23         9.37        46.72        16.04       156.66 
TCGA-49-AARN TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       37.32        41.69        23.05         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-8091 TCGA-55-8204 
       16.01        23.18        14.53        21.44        19.73        16.93 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A4DF 
       32.12        18.15        13.68        16.93        22.65        20.19 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7562 TCGA-95-7947 
       10.55        13.71         1.45         6.12         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       15.65        21.40        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        27.19         5.29 
TCGA-MP-A4TA TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 TCGA-05-4420 TCGA-05-4422 
       31.23         0.00        24.03        19.00        29.98        12.00 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 
       26.01        25.02        25.02        24.00         4.96        22.03 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
        2.04         7.40         5.98         8.68       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       49.05        44.61         4.37        46.98        44.42        44.94 
TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5644 
       42.77        37.15        38.24        33.73        26.56        28.37 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       28.01        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       61.28        22.72         7.17        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
       12.66         8.55        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4505 TCGA-49-4510 
       13.45        76.21        28.11        12.66        14.07        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 
       29.75        55.89        53.29        55.33        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       62.24        28.90         8.55       123.58       221.33       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       101.72        60.16        47.41 
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 
       48.46        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       25.55        11.05         0.72        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6543 
       34.29        30.54        13.94        35.21        38.73        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 
       24.99        40.54        70.26        28.67        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
       22.03         3.91        23.15        25.41        18.64        11.28 
TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       34.19        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
        5.06        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 
       15.42        17.56        15.72        14.47         0.36        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 
       19.96        26.01        17.10        17.62         1.58        12.33 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        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-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       13.61        39.25        40.96        56.81        39.09        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 
       37.02        38.37         2.04        28.41        51.25        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       20.05        18.84        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 
        4.64        13.61         5.42         6.05        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 
       14.01        13.45         4.24        26.73        19.43         8.42 
TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
       15.35         9.24        50.33        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 
       85.15        49.84        36.66       108.66       163.10        27.16 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 
       19.27       129.53        21.90        39.95        38.50        32.09 
TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
        5.88         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
       31.20        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8662 TCGA-83-5908 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
       39.75       110.50        27.09        34.39        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       19.89        35.24         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
       22.82        32.65        31.04        31.20        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
       11.61        13.91        27.58         0.62        28.34        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6831 
       29.46         3.81        13.64        26.47        41.36        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        2.60        12.23        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
       14.27        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 
       19.00        41.82        18.67        27.29         2.76        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       64.60        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
       15.91        18.67         5.39        18.12        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 
       21.60        20.58        21.44        19.76        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD 
       34.85        36.76         1.45        21.57        21.63        18.08 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       35.47        32.48        19.00        14.30        14.53         1.91 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       18.58        15.65        38.63         2.76        86.14        58.45 
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-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        0.13         1.64         0.49         0.43        19.82        16.87 

  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                          0.46                           0.00 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                        119.51                         238.29 
  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE 
                         20.15                          22.77 
[1] "0.5 - 119.5 (20.1)" "0.0 - 238.3 (22.8)"
[1] "hr=" "1.2"
D30V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  1(1P36.13) MUTATED         0       29       24        0        11
  DEL PEAK  1(1P36.13) WILD-TYPE       5      104      115        1        39
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  1(1P36.13) MUTATED          18         27          4        7
  DEL PEAK  1(1P36.13) WILD-TYPE        54         45          7       18
D30V3, multiclass
            clus
vv           DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                             29                            104
  STAGE IB                             24                            115
  STAGE II                              0                              1
  STAGE IIA                            11                             39
  STAGE IIB                            18                             54
  STAGE IIIA                           27                             45
  STAGE IIIB                            4                              7
  STAGE IV                              7                             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  1(1P36.13) MUTATED    37  62  17   6
  DEL PEAK  1(1P36.13) WILD-TYPE 134 216  29  13
D30V4, multiclass
    clus
vv   DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  T1                           37                            134
  T2                           62                            216
  T3                           17                             29
  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  1(1P36.13) MUTATED    69  26    26
  DEL PEAK  1(1P36.13) WILD-TYPE 264  70    50
D30V5, multiclass
       clus
vv      DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  N0                              69                            264
  N1                              26                             70
  N2+N3                           26                             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.13) MUTATED    88   7
  DEL PEAK  1(1P36.13) WILD-TYPE 261  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED     88    7
  DEL PEAK  1(1P36.13) WILD-TYPE  261   18
   clus
vv  DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  0                           88                            261
  1                            7                             18
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.13) MUTATED    57  65
  DEL PEAK  1(1P36.13) WILD-TYPE 219 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED     57   65
  DEL PEAK  1(1P36.13) WILD-TYPE  219  175
        clus
vv       DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  FEMALE                           57                            219
  MALE                             65                            175
[1] 2 2
[1] FALSE
D30V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.13) MUTATED    99  13
  DEL PEAK  1(1P36.13) WILD-TYPE 311  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED     99   13
  DEL PEAK  1(1P36.13) WILD-TYPE  311   47
     clus
vv    DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  NO                            99                            311
  YES                           13                             47
[1] 2 2
[1] FALSE
D30V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                            6
  DEL PEAK  1(1P36.13) WILD-TYPE                         12
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  1(1P36.13) MUTATED                                  28
  DEL PEAK  1(1P36.13) WILD-TYPE                                79
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  1(1P36.13) MUTATED                                                   78
  DEL PEAK  1(1P36.13) WILD-TYPE                                                243
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  1(1P36.13) MUTATED                                            0
  DEL PEAK  1(1P36.13) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  1(1P36.13) MUTATED                                               3
  DEL PEAK  1(1P36.13) WILD-TYPE                                            16
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                                1
  DEL PEAK  1(1P36.13) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                                    0
  DEL PEAK  1(1P36.13) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                              0
  DEL PEAK  1(1P36.13) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                               1
  DEL PEAK  1(1P36.13) WILD-TYPE                            22
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                                 1
  DEL PEAK  1(1P36.13) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                                               2
  DEL PEAK  1(1P36.13) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  1(1P36.13) MUTATED                              2
  DEL PEAK  1(1P36.13) WILD-TYPE                            8
D30V10, multiclass
                                                    clus
vv                                                   DEL PEAK  1(1P36.13) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  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                                                 1
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK  1(1P36.13) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              79
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            243
  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                                                  22
  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"
D30V11, continuous
D30V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.13) MUTATED    82   3   2   6
  DEL PEAK  1(1P36.13) WILD-TYPE 262  10   2  20
D30V13, multiclass
    clus
vv   DEL PEAK  1(1P36.13) MUTATED DEL PEAK  1(1P36.13) WILD-TYPE
  R0                           82                            262
  R1                            3                             10
  R2                            2                              2
  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(1P36.13) MUTATED                                  0     2
  DEL PEAK  1(1P36.13) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.13) MUTATED                           9    89
  DEL PEAK  1(1P36.13) WILD-TYPE                        43   301
D30V14, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      89
                                  clus
vv                                 DEL PEAK  1(1P36.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    43
  WHITE                                                       301
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V15, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.13) MUTATED     1  86
  DEL PEAK  1(1P36.13) WILD-TYPE   6 298
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.13) MUTATED      1   86
  DEL PEAK  1(1P36.13) WILD-TYPE    6  298
                        clus
vv                       DEL PEAK  1(1P36.13) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       DEL PEAK  1(1P36.13) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            298
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  2(1P13.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P13.1) MUTATED    96  54
  DEL PEAK  2(1P13.1) WILD-TYPE 227 127
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                          150                           354 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           54                           127 
$`DEL PEAK  2(1P13.1) MUTATED`
TCGA-05-4434 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-50-5932 
       15.02        11.08        46.72        17.16        11.64        40.60 
TCGA-50-5935 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8205 TCGA-55-A492 
       21.47        19.66        19.73        17.98        19.69        19.59 
TCGA-55-A4DF TCGA-73-4662 TCGA-73-7498 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 
       20.19        82.68        39.09        85.32        13.71        16.18 
TCGA-93-8067 TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VN TCGA-97-8172 TCGA-J2-8192 
        6.12        16.54        15.68        18.18        17.92        24.30 
TCGA-L9-A444 TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
       10.09        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4433 
       24.03        47.05         2.99        14.96        12.00        24.00 
TCGA-05-5715 TCGA-38-4625 TCGA-38-4628 TCGA-44-2665 TCGA-44-2668 TCGA-44-3918 
        2.04        97.74        49.05        42.77        25.02        34.06 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 
       33.30        28.37        23.77        35.54        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-AARE TCGA-49-AARQ 
       29.46        29.75        55.89        53.29        40.41       221.33 
TCGA-50-5044 TCGA-50-5051 TCGA-50-5936 TCGA-50-5946 TCGA-50-6591 TCGA-50-6594 
       20.52        15.72         8.45        53.16         3.91        12.16 
TCGA-50-6595 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 TCGA-55-6971 
        6.21        13.94        35.21        67.89        30.58        46.03 
TCGA-55-6972 TCGA-55-6986 TCGA-55-7283 TCGA-55-7907 TCGA-55-7911 TCGA-55-7913 
       53.65       107.21        20.02        11.28        17.65        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8092 TCGA-55-8094 TCGA-55-8505 TCGA-55-8507 
       19.82        29.23         5.06        17.79        14.47        13.74 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8615 TCGA-55-A48Y TCGA-62-8402 TCGA-62-A46S 
       20.28        19.96        14.66        20.71        49.25        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-64-1678 TCGA-64-5774 TCGA-64-5775 
       67.96        72.30        39.25        39.09        87.98         2.04 
TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 
       42.90        28.41        20.05        20.05        18.84        12.66 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 
        6.12        22.68         7.56         8.42        23.38        26.30 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-73-A9RS TCGA-75-6206 TCGA-75-7027 
        4.31        30.31         1.25        11.18        85.15       100.57 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7160 
        5.69        20.58       129.53       119.51        19.50        22.92 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7539 TCGA-80-5608 TCGA-86-6851 
      238.29        88.14        26.53        26.01        93.11         5.88 
TCGA-86-7701 TCGA-86-8054 TCGA-86-8278 TCGA-86-8668 TCGA-86-8669 TCGA-86-A4D0 
       31.13        37.74        31.04        13.91        30.84         3.81 
TCGA-86-A4JF TCGA-91-6828 TCGA-91-6848 TCGA-91-8497 TCGA-93-7348 TCGA-95-7039 
       24.23        10.62         7.36        14.27        17.46        41.82 
TCGA-95-7567 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7554 TCGA-97-8547 TCGA-97-8552 
       18.67        27.29        19.89        25.48        21.60        20.58 
TCGA-97-A4M5 TCGA-L9-A50W TCGA-MP-A4SW TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TH 
       20.84        14.53        58.45        58.85         5.49        24.36 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A7XG 
       11.15        19.13        73.91         0.13        47.08        20.28 

$`DEL PEAK  2(1P13.1) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       26.01        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 
       26.30        43.53        38.10        42.08        23.93        27.78 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-49-6742 
       86.01        18.31        29.00        29.23         9.37        16.04 
TCGA-49-AAR0 TCGA-49-AARN TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 
      156.66        37.32        41.69        23.05        48.62         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
        6.15        16.93        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A491 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-78-7166 
       22.65        20.58        20.65        13.87        52.60         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7948 
       50.24        10.55         1.45        17.29         2.86        15.65 
TCGA-95-A4VK TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 
       21.40        20.19        20.52        17.75        20.68        23.80 
TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        21.83        27.19         5.29        31.23         2.43 
TCGA-05-4395 TCGA-05-4403 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        0.00        19.00        29.98        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        25.02         4.96        29.00        22.03         9.04 
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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2666 
       44.61         4.37        46.98        44.42        44.94         3.19 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       37.15        38.24        38.89        33.73        26.56        28.01 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       19.56        23.15        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       16.44        22.72        19.46         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       23.64        12.66         8.55        15.98        15.32         9.44 
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-49-4505 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 
       12.66        14.07        55.33        22.26        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V 
       62.24        28.90         8.55       123.58       164.12         9.86 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
       71.47       101.72        60.16        47.41        49.28         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
        9.27        14.27        78.67        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6673 TCGA-50-7109 
       57.53        42.35        25.55        11.05         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 
       36.99        36.79        27.25        34.29        30.54        38.73 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       14.30        80.52         5.62        42.51        40.73        15.25 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
        3.88        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       40.54        70.26        28.67        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-8085 
        3.91        23.15        25.41        18.64        34.19        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       15.19        23.08        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8513 
       15.42        17.56        15.72         0.36        17.72        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
       17.10        17.62         1.58        12.33        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        19.99        17.95         4.57        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-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 
       13.61        40.96        29.92        56.81        81.80        37.02 
TCGA-64-1681 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 
       38.37        51.25        28.47        14.04        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
        4.64         6.64        13.61         5.42         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
       13.41        13.51        14.01        13.45         4.24        26.73 
TCGA-69-A59K TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       19.43        15.35         9.24        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 
       43.82        49.84        36.66       108.66       163.10        27.16 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       19.27        21.90        39.95        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
       64.90         9.57       104.19        31.20         8.02        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       27.09        12.36        34.39        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       19.89        35.24         4.08         4.57        24.33         0.79 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       22.82        32.65        31.20        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       11.61        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
       13.64        26.47        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BD 
       12.23        27.68         1.15        16.60         1.18        19.82 
TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 TCGA-95-8494 
       22.45        23.61         1.08        19.00        12.39         2.76 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
       42.25        64.60        63.52        61.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 
       14.30        21.44        19.76        18.67        24.56        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE 
       36.76         1.45        21.57        21.63        18.08        35.47 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
       32.48        19.00        14.30         1.91        18.58        15.65 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       38.63         2.76        86.14        49.35        37.35        86.04 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-NJ-A4YF TCGA-NJ-A4YG 
       41.59        29.46        11.05        14.10        71.05        74.33 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
        1.64         0.49         0.43        19.82        59.11        16.87 

  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                       238.29                        232.18 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                       20.775                        21.865 
[1] "0.1 - 238.3 (20.8)" "0.0 - 232.2 (21.9)"
[1] "hr=" "1.1"
D31V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  2(1P13.1) MUTATED         2       34       34        0        11
  DEL PEAK  2(1P13.1) WILD-TYPE       3       99      105        1        39
                               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        51         41          6       15
D31V3, multiclass
            clus
vv           DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            34                            99
  STAGE IB                            34                           105
  STAGE II                             0                             1
  STAGE IIA                           11                            39
  STAGE IIB                           21                            51
  STAGE IIIA                          31                            41
  STAGE IIIB                           5                             6
  STAGE IV                            10                            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  2(1P13.1) MUTATED    44  84  14   9
  DEL PEAK  2(1P13.1) WILD-TYPE 127 194  32  10
D31V4, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  T1                          44                           127
  T2                          84                           194
  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    92  30    29
  DEL PEAK  2(1P13.1) WILD-TYPE 241  66    47
D31V5, multiclass
       clus
vv      DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  N0                             92                           241
  N1                             30                            66
  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"
D31V6, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED   102  10
  DEL PEAK  2(1P13.1) WILD-TYPE 247  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED    102   10
  DEL PEAK  2(1P13.1) WILD-TYPE  247   15
   clus
vv  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  0                         102                           247
  1                          10                            15
[1] 2 2
[1] FALSE
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED    82  69
  DEL PEAK  2(1P13.1) WILD-TYPE 194 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED     82   69
  DEL PEAK  2(1P13.1) WILD-TYPE  194  171
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  FEMALE                          82                           194
  MALE                            69                           171
[1] 2 2
[1] FALSE
D31V8, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P13.1) MUTATED   125  14
  DEL PEAK  2(1P13.1) WILD-TYPE 285  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED    125   14
  DEL PEAK  2(1P13.1) WILD-TYPE  285   46
     clus
vv    DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  NO                          125                           285
  YES                          14                            46
[1] 2 2
[1] FALSE
D31V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  2(1P13.1) MUTATED                            8
  DEL PEAK  2(1P13.1) WILD-TYPE                         10
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  2(1P13.1) MUTATED                                  30
  DEL PEAK  2(1P13.1) WILD-TYPE                                77
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  2(1P13.1) MUTATED                                                   92
  DEL PEAK  2(1P13.1) WILD-TYPE                                                229
                               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
D31V10, multiclass
                                                    clus
vv                                                   DEL PEAK  2(1P13.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          92
  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                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             77
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           229
  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"
D31V11, continuous
D31V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  2(1P13.1) MUTATED   102   2   2   9
  DEL PEAK  2(1P13.1) WILD-TYPE 242  11   2  17
D31V13, multiclass
    clus
vv   DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  R0                         102                           242
  R1                           2                            11
  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                          11   116
  DEL PEAK  2(1P13.1) WILD-TYPE                        41   274
D31V14, multiclass
                                  clus
vv                                 DEL PEAK  2(1P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    116
                                  clus
vv                                 DEL PEAK  2(1P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   41
  WHITE                                                      274
[1] 4 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  2(1P13.1) MUTATED     1 109
  DEL PEAK  2(1P13.1) WILD-TYPE   6 275
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      1  109
  DEL PEAK  2(1P13.1) WILD-TYPE    6  275
                        clus
vv                       DEL PEAK  2(1P13.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         109
                        clus
vv                       DEL PEAK  2(1P13.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           275
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED    30  15
  DEL PEAK  3(2Q22.1) WILD-TYPE 293 166
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           45                           459 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           15                           166 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-05-4418 TCGA-44-8119 TCGA-55-A492 TCGA-55-A4DF TCGA-93-8067 TCGA-97-8172 
        9.01         9.37        19.59        20.19         6.12        17.92 
TCGA-L9-A444 TCGA-05-4415 TCGA-38-4625 TCGA-44-2656 TCGA-44-2659 TCGA-44-6778 
       10.09         2.99        97.74        46.98        44.94        61.28 
TCGA-44-6779 TCGA-44-A4SS TCGA-49-AARO TCGA-50-5051 TCGA-50-5936 TCGA-50-5946 
       16.44        13.64       123.58        15.72         8.45        53.16 
TCGA-50-6591 TCGA-53-7624 TCGA-55-6986 TCGA-55-8097 TCGA-55-8508 TCGA-62-8397 
        3.91        34.29       107.21        15.65        20.28        42.38 
TCGA-62-A470 TCGA-64-1676 TCGA-67-3772 TCGA-69-7760 TCGA-71-6725 TCGA-73-4670 
       39.25        56.81        18.84         6.64         8.42         4.31 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-78-7150 TCGA-78-7153 TCGA-78-7220 
       50.33        66.64        43.82        21.90       119.51        26.53 
TCGA-78-7536 TCGA-86-7701 TCGA-86-8054 TCGA-86-8074 TCGA-86-8358 TCGA-91-6829 
        8.02        31.13        37.74         0.79        21.47        41.36 
TCGA-91-6848 TCGA-95-7039 TCGA-97-7554 
        7.36        41.82        25.48 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 
       19.96        14.01         9.96         8.02        20.05        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       15.02        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 
       26.30        43.53        38.10        42.08        23.93        27.78 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 
       86.01        18.31        29.00        29.23        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       16.04        17.16        11.64       156.66        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       21.47        41.69        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
        7.99        16.01        23.18        14.53        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       19.66        19.73        17.98        16.93        19.69        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-64-1677 
       18.15        13.68        16.93        22.65        20.58        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ 
       10.55        85.32        13.71        16.18         1.45        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN 
       16.54         2.86        15.68        15.65        21.40        18.18 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       24.03        47.05        19.00        14.96        29.98        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-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
        4.96        29.00        22.03         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-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.61         4.37        44.42        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        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.30        28.37        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       21.63        23.18        32.45        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         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-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       28.57        12.66        35.54        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
       29.46        29.75        55.89        53.29        55.33        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
       22.26        73.12        62.24        28.90         8.55        40.41 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 
      221.33       164.12         9.86        20.52        71.47       101.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       60.16        47.41        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        48.46        60.72        57.53        42.35 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       25.55        11.05        12.16         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       36.99        36.79        27.25        30.54        13.94        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       38.73        67.89        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       70.26        28.67        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
        3.91        23.15        25.41        18.64        11.28        34.19 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 
       23.08         5.06        17.79        23.64        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       17.72        19.96        26.01        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 
       15.81        19.99        17.95         4.57        39.98        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        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-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       81.80        37.02        38.37        87.98         2.04        42.90 
TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3773 
       28.41        51.25        28.47        20.05        20.05        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
       12.66        14.73         5.72         4.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       13.61         5.42         7.56         6.05         4.41        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K 
       13.51        14.01        13.45         4.24        26.73        19.43 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       23.38        26.30        15.35        30.31         9.24         1.25 
TCGA-73-A9RS TCGA-75-5146 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       11.18        77.85        85.15        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      100.57       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 
      129.53        39.95        19.50        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
       64.90        22.92         9.57       104.19       238.29        88.14 
TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
       31.20        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
        5.88        34.39        38.04        20.55        32.78        19.89 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 
       35.24         4.08         4.57        24.33        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.04        31.20        23.05        14.60        11.61        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        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 
        3.81        24.23        13.64        26.47        10.62         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-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.08        19.00        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 
       19.89        42.25        64.60        63.52        61.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
        0.59        15.91        18.67         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-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 
       20.84        18.67        24.56        34.85        36.76         1.45 
TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
       21.57        21.63        18.08        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       14.30        14.53         1.91        18.58        15.65        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-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       14.10        11.15        19.13        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
        0.13         1.64        47.08         0.49         0.43        19.82 
TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       20.28        59.11        16.87 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         0.79                          0.00 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                       123.58                        238.29 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                        21.47                         21.63 
[1] "0.8 - 123.6 (21.5)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1.2"
D32V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  3(2Q22.1) MUTATED         0        9       14        0         2
  DEL PEAK  3(2Q22.1) WILD-TYPE       5      124      125        1        48
                               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        63         65         10       21
D32V3, multiclass
            clus
vv           DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                              0                             5
  STAGE IA                             9                           124
  STAGE IB                            14                           125
  STAGE II                             0                             1
  STAGE IIA                            2                            48
  STAGE IIB                            9                            63
  STAGE IIIA                           7                            65
  STAGE IIIB                           1                            10
  STAGE IV                             4                            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  3(2Q22.1) MUTATED    11  29   5   1
  DEL PEAK  3(2Q22.1) WILD-TYPE 160 249  41  18
D32V4, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                          11                           160
  T2                          29                           249
  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    31   7     8
  DEL PEAK  3(2Q22.1) WILD-TYPE 302  89    68
D32V5, multiclass
       clus
vv      DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  N0                             31                           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"
D32V6, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    29   4
  DEL PEAK  3(2Q22.1) WILD-TYPE 320  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     29    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                          29                           320
  1                           4                            21
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    25  21
  DEL PEAK  3(2Q22.1) WILD-TYPE 251 219
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     25   21
  DEL PEAK  3(2Q22.1) WILD-TYPE  251  219
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                          25                           251
  MALE                            21                           219
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED    39   4
  DEL PEAK  3(2Q22.1) WILD-TYPE 371  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED     39    4
  DEL PEAK  3(2Q22.1) WILD-TYPE  371   56
     clus
vv    DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  NO                           39                           371
  YES                           4                            56
[1] 2 2
[1] FALSE
D32V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  3(2Q22.1) MUTATED                            3
  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                                                   28
  DEL PEAK  3(2Q22.1) WILD-TYPE                                                293
                               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
D32V10, multiclass
                                                    clus
vv                                                   DEL PEAK  3(2Q22.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          28
  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)                           293
  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"
D32V11, continuous
D32V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(2Q22.1) MUTATED    30   0   0   2
  DEL PEAK  3(2Q22.1) WILD-TYPE 314  13   4  24
D32V13, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  R0                          30                           314
  R1                           0                            13
  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                           3    36
  DEL PEAK  3(2Q22.1) WILD-TYPE                        49   354
D32V14, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     36
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   49
  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"
D32V15, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     1  32
  DEL PEAK  3(2Q22.1) WILD-TYPE   6 352
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      1   32
  DEL PEAK  3(2Q22.1) WILD-TYPE    6  352
                        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                           352
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  4(3P26.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(3P26.2) MUTATED   145  84
  DEL PEAK  4(3P26.2) WILD-TYPE 178  97
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                          229                           275 
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                           84                            97 
$`DEL PEAK  4(3P26.2) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4434 TCGA-38-6178 TCGA-44-6147 TCGA-44-6776 
       19.96         8.02        15.02        14.73        27.78        86.01 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6742 
       29.00        29.23         9.37        11.08        46.72        16.04 
TCGA-49-6745 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       17.16       156.66        37.32        40.60        21.47        41.69 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8204 
       16.01        23.18        21.44         6.15        19.66        16.93 
TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-7498 
       20.58        19.59        20.19        20.65        13.87        39.09 
TCGA-78-8660 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 
       10.55         1.45        17.29        16.54        15.68        15.65 
TCGA-97-A4LX TCGA-97-A4M7 TCGA-J2-8192 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC 
       20.19        20.68        24.30        27.19         5.29         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 
       10.09        50.07        45.01        37.02         0.00        24.03 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4432 TCGA-05-5425 TCGA-05-5715 TCGA-35-5375 
        2.99        29.98        25.02        29.00         2.04         8.68 
TCGA-38-4627 TCGA-38-4628 TCGA-44-2656 TCGA-44-2657 TCGA-44-2668 TCGA-44-3917 
       37.71        49.05        46.98        44.42        25.02        38.89 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6774 TCGA-44-6778 
       33.30        28.37        23.77        19.56        21.63        61.28 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       16.44        19.46        23.64        12.66         8.55        15.98 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV 
       14.07        32.84        55.89        53.29        55.33        22.26 
TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AARE TCGA-50-5049 TCGA-50-5068 TCGA-50-5072 
       73.12        28.90        40.41       101.72        49.28         8.22 
TCGA-50-5931 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 
       14.27        15.12        48.46        57.53        42.35         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 
       11.05        12.16         6.21         0.72        10.13        36.99 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 
       34.29        30.54        13.94        35.21        38.73        67.89 
TCGA-55-6968 TCGA-55-6975 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-7570 
       42.51         3.88        32.71        92.81        40.54        27.09 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8092 
       22.03         3.91        11.28        34.19        29.23         5.06 
TCGA-55-8094 TCGA-55-8206 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 
       17.79        29.19         0.36        13.74        20.28        17.10 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 
       17.62        14.66        12.33        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        81.80        87.98        28.41 
TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-69-7763 TCGA-69-7764 
       51.25        20.05        20.05        18.84        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         4.41        13.41        14.01         8.42 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS 
       26.30        15.35         4.31        30.31        50.33        11.18 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7147 
       77.85        43.82        36.66       100.57         5.69        19.27 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7159 TCGA-78-7160 TCGA-78-7167 TCGA-78-7535 
       20.58        21.90        64.90        22.92        88.14        31.20 
TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
        8.02        10.55       232.18        93.11        27.09        12.36 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
        5.88        31.13        34.39        38.04        32.78        19.89 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8280 
       37.74         4.08        24.33         0.79        22.82        23.05 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8672 TCGA-86-A4D0 TCGA-86-A4JF 
       21.47        11.61        30.84         0.62         3.81        24.23 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-8499 
       41.36         1.97         2.60        12.23        27.68         1.18 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       17.46        41.82        18.67        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 
       42.25        64.60        25.48        18.54         5.39        16.41 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8033 TCGA-J2-A4AG 
       21.44        19.76        20.84        18.67        21.57        32.48 
TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4TF 
       14.53        18.58        38.63        86.04        58.85        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        47.08         0.43        20.28 
TCGA-O1-A52J 
       59.11 

$`DEL PEAK  4(3P26.2) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-5420 
       14.01         9.96        20.05         9.01        26.01        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       28.41        35.28        11.64        26.30        43.53        38.10 
TCGA-44-2662 TCGA-44-6146 TCGA-44-7661 TCGA-49-6761 TCGA-55-1592 TCGA-55-1595 
       42.08        23.93        18.31        11.64        23.05        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7725 TCGA-55-8091 TCGA-55-8203 
        5.79         7.79         7.99        14.53        19.73        17.98 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.69        32.12        18.15        13.68        16.93        22.65 
TCGA-73-4658 TCGA-73-4662 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 
       52.60        82.68         8.48        50.24        85.32        13.71 
TCGA-91-7771 TCGA-93-8067 TCGA-95-7562 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 
       16.18         6.12         2.86        21.40        18.18        17.92 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
       20.52        17.75        23.80         6.35        10.09        21.83 
TCGA-MP-A4TA TCGA-05-4250 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 
       31.23         3.98        47.05        19.00        14.96        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 
       30.02        21.99        26.01        25.02        24.00         4.96 
TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 
       22.03         9.04         0.46         7.40         5.98        97.74 
TCGA-38-4626 TCGA-38-4632 TCGA-38-A44F TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 
      120.79        44.61         4.37        44.94        42.77         3.19 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       37.15        38.24        34.06        33.73        26.56        28.01 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 
       23.15        23.18        32.45        22.72         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-49-4507 
       76.21        28.11        28.57        12.66        35.54         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARO 
       29.46        29.75        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 
      221.33       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        47.41         9.27        78.67         8.45        60.72 
TCGA-50-5946 TCGA-50-6592 TCGA-50-8459 TCGA-50-8460 TCGA-55-5899 TCGA-55-6543 
       53.16        25.55        36.79        27.25        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
       80.52         5.62        40.73        15.25        46.03        53.65 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       69.34        45.34        24.99       107.21        70.26        28.67 
TCGA-55-7283 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 
       20.02        32.71        23.15        25.41        18.64        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8096 
       18.44        19.82        29.72        15.19        23.08        23.64 
TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
       15.65        22.16        15.42        17.56        15.72        14.47 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z 
       17.72        19.96        26.01         1.58        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8402 
        3.25         0.92        15.81        17.95        39.98        49.25 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1680 
       19.53        54.35        67.96        72.30        29.92        37.02 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 
       38.37         2.04        42.90        28.47        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7974 
       14.73         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-73-4659 
       13.51        13.45         4.24        26.73        19.43        23.38 
TCGA-73-4676 TCGA-73-4677 TCGA-75-5125 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 
        9.24         1.25        66.64        85.15        49.84       108.66 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
      163.10        27.16       129.53        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
       38.50        32.09         5.88         9.57       104.19       238.29 
TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 
       26.53        53.33        26.01        39.35        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        35.24         4.57        32.65        31.04 
TCGA-86-8279 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
       31.20        14.60        13.91        27.58        28.34        26.50 
TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6831 TCGA-91-6848 
       29.46        13.64        26.47        10.62        10.19         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN 
        1.15        16.60        14.27        19.82        22.45        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 
        1.08        19.00        12.39        63.52        61.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 
       15.91        18.67        18.12        15.39        14.30        21.60 
TCGA-97-8552 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R 
       20.58        24.56        34.85        36.76         1.45        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A8F4 
       18.08        35.47        19.00        14.30         1.91        15.65 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T7 
        2.76        86.14        58.45        49.35        37.35         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG 
       41.59        29.46        24.36        19.13        73.91        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55R TCGA-S2-AA1A 
        0.13         1.64         0.49        19.82        16.87 

  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                         0.00                          0.13 
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                       232.18                        238.29 
  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE 
                        21.47                         21.99 
[1] "0.0 - 232.2 (21.5)" "0.1 - 238.3 (22.0)"
[1] "hr=" "1.1"
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  4(3P26.2) MUTATED         1       57       57        1        32
  DEL PEAK  4(3P26.2) WILD-TYPE       4       76       82        0        18
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  4(3P26.2) MUTATED          32         33          4       14
  DEL PEAK  4(3P26.2) WILD-TYPE        40         39          7       11
D33V3, multiclass
            clus
vv           DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                            57                            76
  STAGE IB                            57                            82
  STAGE II                             1                             0
  STAGE IIA                           32                            18
  STAGE IIB                           32                            40
  STAGE IIIA                          33                            39
  STAGE IIIB                           4                             7
  STAGE IV                            14                            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    79 134  11   8
  DEL PEAK  4(3P26.2) WILD-TYPE  92 144  35  11
D33V4, multiclass
    clus
vv   DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  T1                          79                            92
  T2                         134                           144
  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   138  54    36
  DEL PEAK  4(3P26.2) WILD-TYPE 195  42    40
D33V5, multiclass
       clus
vv      DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  N0                            138                           195
  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"
D33V6, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P26.2) MUTATED   160  14
  DEL PEAK  4(3P26.2) WILD-TYPE 189  11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P26.2) MUTATED    160   14
  DEL PEAK  4(3P26.2) WILD-TYPE  189   11
   clus
vv  DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  0                         160                           189
  1                          14                            11
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P26.2) MUTATED   123 110
  DEL PEAK  4(3P26.2) WILD-TYPE 153 130
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P26.2) MUTATED    123  110
  DEL PEAK  4(3P26.2) WILD-TYPE  153  130
        clus
vv       DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  FEMALE                         123                           153
  MALE                           110                           130
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P26.2) MUTATED   193  25
  DEL PEAK  4(3P26.2) WILD-TYPE 217  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P26.2) MUTATED    193   25
  DEL PEAK  4(3P26.2) WILD-TYPE  217   35
     clus
vv    DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  NO                          193                           217
  YES                          25                            35
[1] 2 2
[1] FALSE
D33V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  4(3P26.2) MUTATED                           11
  DEL PEAK  4(3P26.2) WILD-TYPE                          7
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  4(3P26.2) MUTATED                                  50
  DEL PEAK  4(3P26.2) WILD-TYPE                                57
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  4(3P26.2) MUTATED                                                  150
  DEL PEAK  4(3P26.2) WILD-TYPE                                                171
                               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
D33V10, multiclass
                                                    clus
vv                                                   DEL PEAK  4(3P26.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           50
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         150
  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                                                     7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             57
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           171
  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"
D33V11, continuous
D33V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  4(3P26.2) MUTATED   150   2   2  10
  DEL PEAK  4(3P26.2) WILD-TYPE 194  11   2  16
D33V13, multiclass
    clus
vv   DEL PEAK  4(3P26.2) MUTATED DEL PEAK  4(3P26.2) WILD-TYPE
  R0                         150                           194
  R1                           2                            11
  R2                           2                             2
  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  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                          27   177
  DEL PEAK  4(3P26.2) WILD-TYPE                        25   213
D33V14, multiclass
                                  clus
vv                                 DEL PEAK  4(3P26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    177
                                  clus
vv                                 DEL PEAK  4(3P26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   25
  WHITE                                                      213
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V15, binary
                               cls
clus                              0   1
  DEL PEAK  4(3P26.2) MUTATED     4 178
  DEL PEAK  4(3P26.2) WILD-TYPE   3 206
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3P26.2) MUTATED      4  178
  DEL PEAK  4(3P26.2) WILD-TYPE    3  206
                        clus
vv                       DEL PEAK  4(3P26.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         178
                        clus
vv                       DEL PEAK  4(3P26.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           206
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  5(3P21.31) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  5(3P21.31) MUTATED   158  87
  DEL PEAK  5(3P21.31) WILD-TYPE 165  94
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                           245                            259 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                            87                             94 
$`DEL PEAK  5(3P21.31) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-6178 
       19.96         8.02        15.02        15.02        35.28        14.73 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F 
       27.78        86.01        29.00        29.23         9.37        11.08 
TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       46.72        16.04        17.16       156.66        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 
       21.47        41.69        16.01        23.18        21.44         6.15 
TCGA-55-8090 TCGA-55-8204 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 
       19.66        16.93        20.58        19.59        20.19        13.87 
TCGA-73-7498 TCGA-78-8660 TCGA-80-5611 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 
       39.09        10.55        85.32         1.45        17.29        16.54 
TCGA-95-7947 TCGA-95-7948 TCGA-97-A4LX TCGA-97-A4M7 TCGA-J2-8192 TCGA-MN-A4N1 
       15.68        15.65        20.19        20.68        24.30        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 
        5.29         2.43        10.09        50.07        45.01        37.02 
TCGA-05-4397 TCGA-05-4415 TCGA-05-4420 TCGA-05-4432 TCGA-05-5425 TCGA-05-5715 
       24.03         2.99        29.98        25.02        29.00         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4627 TCGA-38-4628 TCGA-44-2656 
        7.40         5.98         8.68        37.71        49.05        46.98 
TCGA-44-2657 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 
       44.42        25.02        38.89        34.06        33.30        28.37 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       23.77        19.56        21.63        61.28        16.44        19.46 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-49-4505 TCGA-49-4506 
       23.64        12.66         8.55        15.98        14.07        32.84 
TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 
        8.81        55.89        53.29        55.33        22.26        73.12 
TCGA-49-AAR9 TCGA-49-AARE TCGA-50-5049 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 
        8.55        40.41       101.72        49.28         8.22        14.27 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-6591 TCGA-50-6593 
        8.45        15.12        48.46        57.53         3.91        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 
       12.16         6.21         0.72        10.13        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 
       13.94        35.21        38.73        67.89        30.58        42.51 
TCGA-55-6975 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-7570 TCGA-55-7576 
        3.88        32.71        92.81        40.54        27.09        22.03 
TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 TCGA-55-7995 TCGA-55-8094 
        3.91        11.28        34.19        18.44        29.23        17.79 
TCGA-55-8206 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 
       29.19         0.36        13.74        20.28        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A4DG 
       14.66         1.58        12.33        21.40         3.25        19.99 
TCGA-62-8394 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46R 
        4.57        42.38        14.60        88.64        47.80        56.71 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       13.61        39.25        40.96        56.81        39.09        81.80 
TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       87.98        28.41        51.25        28.47        20.05        20.05 
TCGA-67-3772 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 
       18.84        22.68        13.61         5.42         7.56         4.41 
TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 
       13.41        14.01        13.45         8.42        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 
        4.31        30.31        50.33        11.18        77.85        43.82 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 
       36.66       100.57         5.69        19.27        20.58        21.90 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
       64.90        22.92        88.14        26.53        31.20         8.02 
TCGA-78-7542 TCGA-78-8640 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       10.55       232.18        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
       31.13        34.39        32.78        19.89        37.74         4.08 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 
       24.33         0.79        22.82        31.04        23.05        21.47 
TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6829 TCGA-91-6830 
       11.61        30.84         3.81        24.23        41.36         1.97 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 
       10.19         2.60        12.23        27.68         7.36         1.18 
TCGA-93-7348 TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       17.46        41.82        18.67        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8176 
       42.25        64.60        25.48        18.54         5.39        15.39 
TCGA-97-8177 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8032 
       16.41        21.44        19.76        20.84        18.67         1.45 
TCGA-99-8033 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N4 
       21.57        32.48        19.00        14.53        18.58        38.63 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ 
       58.45        37.35        58.85        11.05        14.10        11.15 
TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
       71.05        47.08         0.43        20.28        59.11 

$`DEL PEAK  5(3P21.31) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 
       14.01         9.96        20.05         9.01        26.01        28.41 
TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       11.64        26.30        43.53        38.10        42.08        23.93 
TCGA-44-7661 TCGA-49-6761 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       18.31        11.64        23.05        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7725 TCGA-55-8091 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 
        7.99        14.53        19.73        17.98        19.69        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-64-1677 TCGA-73-4658 
       18.15        13.68        16.93        22.65        20.65        52.60 
TCGA-73-4662 TCGA-78-7166 TCGA-78-7633 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 
       82.68         8.48        50.24        13.71        16.18         6.12 
TCGA-95-7562 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 
        2.86        21.40        18.18        17.92        20.52        17.75 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4TA TCGA-05-4250 
       23.80         6.35        10.09        21.83        31.23         3.98 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
        0.00        47.05        19.00        14.96        12.00        30.02 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 
       21.99        26.01        25.02        24.00         4.96        22.03 
TCGA-05-5429 TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-4632 TCGA-38-A44F 
        9.04         0.46        97.74       120.79        44.61         4.37 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 
       44.94        42.77         3.19        37.15        38.24        33.73 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 
       26.56        28.01        23.15        23.18        32.45        22.72 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
        7.17        36.07        18.87        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-49-4510 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AAR4 
       35.54        29.46        29.75        22.26        62.24        28.90 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
      123.58       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5933 TCGA-50-5942 
       15.72        60.16        47.41         9.27        78.67        60.72 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       53.16        42.35        25.55        36.99        36.79        27.25 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       14.30        80.52         5.62        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 
       53.65        69.34        45.34        24.99       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       28.67        20.02        32.71        23.15        25.41        18.64 
TCGA-55-7911 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       17.65        19.82        29.72        15.19        23.08         5.06 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       23.64        15.65        22.16        15.42        17.56        15.72 
TCGA-55-8505 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-A48Y TCGA-55-A493 
       14.47        17.72        19.96        26.01        20.71         0.92 
TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46S 
       15.81        17.95        39.98        49.25        19.53        54.35 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
       67.96        72.30        29.92        37.02        38.37         2.04 
TCGA-64-5778 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       42.90        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7974 TCGA-69-7980 TCGA-69-8255 TCGA-69-8453 
        6.64         6.12         6.05        13.51         4.24        26.73 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4676 TCGA-73-4677 TCGA-75-5125 TCGA-75-6206 
       19.43        23.38         9.24         1.25        66.64        85.15 
TCGA-75-6212 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7149 TCGA-78-7152 
       49.84       108.66       163.10        27.16       129.53        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 
      119.51        19.50        38.50        32.09         5.88         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8648 
      104.19       238.29        53.33        26.01        39.35        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-86-7713 TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 
       77.59       110.50        38.04        20.55        35.24         4.57 
TCGA-86-8076 TCGA-86-8279 TCGA-86-8359 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
       32.65        31.20        14.60        13.91        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       28.34        26.50        29.46        13.64        26.47        10.62 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN 
        1.15        16.60        14.27        19.82        22.45        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 
        1.08        19.00        12.39        63.52        61.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
       15.91        18.67        18.12        14.30        21.60        20.58 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE 
       24.56        34.85        36.76        21.63        18.08        35.47 
TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY 
       14.30         1.91        15.65         2.76        86.14        49.35 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK 
       86.04         5.49        41.59        29.46        24.36        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55R 
       73.91        74.33         0.13         1.64         0.49        19.82 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                          0.36                           0.00 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                        232.18                         238.29 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                         20.84                          22.45 
[1] "0.4 - 232.2 (20.8)" "0.0 - 238.3 (22.4)"
[1] "hr=" "1.1"
D34V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  5(3P21.31) MUTATED         2       62       60        1        32
  DEL PEAK  5(3P21.31) WILD-TYPE       3       71       79        0        18
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  5(3P21.31) MUTATED          33         37          4       13
  DEL PEAK  5(3P21.31) WILD-TYPE        39         35          7       12
D34V3, multiclass
            clus
vv           DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             62                             71
  STAGE IB                             60                             79
  STAGE II                              1                              0
  STAGE IIA                            32                             18
  STAGE IIB                            33                             39
  STAGE IIIA                           37                             35
  STAGE IIIB                            4                              7
  STAGE IV                             13                             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    87 141  12   7
  DEL PEAK  5(3P21.31) WILD-TYPE  84 137  34  12
D34V4, multiclass
    clus
vv   DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  T1                           87                             84
  T2                          141                            137
  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   146  59    37
  DEL PEAK  5(3P21.31) WILD-TYPE 187  37    39
D34V5, multiclass
       clus
vv      DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  N0                             146                            187
  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"
D34V6, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED   171  13
  DEL PEAK  5(3P21.31) WILD-TYPE 178  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED    171   13
  DEL PEAK  5(3P21.31) WILD-TYPE  178   12
   clus
vv  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  0                          171                            178
  1                           13                             12
[1] 2 2
[1] FALSE
D34V7, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED   128 120
  DEL PEAK  5(3P21.31) WILD-TYPE 148 120
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED    128  120
  DEL PEAK  5(3P21.31) WILD-TYPE  148  120
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  FEMALE                          128                            148
  MALE                            120                            120
[1] 2 2
[1] FALSE
D34V8, binary
                                cls
clus                               0   1
  DEL PEAK  5(3P21.31) MUTATED   203  28
  DEL PEAK  5(3P21.31) WILD-TYPE 207  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED    203   28
  DEL PEAK  5(3P21.31) WILD-TYPE  207   32
     clus
vv    DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  NO                           203                            207
  YES                           28                             32
[1] 2 2
[1] FALSE
D34V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  5(3P21.31) MUTATED                           12
  DEL PEAK  5(3P21.31) WILD-TYPE                          6
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  5(3P21.31) MUTATED                                  52
  DEL PEAK  5(3P21.31) WILD-TYPE                                55
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  5(3P21.31) MUTATED                                                  159
  DEL PEAK  5(3P21.31) WILD-TYPE                                                162
                                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
D34V10, multiclass
                                                    clus
vv                                                   DEL PEAK  5(3P21.31) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          159
  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                                                      6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            162
  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"
D34V11, continuous
D34V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  5(3P21.31) MUTATED   163   3   2   9
  DEL PEAK  5(3P21.31) WILD-TYPE 181  10   2  17
D34V13, multiclass
    clus
vv   DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  R0                          163                            181
  R1                            3                             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  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                          27   192
  DEL PEAK  5(3P21.31) WILD-TYPE                        25   198
D34V14, multiclass
                                  clus
vv                                 DEL PEAK  5(3P21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     192
                                  clus
vv                                 DEL PEAK  5(3P21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       198
[1] 4 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  5(3P21.31) MUTATED     4 192
  DEL PEAK  5(3P21.31) WILD-TYPE   3 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      4  192
  DEL PEAK  5(3P21.31) WILD-TYPE    3  192
                        clus
vv                       DEL PEAK  5(3P21.31) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          192
                        clus
vv                       DEL PEAK  5(3P21.31) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            192
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK  6(3Q11.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3Q11.1) MUTATED    89  50
  DEL PEAK  6(3Q11.1) WILD-TYPE 234 131
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                          139                           365 
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                           50                           131 
$`DEL PEAK  6(3Q11.1) MUTATED`
TCGA-05-5420 TCGA-44-6147 TCGA-44-6776 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F 
       15.02        27.78        86.01        29.23         9.37        11.08 
TCGA-49-6742 TCGA-49-AAR0 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       16.04       156.66        40.60        21.47        41.69        23.05 
TCGA-55-7573 TCGA-55-8090 TCGA-55-8205 TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 
       16.01        19.66        19.69        19.59        20.19        13.87 
TCGA-73-7498 TCGA-78-8660 TCGA-91-7771 TCGA-95-7948 TCGA-97-8172 TCGA-J2-8192 
       39.09        10.55        16.18        15.65        17.92        24.30 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 
        2.43        10.09        50.07        45.01        37.02         2.99 
TCGA-05-5425 TCGA-05-5715 TCGA-44-3917 TCGA-44-6144 TCGA-44-6145 TCGA-44-6774 
       29.00         2.04        38.89        23.77        19.56        21.63 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       16.44        19.46        23.64        12.66         8.55        15.98 
TCGA-49-4490 TCGA-49-4506 TCGA-49-6743 TCGA-49-AAQV TCGA-50-5068 TCGA-50-5072 
       12.66        32.84        53.29        22.26        49.28         8.22 
TCGA-50-5941 TCGA-50-6591 TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-53-7624 
       48.46         3.91        11.05         6.21         0.72        34.29 
TCGA-55-5899 TCGA-55-6975 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 
       30.58         3.88        32.71        92.81        40.54        20.02 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7910 TCGA-55-8206 TCGA-55-8514 TCGA-55-8615 
       22.03         3.91        34.19        29.19        17.10        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 
        1.58        12.33        21.40        19.99         4.57        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46Y TCGA-62-A470 
       14.60        88.64        19.53        56.71        13.61        39.25 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5781 TCGA-67-3770 TCGA-67-3772 TCGA-69-7763 
       39.09        87.98        51.25        20.05        18.84        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8253 TCGA-71-6725 
       13.61         5.42         7.56         6.05        14.01         8.42 
TCGA-73-4659 TCGA-73-4675 TCGA-75-5146 TCGA-75-6214 TCGA-75-7027 TCGA-78-7145 
       23.38        30.31        77.85        36.66       100.57        27.16 
TCGA-78-7148 TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
       20.58        22.92         9.57        88.14        26.53        31.20 
TCGA-78-7536 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7954 
        8.02        93.11        27.09        12.36        31.13        19.89 
TCGA-86-8054 TCGA-86-8073 TCGA-86-8075 TCGA-86-8280 TCGA-86-8585 TCGA-91-6831 
       37.74        24.33        22.82        23.05        11.61        10.19 
TCGA-91-6835 TCGA-91-6847 TCGA-91-8497 TCGA-91-8499 TCGA-93-7348 TCGA-95-7039 
        2.60        27.68        14.27         1.18        17.46        41.82 
TCGA-95-7567 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 
       18.67        27.29        19.89        42.25        25.48        18.54 
TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8032 
        5.39        16.41        19.76        20.84        18.67         1.45 
TCGA-J2-A4AG TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A55O 
       32.48        11.05        14.10        11.15        19.13         0.43 
TCGA-NJ-A7XG 
       20.28 

$`DEL PEAK  6(3Q11.1) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       26.01        15.02        28.41        35.28        11.64        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-7661 
       26.30        43.53        38.10        42.08        23.93        18.31 
TCGA-44-7670 TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-55-1595 
       29.00        46.72        17.16        11.64        37.32        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        5.79         7.79         7.99        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-8511 
        6.15        19.73        17.98        16.93        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-64-1677 TCGA-73-4658 
       13.68        16.93        22.65        20.58        20.65        52.60 
TCGA-73-4662 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC 
       82.68         8.48        50.24        85.32        13.71         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK 
        6.12        17.29        16.54         2.86        15.68        21.40 
TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 
       18.18        20.19        20.52        17.75        20.68        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
        6.35        10.09        21.83        27.19         5.29        31.23 
TCGA-05-4250 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 
        3.98         0.00        24.03        47.05        19.00        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
       29.98        12.00        30.02        21.99        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 
       25.02        24.00         4.96        22.03         9.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       49.05        44.61         4.37        46.98        44.42        44.94 
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-44-6148 
       33.73        26.56        33.30        28.37        28.01        23.15 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 
       23.18        32.45        61.28        22.72         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-49-4494 TCGA-49-4505 TCGA-49-4507 
       76.21        28.11        28.57        35.54        14.07         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAR2 
       29.46        29.75        55.89        55.33        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ 
       62.24        28.90         8.55        40.41       123.58       221.33 
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       101.72        15.72 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       60.16        47.41         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        60.72        57.53        53.16        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        36.99        36.79        27.25        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 
       13.94        35.21        38.73        67.89        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
        5.62        42.51        40.73        15.25        46.03        53.65 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       69.34        45.34        24.99       107.21        70.26        28.67 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
       27.09        32.71        23.15        25.41        18.64        11.28 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       17.65        18.44        19.82        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8208 
       23.08         5.06        17.79        23.64        15.65        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       15.42        17.56        15.72        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-A48Y 
       20.28        17.72        19.96        26.01        17.62        20.71 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 TCGA-62-8402 
        3.25         0.92        15.81        17.95        39.98        49.25 
TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-62-A472 
       47.80        54.35        67.96        72.30        40.96        29.92 
TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
       56.81        81.80        37.02        38.37         2.04        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       28.41        28.47        20.05        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7978 TCGA-69-7979 
        5.72         4.64         6.64         6.12         4.41        13.41 
TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4666 
       13.51        13.45         4.24        26.73        19.43        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS 
       15.35         4.31         9.24         1.25        50.33        11.18 
TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-78-7143 
       66.64        43.82        85.15        49.84       108.66       163.10 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27       129.53        21.90        39.95       119.51 
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-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
      238.29        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 
       39.75        77.59       110.50         5.88        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       20.55        32.78        35.24         4.08         4.57         0.79 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 
       32.65        31.04        31.20        21.47        14.60        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        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
        3.81        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-A4BD 
        1.97        12.23         7.36         1.15        16.60        19.82 
TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 TCGA-95-8494 
       22.45        23.61         1.08        19.00        12.39         2.76 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       64.60        63.52        61.48         0.59        15.91        18.67 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       18.12        15.39        14.30        21.60        20.58        21.44 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD 
       24.56        34.85        36.76        21.57        21.63        18.08 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV 
       35.47        19.00        14.30        14.53         1.91        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       15.65        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       37.35        86.04        58.85         5.49        41.59        29.46 
TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       24.36        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       47.08         0.49        19.82        59.11        16.87 

  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                         0.43                          0.00 
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                       156.66                        238.29 
  DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE 
                        19.99                         22.65 
[1] "0.4 - 156.7 (20.0)" "0.0 - 238.3 (22.6)"
[1] "hr=" "1.2"
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  6(3Q11.1) MUTATED         1       33       37        1        12
  DEL PEAK  6(3Q11.1) WILD-TYPE       4      100      102        0        38
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  6(3Q11.1) MUTATED          19         25          3        7
  DEL PEAK  6(3Q11.1) WILD-TYPE        53         47          8       18
D35V3, multiclass
            clus
vv           DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  STAGE I                              1                             4
  STAGE IA                            33                           100
  STAGE IB                            37                           102
  STAGE II                             1                             0
  STAGE IIA                           12                            38
  STAGE IIB                           19                            53
  STAGE IIIA                          25                            47
  STAGE IIIB                           3                             8
  STAGE IV                             7                            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  82   9   6
  DEL PEAK  6(3Q11.1) WILD-TYPE 127 196  37  13
D35V4, multiclass
    clus
vv   DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  T1                          44                           127
  T2                          82                           196
  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    86  27    27
  DEL PEAK  6(3Q11.1) WILD-TYPE 247  69    49
D35V5, multiclass
       clus
vv      DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  N0                             86                           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"
D35V6, binary
                               cls
clus                              0   1
  DEL PEAK  6(3Q11.1) MUTATED   100   7
  DEL PEAK  6(3Q11.1) WILD-TYPE 249  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3Q11.1) MUTATED    100    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                         100                           249
  1                           7                            18
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3Q11.1) MUTATED    79  62
  DEL PEAK  6(3Q11.1) WILD-TYPE 197 178
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3Q11.1) MUTATED     79   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                          79                           197
  MALE                            62                           178
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(3Q11.1) MUTATED   117  18
  DEL PEAK  6(3Q11.1) WILD-TYPE 293  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3Q11.1) MUTATED    117   18
  DEL PEAK  6(3Q11.1) WILD-TYPE  293   42
     clus
vv    DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  NO                          117                           293
  YES                          18                            42
[1] 2 2
[1] FALSE
D35V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  6(3Q11.1) MUTATED                            6
  DEL PEAK  6(3Q11.1) WILD-TYPE                         12
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  6(3Q11.1) MUTATED                                  33
  DEL PEAK  6(3Q11.1) WILD-TYPE                                74
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  6(3Q11.1) MUTATED                                                   85
  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
D35V10, multiclass
                                                    clus
vv                                                   DEL PEAK  6(3Q11.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           33
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          85
  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                                                    12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             74
  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"
D35V11, continuous
D35V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(3Q11.1) MUTATED    83   3   0   5
  DEL PEAK  6(3Q11.1) WILD-TYPE 261  10   4  21
D35V13, multiclass
    clus
vv   DEL PEAK  6(3Q11.1) MUTATED DEL PEAK  6(3Q11.1) WILD-TYPE
  R0                          83                           261
  R1                           3                            10
  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   113
  DEL PEAK  6(3Q11.1) WILD-TYPE                        41   277
D35V14, multiclass
                                  clus
vv                                 DEL PEAK  6(3Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                    113
                                  clus
vv                                 DEL PEAK  6(3Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   41
  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"
D35V15, binary
                               cls
clus                              0   1
  DEL PEAK  6(3Q11.1) MUTATED     1 107
  DEL PEAK  6(3Q11.1) WILD-TYPE   6 277
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3Q11.1) MUTATED      1  107
  DEL PEAK  6(3Q11.1) WILD-TYPE    6  277
                        clus
vv                       DEL PEAK  6(3Q11.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         107
                        clus
vv                       DEL PEAK  6(3Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           277
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK  7(3Q29) MUTATION ANALYSIS
D36V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  7(3Q29) MUTATED    88  46
  DEL PEAK  7(3Q29) WILD-TYPE 235 135
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                        134                         370 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                         46                         135 
$`DEL PEAK  7(3Q29) MUTATED`
TCGA-05-4405 TCGA-05-5420 TCGA-38-4631 TCGA-44-6776 TCGA-44-7671 TCGA-44-8119 
       20.05        15.02        11.64        86.01        29.23         9.37 
TCGA-44-A47F TCGA-49-6742 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-7573 
       11.08        16.04        40.60        21.47        41.69        16.01 
TCGA-55-7725 TCGA-55-8090 TCGA-55-8203 TCGA-55-A492 TCGA-64-1677 TCGA-73-4662 
       14.53        19.66        17.98        19.59        20.65        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 
       39.09         8.48        10.55        85.32        13.71        16.18 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 
       15.65        21.40        17.92        17.75        24.30        23.80 
TCGA-L9-A443 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4390 TCGA-05-4415 
        6.35         5.29         2.43        50.07        37.02         2.99 
TCGA-05-4417 TCGA-05-4422 TCGA-05-5715 TCGA-44-2656 TCGA-44-3917 TCGA-44-5644 
       14.96        12.00         2.04        46.98        38.89        28.37 
TCGA-44-6144 TCGA-44-6774 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       23.77        21.63        18.87        23.64        12.66         8.55 
TCGA-49-4506 TCGA-49-4510 TCGA-50-5068 TCGA-50-6673 TCGA-53-7626 TCGA-55-5899 
       32.84        29.46        49.28         0.72        30.54        30.58 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6972 TCGA-55-6975 TCGA-55-6982 TCGA-55-6983 
       80.52         5.62        53.65         3.88        32.71        92.81 
TCGA-55-7283 TCGA-55-7727 TCGA-55-7815 TCGA-55-7910 TCGA-55-8094 TCGA-55-8206 
       20.02         3.91        25.41        34.19        17.79        29.19 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Z 
       13.74        20.28        17.10        14.66         1.58        21.40 
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-64-1678 TCGA-64-5774 
       19.53        56.71        13.61        39.25        39.09        87.98 
TCGA-67-3770 TCGA-67-3772 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 
       20.05        18.84        22.68        13.61         5.42         6.05 
TCGA-69-8253 TCGA-69-8255 TCGA-73-4659 TCGA-73-4675 TCGA-73-A9RS TCGA-75-5146 
       14.01         4.24        23.38        30.31        11.18        77.85 
TCGA-75-7027 TCGA-78-7147 TCGA-78-7148 TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 
      100.57        19.27        20.58        22.92         9.57        88.14 
TCGA-78-7535 TCGA-78-7539 TCGA-80-5608 TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 
       31.20        26.01        93.11        12.36        31.13        38.04 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8280 TCGA-91-6828 TCGA-91-6835 
       37.74         4.08        22.82        23.05        10.62         2.60 
TCGA-91-6847 TCGA-91-8497 TCGA-95-7567 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 
       27.68        14.27        18.67        19.89        42.25        25.48 
TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       18.54         5.39        16.41        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8032 TCGA-J2-A4AG TCGA-MP-A4T6 TCGA-MP-A4TI TCGA-MP-A4TJ 
       24.56         1.45        32.48        58.85        14.10        11.15 
TCGA-NJ-A55O TCGA-NJ-A7XG 
        0.43        20.28 

$`DEL PEAK  7(3Q29) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96         8.02         9.01        26.01 
TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       15.02        28.41        35.28        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-7661 TCGA-44-7670 
       38.10        42.08        23.93        27.78        18.31        29.00 
TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-55-1592 
       46.72        17.16        11.64       156.66        37.32        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7724 TCGA-55-7726 
       48.62         5.79         7.79         7.99        23.18        21.44 
TCGA-55-7914 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
        6.15        19.73        16.93        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-67-6217 
       13.68        16.93        22.65        20.58        20.19        13.87 
TCGA-73-4658 TCGA-78-7633 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       52.60        50.24         1.45         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 
        2.86        15.68        18.18        20.19        20.52        20.68 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4250 
       10.09        21.83        27.19        31.23        10.09         3.98 
TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4420 
       45.01         0.00        24.03        47.05        19.00        29.98 
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-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 
        4.96        29.00        22.03         9.04         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-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 
       44.61         4.37        44.42        44.94        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        33.73        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 
       33.30        28.01        19.56        23.15        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       61.28        16.44        22.72        19.46         7.17        36.07 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        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-49-4505 
       76.21        28.11        28.57        12.66        35.54        14.07 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 
        8.81        29.75        55.89        53.29        55.33        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE 
       22.26        73.12        62.24        28.90         8.55        40.41 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
      123.58       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 
      101.72        15.72        60.16        47.41         8.22         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       14.27        78.67         8.45        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       57.53        53.16        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       12.16         6.21        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 
       34.29        13.94        35.21        38.73        67.89        14.30 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6980 TCGA-55-6981 
       42.51        40.73        15.25        46.03        69.34        45.34 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 
       24.99        40.54       107.21        70.26        28.67        27.09 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
       32.71        22.03        23.15        18.64        11.28        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
        5.06        23.64        15.65        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
       15.72        14.47         0.36        17.72        19.96        26.01 
TCGA-55-8614 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       17.62        12.33        20.71         3.25         0.92        15.81 
TCGA-55-A57B TCGA-62-8394 TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V 
       17.95         4.57        47.80        54.35        67.96        72.30 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       40.96        29.92        56.81        81.80        37.02        38.37 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 
        6.12         7.56         4.41        13.41        13.51        13.45 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       26.73        19.43         8.42        26.30        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 
        9.24         1.25        50.33        66.64        43.82        85.15 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       49.84        36.66       108.66       163.10        27.16         5.69 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
      129.53        21.90        39.95       119.51        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       238.29        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
        8.02        53.33        39.35        10.55       232.18        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 
       77.59       110.50        27.09         5.88        34.39        20.55 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       32.78        19.89        35.24         4.57        24.33         0.79 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       32.65        31.04        31.20        21.47        14.60        11.61 
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        28.34        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
       29.46         3.81        24.23        13.64        26.47        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        1.97        10.19        12.23         7.36         1.15        16.60 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
        1.18        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7547 
       19.00        41.82        12.39        27.29         2.76        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 
       63.52        61.48         0.59        15.91        18.67        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-99-8025 
       15.39        14.30        21.60        20.58        21.44        34.85 
TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 
       36.76        21.57        21.63        18.08        35.47        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       14.30        14.53         1.91        18.58        15.65        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-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK 
        5.49        41.59        29.46        11.05        24.36        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
        0.49        19.82        59.11        16.87 

  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                       0.43                        0.00 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                     100.57                      238.29 
  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE 
                     20.050                      22.355 
[1] "0.4 - 100.6 (20.1)" "0.0 - 238.3 (22.4)"
[1] "hr=" "1.1"
D36V2, 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      102      102        1        34
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  7(3Q29) MUTATED          21         21          2        4
  DEL PEAK  7(3Q29) WILD-TYPE        51         51          9       21
D36V3, multiclass
            clus
vv           DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  STAGE I                            1                           4
  STAGE IA                          31                         102
  STAGE IB                          37                         102
  STAGE II                           0                           1
  STAGE IIA                         16                          34
  STAGE IIB                         21                          51
  STAGE IIIA                        21                          51
  STAGE IIIB                         2                           9
  STAGE IV                           4                          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  79  10   5
  DEL PEAK  7(3Q29) WILD-TYPE 129 199  36  14
D36V4, multiclass
    clus
vv   DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  T1                        42                         129
  T2                        79                         199
  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    87  28    21
  DEL PEAK  7(3Q29) WILD-TYPE 246  68    55
D36V5, multiclass
       clus
vv      DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  N0                           87                         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"
D36V6, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED   100   4
  DEL PEAK  7(3Q29) WILD-TYPE 249  21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED    100    4
  DEL PEAK  7(3Q29) WILD-TYPE  249   21
   clus
vv  DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  0                       100                         249
  1                         4                          21
[1] 2 2
[1] FALSE
D36V7, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED    72  64
  DEL PEAK  7(3Q29) WILD-TYPE 204 176
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED     72   64
  DEL PEAK  7(3Q29) WILD-TYPE  204  176
        clus
vv       DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  FEMALE                        72                         204
  MALE                          64                         176
[1] 2 2
[1] FALSE
D36V8, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED   113  16
  DEL PEAK  7(3Q29) WILD-TYPE 297  44
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED    113   16
  DEL PEAK  7(3Q29) WILD-TYPE  297   44
     clus
vv    DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  NO                        113                         297
  YES                        16                          44
[1] 2 2
[1] FALSE
D36V9, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  7(3Q29) MUTATED                            5
  DEL PEAK  7(3Q29) WILD-TYPE                         13
                             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                                                   80
  DEL PEAK  7(3Q29) WILD-TYPE                                                241
                             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
D36V10, multiclass
                                                    clus
vv                                                   DEL PEAK  7(3Q29) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        80
  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                                                  13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           73
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         241
  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"
D36V11, continuous
D36V12, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  7(3Q29) MUTATED    87   3   0   3
  DEL PEAK  7(3Q29) WILD-TYPE 257  10   4  23
D36V13, multiclass
    clus
vv   DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  R0                        87                         257
  R1                         3                          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   107
  DEL PEAK  7(3Q29) WILD-TYPE                        41   283
D36V14, multiclass
                                  clus
vv                                 DEL PEAK  7(3Q29) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                               11
  WHITE                                                  107
                                  clus
vv                                 DEL PEAK  7(3Q29) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      7
  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"
D36V15, binary
                             cls
clus                            0   1
  DEL PEAK  7(3Q29) MUTATED     1 103
  DEL PEAK  7(3Q29) WILD-TYPE   6 281
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(3Q29) MUTATED      1  103
  DEL PEAK  7(3Q29) WILD-TYPE    6  281
                        clus
vv                       DEL PEAK  7(3Q29) MUTATED DEL PEAK  7(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             1                           6
  NOT HISPANIC OR LATINO                       103                         281
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK  8(4P16.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(4P16.3) MUTATED    85  41
  DEL PEAK  8(4P16.3) WILD-TYPE 238 140
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                          126                           378 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                           41                           140 
$`DEL PEAK  8(4P16.3) MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-5420 TCGA-44-6146 TCGA-44-6147 TCGA-44-7670 
        8.02        20.05        15.02        23.93        27.78        29.00 
TCGA-49-4501 TCGA-49-6742 TCGA-49-AAR0 TCGA-55-7724 TCGA-55-7726 TCGA-55-8203 
       46.72        16.04       156.66        23.18        21.44        17.98 
TCGA-55-8204 TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-80-5611 TCGA-91-7771 
       16.93        20.58        20.19        20.65        85.32        16.18 
TCGA-95-7043 TCGA-95-A4VN TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4397 TCGA-05-4398 
       16.54        18.18        10.09        50.07        24.03        47.05 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-5425 TCGA-35-4123 
        2.99        14.96        29.98        30.02        29.00         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4632 TCGA-44-2659 TCGA-44-3918 TCGA-44-5643 
        8.68        97.74        44.61        44.94        34.06        33.30 
TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 
       28.37        23.77        19.56        61.28        19.46        36.07 
TCGA-44-8117 TCGA-44-A479 TCGA-49-4487 TCGA-49-4506 TCGA-49-4510 TCGA-49-6743 
       12.66        15.98        28.11        32.84        29.46        53.29 
TCGA-49-AAR2 TCGA-49-AARE TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5946 
       73.12        40.41       101.72        15.72        47.41        53.16 
TCGA-50-6590 TCGA-50-6673 TCGA-50-7109 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-5899 
       42.35         0.72        10.13        30.54        35.21        30.58 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6985 TCGA-55-7574 TCGA-55-7815 
       42.51        40.73        46.03        40.54        32.71        25.41 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7913 TCGA-55-7995 TCGA-55-8096 TCGA-55-8505 
       18.64        34.19        18.44        29.23        23.64        14.47 
TCGA-55-8507 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       13.74        17.10        17.62        14.66         1.58        12.33 
TCGA-55-A48Z TCGA-55-A4DG TCGA-62-8394 TCGA-62-8398 TCGA-62-A46V TCGA-62-A472 
       21.40        19.99         4.57        14.60        72.30        29.92 
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        13.41        26.73         8.42        23.38         4.31 
TCGA-73-4675 TCGA-78-7143 TCGA-78-7159 TCGA-78-7536 TCGA-78-8640 TCGA-78-8662 
       30.31       163.10        64.90         8.02       232.18       110.50 
TCGA-86-7713 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-A4JF TCGA-91-6830 
       38.04         4.08         0.79        22.82        24.23         1.97 
TCGA-91-6840 TCGA-91-6848 TCGA-93-A4JO TCGA-95-7567 TCGA-95-7944 TCGA-97-8547 
       12.23         7.36         1.08        18.67        12.39        21.60 
TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 
       21.44        19.76        34.85        21.57        18.08        19.00 
TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4T4 TCGA-MP-A4TJ TCGA-NJ-A4YI TCGA-O1-A52J 
       18.58        38.63        86.04        11.15         0.13        59.11 

$`DEL PEAK  8(4P16.3) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96         9.01        26.01        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       28.41        35.28        11.64        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 
       38.10        42.08        86.01        18.31        29.23         9.37 
TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 
       11.08        17.16        11.64        37.32        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
       41.69        23.05        48.62         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8205 
       16.01        14.53         6.15        19.66        19.73        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 
       32.12        18.15        13.68        16.93        22.65        19.59 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 
       10.55        13.71         1.45         6.12        17.29         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.68        15.65        21.40        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       17.75        20.68        24.30        23.80         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4250 
       21.83        27.19         5.29        31.23         2.43         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4403 TCGA-05-4422 TCGA-05-4425 
       45.01        37.02         0.00        19.00        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 
       26.01        25.02        25.02        24.00         4.96        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-38-4626 TCGA-38-4627 
        9.04         2.04         0.46         7.40       120.79        37.71 
TCGA-38-4628 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 
       49.05         4.37        46.98        44.42        42.77         3.19 
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        33.73        26.56 
TCGA-44-5645 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 
       28.01        23.15        21.63        23.18        32.45        16.44 
TCGA-44-7659 TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-8120 TCGA-44-A47A 
       22.72         7.17        18.87        23.64         8.55        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 
        9.44        11.54        13.64        13.45        76.21        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 
       12.66        35.54        14.07         8.81        29.75        55.89 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       55.33        22.26        22.26        62.24        28.90         8.55 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
      123.58       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       60.16        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6591 
        8.45        15.12        48.46        60.72        57.53         3.91 
TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-8457 TCGA-50-8459 
       25.55        11.05        12.16         6.21        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 
       27.25        34.29        13.94        38.73        67.89        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       80.52         5.62        15.25        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 
       45.34        32.71        92.81        24.99       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       28.67        20.02        27.09        22.03         3.91        23.15 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       11.28        17.65        19.82        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
        5.06        17.79        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 
       17.56        15.72         0.36        20.28        17.72        19.96 
TCGA-55-8513 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B 
       26.01        20.71         3.25         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        81.80        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        20.05        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
       14.73         5.72         4.64         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         4.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       19.43        26.30        15.35         9.24         1.25        50.33 
TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       11.18        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       36.66       108.66       100.57        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
       20.58       129.53        21.90        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       38.50        32.09         5.88        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
      238.29        88.14        26.53        31.20        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 
       39.35        10.55        39.75        77.59        93.11        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 
       12.36         5.88        31.13        34.39        20.55        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
       19.89        35.24        37.74         4.57        24.33        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       31.04        31.20        23.05        21.47        14.60        11.61 
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        28.34        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       29.46         3.81        13.64        26.47        10.62        41.36 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       10.19         2.60        27.68         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP 
        1.18        19.82        22.45        17.46        23.61        19.00 
TCGA-95-7039 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       41.82        27.29         2.76        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8552 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       20.58        20.84        18.67        24.56        36.76         1.45 
TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       21.63        35.47        32.48        14.30        14.53         1.91 
TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 
       15.65         2.76        86.14        58.45        49.35        37.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
       58.85         5.49        41.59        29.46        11.05        24.36 
TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP 
       14.10        19.13        73.91        71.05        74.33         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       47.08         0.49         0.43        19.82        20.28        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 
                       232.18                        238.29 
  DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE 
                        22.75                         21.47 
[1] "0.1 - 232.2 (22.8)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.2"
D37V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  8(4P16.3) MUTATED         2       33       37        0        12
  DEL PEAK  8(4P16.3) WILD-TYPE       3      100      102        1        38
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  8(4P16.3) MUTATED          16         19          4        6
  DEL PEAK  8(4P16.3) WILD-TYPE        56         53          7       19
D37V3, multiclass
            clus
vv           DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            33                           100
  STAGE IB                            37                           102
  STAGE II                             0                             1
  STAGE IIA                           12                            38
  STAGE IIB                           16                            56
  STAGE IIIA                          19                            53
  STAGE IIIB                           4                             7
  STAGE IV                             6                            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  8(4P16.3) MUTATED    46  68  12   3
  DEL PEAK  8(4P16.3) WILD-TYPE 125 210  34  16
D37V4, multiclass
    clus
vv   DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  T1                          46                           125
  T2                          68                           210
  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    82  22    22
  DEL PEAK  8(4P16.3) WILD-TYPE 251  74    54
D37V5, multiclass
       clus
vv      DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  N0                             82                           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"
D37V6, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED    85   6
  DEL PEAK  8(4P16.3) WILD-TYPE 264  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED     85    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                          85                           264
  1                           6                            19
[1] 2 2
[1] FALSE
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED    70  60
  DEL PEAK  8(4P16.3) WILD-TYPE 206 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED     70   60
  DEL PEAK  8(4P16.3) WILD-TYPE  206  180
        clus
vv       DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  FEMALE                          70                           206
  MALE                            60                           180
[1] 2 2
[1] FALSE
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED   104  17
  DEL PEAK  8(4P16.3) WILD-TYPE 306  43
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED    104   17
  DEL PEAK  8(4P16.3) WILD-TYPE  306   43
     clus
vv    DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  NO                          104                           306
  YES                          17                            43
[1] 2 2
[1] FALSE
D37V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  8(4P16.3) MUTATED                            4
  DEL PEAK  8(4P16.3) WILD-TYPE                         14
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  8(4P16.3) MUTATED                                  27
  DEL PEAK  8(4P16.3) WILD-TYPE                                80
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  8(4P16.3) MUTATED                                                   88
  DEL PEAK  8(4P16.3) WILD-TYPE                                                233
                               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
D37V10, multiclass
                                                    clus
vv                                                   DEL PEAK  8(4P16.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           27
  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                                             80
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           233
  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"
D37V11, continuous
D37V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(4P16.3) MUTATED    84   3   2   8
  DEL PEAK  8(4P16.3) WILD-TYPE 260  10   2  18
D37V13, multiclass
    clus
vv   DEL PEAK  8(4P16.3) MUTATED DEL PEAK  8(4P16.3) WILD-TYPE
  R0                          84                           260
  R1                           3                            10
  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                        37   297
D37V14, 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                                   37
  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"
D37V15, binary
                               cls
clus                              0   1
  DEL PEAK  8(4P16.3) MUTATED     2  94
  DEL PEAK  8(4P16.3) WILD-TYPE   5 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4P16.3) MUTATED      2   94
  DEL PEAK  8(4P16.3) WILD-TYPE    5  290
                        clus
vv                       DEL PEAK  8(4P16.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          94
                        clus
vv                       DEL PEAK  8(4P16.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           290
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK  9(4Q22.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4Q22.1) MUTATED    99  56
  DEL PEAK  9(4Q22.1) WILD-TYPE 224 125
  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                          155                           349 
  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                           56                           125 
$`DEL PEAK  9(4Q22.1) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4405 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 
       19.96         8.02        20.05        15.02        15.02        35.28 
TCGA-38-6178 TCGA-44-6147 TCGA-49-4501 TCGA-49-AAR0 TCGA-55-1592 TCGA-55-1595 
       14.73        27.78        46.72       156.66        23.05        48.62 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-8203 TCGA-55-8204 TCGA-55-A491 
       16.01        23.18        21.44        17.98        16.93        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4662 TCGA-91-A4BC TCGA-93-8067 
       19.59        20.19        20.65        82.68         1.45         6.12 
TCGA-95-7043 TCGA-95-A4VN TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4390 
       16.54        18.18        31.23        10.09        50.07        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4415 TCGA-05-4424 TCGA-05-5425 
        0.00        24.03        47.05         2.99        30.02        29.00 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4628 TCGA-44-2656 TCGA-44-5643 TCGA-44-5644 
        5.98         8.68        49.05        46.98        33.30        28.37 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-A479 
       23.77        19.56        61.28        19.46        36.07        15.98 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4506 TCGA-49-4507 TCGA-49-6743 TCGA-49-AARE 
       13.45        28.11        32.84         8.81        53.29        40.41 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5072 TCGA-50-5936 TCGA-50-5946 
      101.72        15.72        47.41         8.22         8.45        53.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 
        6.21         0.72        10.13        35.21        38.73        67.89 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6985 TCGA-55-7574 TCGA-55-7815 
       42.51        40.73        46.03        40.54        32.71        25.41 
TCGA-55-7910 TCGA-55-7913 TCGA-55-8092 TCGA-55-8094 TCGA-55-8301 TCGA-55-8505 
       34.19        18.44         5.06        17.79        17.56        14.47 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z 
       13.74        20.28        17.10         1.58        20.71        21.40 
TCGA-55-A4DG TCGA-62-8394 TCGA-62-A46O TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y 
       19.99         4.57        47.80        67.96        72.30        13.61 
TCGA-62-A472 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-64-5779 TCGA-67-3771 
       29.92        81.80        38.37        42.90        28.41        20.05 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 
       22.68        13.61         7.56         4.24        26.73         8.42 
TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-75-5146 TCGA-75-6214 TCGA-75-7027 
       23.38         4.31        30.31        77.85        36.66       100.57 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7154 TCGA-78-7167 TCGA-78-7220 
        5.69        19.27        20.58        19.50        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-8640 TCGA-86-7713 TCGA-86-7954 
       31.20         8.02        26.01       232.18        38.04        19.89 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 
       37.74         4.08         0.79        22.82        31.20        21.47 
TCGA-86-8669 TCGA-86-8672 TCGA-86-A4JF TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       30.84         0.62        24.23        41.36         1.97        10.19 
TCGA-91-6840 TCGA-91-6847 TCGA-93-A4JO TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VP 
       12.23        27.68         1.08        18.67        12.39        19.89 
TCGA-97-7937 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-8025 TCGA-99-8028 
       18.54        21.60        21.44        19.76        34.85        36.76 
TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4TF 
       21.57        18.08        19.00        15.65        38.63        11.05 
TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-O1-A52J 
       11.15        71.05         0.13        47.08        59.11 

$`DEL PEAK  9(4Q22.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 TCGA-38-4631 
       14.01         9.96         9.01        26.01        28.41        11.64 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6776 
       26.30        43.53        38.10        42.08        23.93        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 
       18.31        29.00        29.23         9.37        11.08        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       17.16        11.64        37.32        40.60        21.47        41.69 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 
        5.79         7.79         7.99        14.53         6.15        19.66 
TCGA-55-8091 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       19.73        19.69        32.12        18.15        13.68        16.93 
TCGA-55-A48X TCGA-67-6217 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       22.65        13.87        52.60        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-93-A4JQ TCGA-95-7562 
       10.55        85.32        13.71        16.18        17.29         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.68        15.65        21.40        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       17.75        20.68        24.30        23.80         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4389 
       21.83        27.19         5.29         2.43         3.98        45.01 
TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
       19.00        14.96        29.98        12.00        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       25.02        25.02        24.00         4.96        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        2.04         0.46         7.40        97.74       120.79        37.71 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 
       44.61         4.37        44.42        44.94        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        33.73 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       26.56        28.01        23.15        21.63        23.18        32.45 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       16.44        22.72         7.17        18.87        23.64        12.66 
TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
        8.55        15.32         9.44        11.54        13.64        76.21 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 
       28.57        12.66        35.54        14.07        29.46        29.75 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       55.89        55.33        22.26        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       28.90         8.55       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
       20.52        71.47        60.16        49.28         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        48.46        60.72        57.53        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 TCGA-50-8459 
        3.91        25.55        11.05        12.16        36.99        36.79 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-5899 TCGA-55-6543 
       27.25        34.29        30.54        13.94        30.58        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
       80.52         5.62        15.25        53.65         3.88        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 
       45.34        32.71        92.81        24.99       107.21        70.26 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       28.67        20.02        27.09        22.03         3.91        23.15 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       18.64        11.28        17.65        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       15.19        23.08        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
       15.42        15.72         0.36        17.72        19.96        26.01 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 
       17.62        14.66        12.33         3.25         0.92        15.81 
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-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 
       19.53        56.71        54.35        39.25        40.96        56.81 
TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 
       39.09        37.02        87.98         2.04        51.25        28.47 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       20.05        18.84        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 
        4.64         6.64         6.12         5.42         6.05         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-73-4666 
       13.41        13.51        14.01        13.45        19.43        26.30 
TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 
       15.35         9.24         1.25        50.33        11.18        66.64 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 
       43.82        85.15        49.84       108.66       163.10        27.16 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 
      129.53        21.90        39.95       119.51        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
        5.88        64.90        22.92         9.57       104.19       238.29 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       53.33        39.35        10.55        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 
       20.55        32.78        35.24         4.57        24.33        32.65 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
       31.04        23.05        14.60        11.61        13.91        27.58 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46         3.81        13.64        26.47 
TCGA-91-6828 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       10.62         2.60         7.36         1.15        16.60        14.27 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP 
        1.18        19.82        22.45        17.46        23.61        19.00 
TCGA-95-7039 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       41.82        27.29         2.76        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       61.48        25.48         0.59        15.91        18.67         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M5 
       18.12        15.39        16.41        14.30        20.58        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG 
       18.67        24.56         1.45        21.63        35.47        32.48 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4SV 
       14.30        14.53         1.91        18.58         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-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 
       41.59        29.46        24.36        14.10        19.13        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       74.33         1.64         0.49         0.43        19.82        20.28 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                         0.00                          0.36 
  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                       232.18                        238.29 
  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE 
                        21.44                         21.99 
[1] "0.0 - 232.2 (21.4)" "0.4 - 238.3 (22.0)"
[1] "hr=" "1.1"
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK  9(4Q22.1) MUTATED         2       43       41        0        14
  DEL PEAK  9(4Q22.1) WILD-TYPE       3       90       98        1        36
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK  9(4Q22.1) MUTATED          17         28          5        8
  DEL PEAK  9(4Q22.1) WILD-TYPE        55         44          6       17
D38V3, multiclass
            clus
vv           DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            43                            90
  STAGE IB                            41                            98
  STAGE II                             0                             1
  STAGE IIA                           14                            36
  STAGE IIB                           17                            55
  STAGE IIIA                          28                            44
  STAGE IIIB                           5                             6
  STAGE IV                             8                            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  9(4Q22.1) MUTATED    51  90  11   5
  DEL PEAK  9(4Q22.1) WILD-TYPE 120 188  35  14
D38V4, multiclass
    clus
vv   DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  T1                          51                           120
  T2                          90                           188
  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  9(4Q22.1) MUTATED   102  21    32
  DEL PEAK  9(4Q22.1) WILD-TYPE 231  75    44
D38V5, multiclass
       clus
vv      DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  N0                            102                           231
  N1                             21                            75
  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"
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q22.1) MUTATED   105   8
  DEL PEAK  9(4Q22.1) WILD-TYPE 244  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED    105    8
  DEL PEAK  9(4Q22.1) WILD-TYPE  244   17
   clus
vv  DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  0                         105                           244
  1                           8                            17
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q22.1) MUTATED    85  73
  DEL PEAK  9(4Q22.1) WILD-TYPE 191 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED     85   73
  DEL PEAK  9(4Q22.1) WILD-TYPE  191  167
        clus
vv       DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  FEMALE                          85                           191
  MALE                            73                           167
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q22.1) MUTATED   119  25
  DEL PEAK  9(4Q22.1) WILD-TYPE 291  35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED    119   25
  DEL PEAK  9(4Q22.1) WILD-TYPE  291   35
     clus
vv    DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  NO                          119                           291
  YES                          25                            35
[1] 2 2
[1] FALSE
D38V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK  9(4Q22.1) MUTATED                            4
  DEL PEAK  9(4Q22.1) WILD-TYPE                         14
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK  9(4Q22.1) MUTATED                                  32
  DEL PEAK  9(4Q22.1) WILD-TYPE                                75
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK  9(4Q22.1) MUTATED                                                  106
  DEL PEAK  9(4Q22.1) WILD-TYPE                                                215
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK  9(4Q22.1) MUTATED                                            0
  DEL PEAK  9(4Q22.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK  9(4Q22.1) MUTATED                                               3
  DEL PEAK  9(4Q22.1) WILD-TYPE                                            16
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK  9(4Q22.1) MUTATED                                2
  DEL PEAK  9(4Q22.1) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK  9(4Q22.1) MUTATED                                    1
  DEL PEAK  9(4Q22.1) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(4Q22.1) MUTATED                              0
  DEL PEAK  9(4Q22.1) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK  9(4Q22.1) MUTATED                               4
  DEL PEAK  9(4Q22.1) WILD-TYPE                            19
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK  9(4Q22.1) MUTATED                                 1
  DEL PEAK  9(4Q22.1) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK  9(4Q22.1) MUTATED                                               2
  DEL PEAK  9(4Q22.1) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK  9(4Q22.1) MUTATED                              3
  DEL PEAK  9(4Q22.1) WILD-TYPE                            7
D38V10, multiclass
                                                    clus
vv                                                   DEL PEAK  9(4Q22.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         106
  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                                              1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                2
  MUCINOUS (COLLOID) CARCINOMA                                                 3
                                                    clus
vv                                                   DEL PEAK  9(4Q22.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             75
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           215
  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                                                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"
D38V11, continuous
D38V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(4Q22.1) MUTATED   103   5   2  10
  DEL PEAK  9(4Q22.1) WILD-TYPE 241   8   2  16
D38V13, multiclass
    clus
vv   DEL PEAK  9(4Q22.1) MUTATED DEL PEAK  9(4Q22.1) WILD-TYPE
  R0                         103                           241
  R1                           5                             8
  R2                           2                             2
  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  9(4Q22.1) MUTATED                                  0     4
  DEL PEAK  9(4Q22.1) WILD-TYPE                                1     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q22.1) MUTATED                          15   116
  DEL PEAK  9(4Q22.1) WILD-TYPE                        37   274
D38V14, multiclass
                                  clus
vv                                 DEL PEAK  9(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                    116
                                  clus
vv                                 DEL PEAK  9(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   37
  WHITE                                                      274
[1] 4 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  9(4Q22.1) MUTATED     2 114
  DEL PEAK  9(4Q22.1) WILD-TYPE   5 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q22.1) MUTATED      2  114
  DEL PEAK  9(4Q22.1) WILD-TYPE    5  270
                        clus
vv                       DEL PEAK  9(4Q22.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         114
                        clus
vv                       DEL PEAK  9(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           270
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 10(4Q34.3) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q34.3) MUTATED   119  65
  DEL PEAK 10(4Q34.3) WILD-TYPE 204 116
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                          184                           320 
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                           65                           116 
$`DEL PEAK 10(4Q34.3) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 
       19.96         8.02        20.05        26.01        15.02        15.02 
TCGA-38-6178 TCGA-44-6147 TCGA-44-7670 TCGA-49-4501 TCGA-49-AAR0 TCGA-55-1592 
       14.73        27.78        29.00        46.72       156.66        23.05 
TCGA-55-1595 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-8203 TCGA-55-8204 
       48.62        16.01        23.18        21.44        17.98        16.93 
TCGA-55-8205 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4662 
       19.69        20.58        19.59        20.19        20.65        82.68 
TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 
       85.32        16.18         1.45        17.29        16.54        15.68 
TCGA-95-A4VN TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 
       18.18        27.19         5.29        31.23        10.09        50.07 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 
       45.01        37.02         0.00        47.05         2.99        14.96 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-35-4123 
       29.98        30.02        25.02        29.00        22.03         5.98 
TCGA-35-5375 TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
        8.68        38.89        33.30        28.37        23.77        19.56 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-A479 TCGA-49-4487 TCGA-49-4506 
       61.28        19.46        36.07        15.98        28.11        32.84 
TCGA-49-4507 TCGA-49-6743 TCGA-49-AARE TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
        8.81        53.29        40.41        71.47       101.72        15.72 
TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 
       47.41         8.22         9.27        14.27         8.45        15.12 
TCGA-50-5941 TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-53-7624 
       48.46        25.55         6.21         0.72        10.13        34.29 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6971 
       35.21        38.73        67.89        30.58        42.51        46.03 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7815 TCGA-55-7910 TCGA-55-7913 
       27.09        32.71        22.03        25.41        34.19        18.44 
TCGA-55-8085 TCGA-55-8092 TCGA-55-8094 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       29.72         5.06        17.79        14.47        13.74        20.28 
TCGA-55-8512 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A48Z 
       19.96        17.10        14.66         1.58        20.71        21.40 
TCGA-55-A490 TCGA-62-8394 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46R 
        3.25         4.57        14.60        88.64        47.80        56.71 
TCGA-62-A46U TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1679 TCGA-64-5778 
       67.96        13.61        39.25        29.92        81.80        42.90 
TCGA-64-5779 TCGA-67-3771 TCGA-67-3773 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 
       28.41        20.05        14.04        22.68        13.61         7.56 
TCGA-69-7979 TCGA-69-8255 TCGA-69-8453 TCGA-71-6725 TCGA-73-4659 TCGA-73-4670 
       13.41         4.24        26.73         8.42        23.38         4.31 
TCGA-73-4675 TCGA-75-6214 TCGA-75-7027 TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 
       30.31        36.66       100.57        20.58        21.90        39.95 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
       38.50        64.90        88.14        26.53        31.20         8.02 
TCGA-78-7539 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 
       26.01         5.88        34.39        38.04        19.89        35.24 
TCGA-86-8055 TCGA-86-8075 TCGA-86-8279 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 
        4.08        22.82        31.20        30.84         0.62        29.46 
TCGA-86-A4JF TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 
       24.23        10.62        41.36         1.97        10.19        12.23 
TCGA-91-6847 TCGA-91-8499 TCGA-93-A4JO TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VP 
       27.68         1.18         1.08        18.67        12.39        19.89 
TCGA-97-7937 TCGA-97-8175 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-8025 TCGA-99-8028 
       18.54        18.12        21.44        19.76        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 
        1.45        21.57        18.08        19.00        18.58        15.65 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-NJ-A4YF 
       38.63         2.76        58.45        11.05        11.15        71.05 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A7XG TCGA-O1-A52J 
        0.13        47.08        20.28        59.11 

$`DEL PEAK 10(4Q34.3) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 
       14.01         9.96         9.01        28.41        35.28        11.64 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6776 
       26.30        43.53        38.10        42.08        23.93        86.01 
TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 TCGA-49-6745 
       18.31        29.23         9.37        11.08        16.04        17.16 
TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-6978 
       11.64        37.32        40.60        21.47        41.69         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
        7.79         7.99        14.53         6.15        19.66        19.73 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-67-6217 
       32.12        18.15        13.68        16.93        22.65        13.87 
TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-6836 
       52.60        39.09         8.48        50.24        10.55        13.71 
TCGA-93-8067 TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX 
        6.12         2.86        15.65        21.40        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4397 TCGA-05-4403 
       10.09        21.83         2.43         3.98        24.03        19.00 
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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
       37.71        49.05        44.61         4.37        46.98        44.42 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       44.94        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6148 TCGA-44-6774 
       34.06        33.73        26.56        28.01        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7669 
       23.18        32.45        16.44        22.72         7.17        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       23.64        12.66         8.55        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-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 
       14.07        29.46        29.75        55.89        55.33        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO 
       22.26        73.12        62.24        28.90         8.55       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5055 TCGA-50-5068 
      221.33       164.12         9.86        20.52        60.16        49.28 
TCGA-50-5933 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 
       78.67        60.72        57.53        53.16        42.35         3.91 
TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
       11.05        12.16        36.99        36.79        27.25        30.54 
TCGA-53-7813 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 
       13.94        14.30        80.52         5.62        40.73        15.25 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       53.65         3.88        69.34        45.34        32.71        92.81 
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        28.67        20.02 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 
        3.91        23.15        18.64        11.28        17.65        19.82 
TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       29.23        15.19        23.08        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 
       22.16        15.42        17.56        15.72         0.36        17.72 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8620 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       26.01        17.62        12.33         0.92        15.81        19.99 
TCGA-55-A57B TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46S 
       17.95        39.98        42.38        49.25        19.53        54.35 
TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 
       72.30        40.96        56.81        39.09        37.02        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 
       87.98         2.04        51.25        28.47        20.05        18.84 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       12.66        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 
        5.42         6.05         4.41        13.51        14.01        13.45 
TCGA-69-A59K TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       19.43        26.30        15.35         9.24         1.25        50.33 
TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       11.18        66.64        77.85        43.82        85.15        49.84 
TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
      108.66       163.10        27.16         5.69        19.27       129.53 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 
      119.51        19.50        32.09         5.88        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
      104.19       238.29        53.33        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       31.13        20.55        32.78        37.74         4.57        24.33 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
        0.79        32.65        31.04        23.05        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 
       11.61        13.91        27.58        28.34        26.50         3.81 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       13.64        26.47         2.60         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP 
       14.27        19.82        22.45        17.46        23.61        19.00 
TCGA-95-7039 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       41.82        27.29         2.76        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       61.48        25.48         0.59        15.91        18.67         5.39 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M5 
       15.39        16.41        14.30        21.60        20.58        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       18.67        24.56        21.63        35.47        32.48        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 
       14.53         1.91        86.14        49.35        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI 
       58.85         5.49        41.59        29.46        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       19.13        73.91        74.33         1.64         0.49         0.43 
TCGA-NJ-A55R TCGA-S2-AA1A 
       19.82        16.87 

  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                         0.00                          0.36 
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                       156.66                        238.29 
  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE 
                        21.42                         21.91 
[1] "0.0 - 156.7 (21.4)" "0.4 - 238.3 (21.9)"
[1] "hr=" "1.1"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 10(4Q34.3) MUTATED         2       50       48        0        20
  DEL PEAK 10(4Q34.3) WILD-TYPE       3       83       91        1        30
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 10(4Q34.3) MUTATED          18         32          5       10
  DEL PEAK 10(4Q34.3) WILD-TYPE        54         40          6       15
D39V3, multiclass
            clus
vv           DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            50                            83
  STAGE IB                            48                            91
  STAGE II                             0                             1
  STAGE IIA                           20                            30
  STAGE IIB                           18                            54
  STAGE IIIA                          32                            40
  STAGE IIIB                           5                             6
  STAGE IV                            10                            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 10(4Q34.3) MUTATED    61 107  12   6
  DEL PEAK 10(4Q34.3) WILD-TYPE 110 171  34  13
D39V4, multiclass
    clus
vv   DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  T1                          61                           110
  T2                         107                           171
  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(4Q34.3) MUTATED   119  29    35
  DEL PEAK 10(4Q34.3) WILD-TYPE 214  67    41
D39V5, multiclass
       clus
vv      DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  N0                            119                           214
  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"
D39V6, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q34.3) MUTATED   132  10
  DEL PEAK 10(4Q34.3) WILD-TYPE 217  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q34.3) MUTATED    132   10
  DEL PEAK 10(4Q34.3) WILD-TYPE  217   15
   clus
vv  DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  0                         132                           217
  1                          10                            15
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q34.3) MUTATED    93  94
  DEL PEAK 10(4Q34.3) WILD-TYPE 183 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q34.3) MUTATED     93   94
  DEL PEAK 10(4Q34.3) WILD-TYPE  183  146
        clus
vv       DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  FEMALE                          93                           183
  MALE                            94                           146
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q34.3) MUTATED   145  30
  DEL PEAK 10(4Q34.3) WILD-TYPE 265  30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q34.3) MUTATED    145   30
  DEL PEAK 10(4Q34.3) WILD-TYPE  265   30
     clus
vv    DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  NO                          145                           265
  YES                          30                            30
[1] 2 2
[1] FALSE
D39V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 10(4Q34.3) MUTATED                            6
  DEL PEAK 10(4Q34.3) WILD-TYPE                         12
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 10(4Q34.3) MUTATED                                  41
  DEL PEAK 10(4Q34.3) WILD-TYPE                                66
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 10(4Q34.3) MUTATED                                                  119
  DEL PEAK 10(4Q34.3) WILD-TYPE                                                202
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 10(4Q34.3) MUTATED                                            0
  DEL PEAK 10(4Q34.3) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 10(4Q34.3) MUTATED                                               4
  DEL PEAK 10(4Q34.3) WILD-TYPE                                            15
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 10(4Q34.3) MUTATED                                2
  DEL PEAK 10(4Q34.3) WILD-TYPE                              0
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 10(4Q34.3) MUTATED                                    1
  DEL PEAK 10(4Q34.3) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 10(4Q34.3) MUTATED                              0
  DEL PEAK 10(4Q34.3) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 10(4Q34.3) MUTATED                               6
  DEL PEAK 10(4Q34.3) WILD-TYPE                            17
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 10(4Q34.3) MUTATED                                 1
  DEL PEAK 10(4Q34.3) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 10(4Q34.3) MUTATED                                               4
  DEL PEAK 10(4Q34.3) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 10(4Q34.3) MUTATED                              3
  DEL PEAK 10(4Q34.3) WILD-TYPE                            7
D39V10, multiclass
                                                    clus
vv                                                   DEL PEAK 10(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 10(4Q34.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             66
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           202
  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"
D39V11, continuous
D39V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4Q34.3) MUTATED   124   4   2  11
  DEL PEAK 10(4Q34.3) WILD-TYPE 220   9   2  15
D39V13, multiclass
    clus
vv   DEL PEAK 10(4Q34.3) MUTATED DEL PEAK 10(4Q34.3) WILD-TYPE
  R0                         124                           220
  R1                           4                             9
  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 10(4Q34.3) MUTATED                                  0     4
  DEL PEAK 10(4Q34.3) WILD-TYPE                                1     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(4Q34.3) MUTATED                          21   135
  DEL PEAK 10(4Q34.3) WILD-TYPE                        31   255
D39V14, multiclass
                                  clus
vv                                 DEL PEAK 10(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 21
  WHITE                                                    135
                                  clus
vv                                 DEL PEAK 10(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      255
[1] 4 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 10(4Q34.3) MUTATED     5 136
  DEL PEAK 10(4Q34.3) WILD-TYPE   2 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q34.3) MUTATED      5  136
  DEL PEAK 10(4Q34.3) WILD-TYPE    2  248
                        clus
vv                       DEL PEAK 10(4Q34.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         136
                        clus
vv                       DEL PEAK 10(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           248
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 11(5Q12.1) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(5Q12.1) MUTATED   118  58
  DEL PEAK 11(5Q12.1) WILD-TYPE 205 123
  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                          176                           328 
  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                           58                           123 
$`DEL PEAK 11(5Q12.1) MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 TCGA-38-4630 
       19.96         9.96         8.02        20.05        26.01        35.28 
TCGA-38-4631 TCGA-44-6146 TCGA-44-6147 TCGA-44-7670 TCGA-49-6742 TCGA-55-1592 
       11.64        23.93        27.78        29.00        16.04        23.05 
TCGA-55-6979 TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 TCGA-55-8203 TCGA-55-8204 
        7.79        23.18        21.44         6.15        17.98        16.93 
TCGA-55-8511 TCGA-55-A491 TCGA-55-A492 TCGA-80-5611 TCGA-93-8067 TCGA-95-7043 
       18.15        20.58        19.59        85.32         6.12        16.54 
TCGA-95-7947 TCGA-95-7948 TCGA-97-8172 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 
       15.68        15.65        17.92        10.09        21.83        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4389 TCGA-05-4397 TCGA-05-4398 
        5.29         2.43        50.07        45.01        24.03        47.05 
TCGA-05-4417 TCGA-05-4424 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 
       14.96        30.02        25.02        29.00        22.03         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 TCGA-44-2657 
        7.40         5.98        97.74        49.05        44.61        44.42 
TCGA-44-2659 TCGA-44-3917 TCGA-44-3919 TCGA-44-6144 TCGA-44-6145 TCGA-44-6774 
       44.94        38.89        33.73        23.77        19.56        21.63 
TCGA-44-6775 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 TCGA-44-8120 TCGA-44-A4SS 
       23.18        61.28        19.46         7.17         8.55        13.64 
TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AARE 
       12.66        14.07         8.81        73.12        28.90        40.41 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5944 TCGA-50-5946 
       71.47       101.72        47.41        49.28        57.53        53.16 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
       34.29        30.54        35.21        38.73        67.89        30.58 
TCGA-55-6969 TCGA-55-6972 TCGA-55-6975 TCGA-55-6981 TCGA-55-6985 TCGA-55-7570 
       40.73        53.65         3.88        45.34        40.54        27.09 
TCGA-55-7727 TCGA-55-7910 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8094 
        3.91        34.19        18.44        19.82        29.23        17.79 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 
       14.47         0.36        13.74        17.72        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A57B TCGA-62-8394 
       14.66         1.58        12.33        20.71        17.95         4.57 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A470 TCGA-62-A471 
       14.60        88.64        49.25        47.80        39.25        40.96 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 
       56.81        39.09        81.80        38.37        42.90        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-69-7765 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 
       20.05        18.84         5.42        13.41        13.51         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 TCGA-75-5125 TCGA-75-5146 
       19.43         8.42        15.35         4.31        66.64        77.85 
TCGA-75-5147 TCGA-75-6214 TCGA-75-7027 TCGA-78-7149 TCGA-78-7150 TCGA-78-7154 
       43.82        36.66       100.57       129.53        21.90        19.50 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 
       64.90        22.92         9.57        26.53        31.20         8.02 
TCGA-78-8640 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 
      232.18        93.11        27.09        12.36         5.88        34.39 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8074 TCGA-86-8279 TCGA-86-8359 
       38.04        32.78        35.24         0.79        31.20        14.60 
TCGA-86-8585 TCGA-86-8672 TCGA-91-6829 TCGA-91-6840 TCGA-91-8499 TCGA-93-7348 
       11.61         0.62        41.36        12.23         1.18        17.46 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-97-7937 TCGA-97-8175 TCGA-99-8033 
        1.08        19.00        18.67        18.54        18.12        21.57 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV 
       18.08        19.00        18.58        15.65        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4TE TCGA-MP-A4TK TCGA-MP-A5C7 
       58.45        86.04        58.85        29.46        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YQ 
       71.05        47.08 

$`DEL PEAK 11(5Q12.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-6178 
       14.01         9.01        15.02        15.02        28.41        14.73 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6776 TCGA-44-7661 
       26.30        43.53        38.10        42.08        86.01        18.31 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 
       29.23         9.37        11.08        46.72        17.16        11.64 
TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 
      156.66        37.32        40.60        21.47        41.69        48.62 
TCGA-55-6978 TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 TCGA-55-8090 TCGA-55-8091 
        5.79         7.99        16.01        14.53        19.66        19.73 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A4DF 
       19.69        32.12        13.68        16.93        22.65        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.65        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ 
       50.24        10.55        13.71        16.18         1.45        17.29 
TCGA-95-7562 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
        2.86        21.40        18.18        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-MP-A4TA TCGA-MP-A4TD 
       20.68        24.30        23.80         6.35        31.23        10.09 
TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 TCGA-05-4403 TCGA-05-4415 TCGA-05-4420 
        3.98        37.02         0.00        19.00         2.99        29.98 
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-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F 
        9.04         0.46         8.68       120.79        37.71         4.37 
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-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6148 
       34.06        26.56        33.30        28.37        28.01        23.15 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       32.45        16.44        22.72        36.07        18.87        23.64 
TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SU 
       12.66        15.98        15.32         9.44        11.54        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 
       76.21        28.11        28.57        35.54        32.84        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV 
       29.75        55.89        53.29        55.33        22.26        22.26 
TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       62.24         8.55       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       20.52        15.72        60.16         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-6590 
       78.67         8.45        15.12        48.46        60.72        42.35 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
        3.91        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-55-6543 
       10.13        36.99        36.79        27.25        13.94        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6970 TCGA-55-6971 TCGA-55-6980 
       80.52         5.62        42.51        15.25        46.03        69.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       32.71        92.81        24.99       107.21        70.26        28.67 
TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       20.02        32.71        22.03        23.15        25.41        18.64 
TCGA-55-7907 TCGA-55-7911 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       11.28        17.65        29.72        15.19        23.08         5.06 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-A48Z TCGA-55-A490 
       15.72        20.28        19.96        26.01        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-A46P 
        0.92        15.81        19.99        39.98        42.38        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 
       56.71        54.35        67.96        72.30        13.61        29.92 
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-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 
       14.04        12.66        14.73         5.72         4.64         6.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
        6.12        22.68        13.61         7.56         6.05         4.41 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 
       14.01        13.45        26.73        23.38        26.30        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6206 TCGA-75-6212 
        9.24         1.25        50.33        11.18        85.15        49.84 
TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 
      108.66       163.10        27.16         5.69        19.27        20.58 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 
       39.95       119.51        38.50        32.09         5.88       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
      238.29        88.14        53.33        26.01        39.35        10.55 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-7701 TCGA-86-7714 TCGA-86-7954 
       39.75        77.59       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 
       37.74         4.08         4.57        24.33        22.82        32.65 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       31.04        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 
       28.34        26.50        29.46         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6847 
       26.47        10.62         1.97        10.19         2.60        27.68 
TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 
        7.36         1.15        16.60        14.27        19.82        22.45 
TCGA-93-A4JN TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
       23.61        41.82        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 
       42.25        64.60        63.52        61.48        25.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       15.91        18.67         5.39        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AE 
       24.56        34.85        36.76         1.45        21.63        35.47 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-MP-A4SY 
       32.48        14.30        14.53         1.91         2.76        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       37.35         5.49        41.59        11.05        24.36        14.10 
TCGA-MP-A4TJ TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       11.15        74.33         0.13         1.64         0.49         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                         0.36                          0.00 
  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                       232.18                        238.29 
  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE 
                       21.865                        21.470 
[1] "0.4 - 232.2 (21.9)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.2"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 11(5Q12.1) MUTATED         2       43       51        0        19
  DEL PEAK 11(5Q12.1) WILD-TYPE       3       90       88        1        31
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 11(5Q12.1) MUTATED          26         21          4        9
  DEL PEAK 11(5Q12.1) WILD-TYPE        46         51          7       16
D40V3, multiclass
            clus
vv           DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            43                            90
  STAGE IB                            51                            88
  STAGE II                             0                             1
  STAGE IIA                           19                            31
  STAGE IIB                           26                            46
  STAGE IIIA                          21                            51
  STAGE IIIB                           4                             7
  STAGE IV                             9                            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 11(5Q12.1) MUTATED    60  99  12   6
  DEL PEAK 11(5Q12.1) WILD-TYPE 111 179  34  13
D40V4, multiclass
    clus
vv   DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  T1                          60                           111
  T2                          99                           179
  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 11(5Q12.1) MUTATED   110  40    23
  DEL PEAK 11(5Q12.1) WILD-TYPE 223  56    53
D40V5, multiclass
       clus
vv      DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  N0                            110                           223
  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"
D40V6, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q12.1) MUTATED   126   9
  DEL PEAK 11(5Q12.1) WILD-TYPE 223  16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED    126    9
  DEL PEAK 11(5Q12.1) WILD-TYPE  223   16
   clus
vv  DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  0                         126                           223
  1                           9                            16
[1] 2 2
[1] FALSE
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q12.1) MUTATED    92  87
  DEL PEAK 11(5Q12.1) WILD-TYPE 184 153
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED     92   87
  DEL PEAK 11(5Q12.1) WILD-TYPE  184  153
        clus
vv       DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  FEMALE                          92                           184
  MALE                            87                           153
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q12.1) MUTATED   143  20
  DEL PEAK 11(5Q12.1) WILD-TYPE 267  40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED    143   20
  DEL PEAK 11(5Q12.1) WILD-TYPE  267   40
     clus
vv    DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  NO                          143                           267
  YES                          20                            40
[1] 2 2
[1] FALSE
D40V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 11(5Q12.1) MUTATED                            6
  DEL PEAK 11(5Q12.1) WILD-TYPE                         12
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 11(5Q12.1) MUTATED                                  36
  DEL PEAK 11(5Q12.1) WILD-TYPE                                71
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 11(5Q12.1) MUTATED                                                  122
  DEL PEAK 11(5Q12.1) WILD-TYPE                                                199
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 11(5Q12.1) MUTATED                                            0
  DEL PEAK 11(5Q12.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 11(5Q12.1) MUTATED                                               2
  DEL PEAK 11(5Q12.1) WILD-TYPE                                            17
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 11(5Q12.1) MUTATED                                0
  DEL PEAK 11(5Q12.1) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 11(5Q12.1) MUTATED                                    2
  DEL PEAK 11(5Q12.1) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 11(5Q12.1) MUTATED                              1
  DEL PEAK 11(5Q12.1) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 11(5Q12.1) MUTATED                               5
  DEL PEAK 11(5Q12.1) WILD-TYPE                            18
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 11(5Q12.1) MUTATED                                 0
  DEL PEAK 11(5Q12.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 11(5Q12.1) MUTATED                                               4
  DEL PEAK 11(5Q12.1) WILD-TYPE                                             1
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 11(5Q12.1) MUTATED                              1
  DEL PEAK 11(5Q12.1) WILD-TYPE                            9
D40V10, multiclass
                                                    clus
vv                                                   DEL PEAK 11(5Q12.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           36
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         122
  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 11(5Q12.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             71
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           199
  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"
D40V11, continuous
D40V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(5Q12.1) MUTATED   130   3   1  13
  DEL PEAK 11(5Q12.1) WILD-TYPE 214  10   3  13
D40V13, multiclass
    clus
vv   DEL PEAK 11(5Q12.1) MUTATED DEL PEAK 11(5Q12.1) WILD-TYPE
  R0                         130                           214
  R1                           3                            10
  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 11(5Q12.1) MUTATED                                  1     4
  DEL PEAK 11(5Q12.1) WILD-TYPE                                0     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(5Q12.1) MUTATED                          21   124
  DEL PEAK 11(5Q12.1) WILD-TYPE                        31   266
D40V14, multiclass
                                  clus
vv                                 DEL PEAK 11(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 21
  WHITE                                                    124
                                  clus
vv                                 DEL PEAK 11(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   31
  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"
D40V15, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q12.1) MUTATED     6 127
  DEL PEAK 11(5Q12.1) WILD-TYPE   1 257
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q12.1) MUTATED      6  127
  DEL PEAK 11(5Q12.1) WILD-TYPE    1  257
                        clus
vv                       DEL PEAK 11(5Q12.1) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         127
                        clus
vv                       DEL PEAK 11(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           257
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 12(5Q31.1) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(5Q31.1) MUTATED   141  68
  DEL PEAK 12(5Q31.1) WILD-TYPE 182 113
  DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE 
                          209                           295 
  DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE 
                           68                           113 
$`DEL PEAK 12(5Q31.1) MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4427 TCGA-38-4630 
       19.96         9.96         8.02        20.05        26.01        35.28 
TCGA-38-4631 TCGA-38-7271 TCGA-44-6146 TCGA-44-6147 TCGA-44-7670 TCGA-49-6742 
       11.64        26.30        23.93        27.78        29.00        16.04 
TCGA-55-1592 TCGA-55-6979 TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 TCGA-55-8203 
       23.05         7.79        23.18        21.44         6.15        17.98 
TCGA-55-8204 TCGA-55-8511 TCGA-55-A491 TCGA-55-A492 TCGA-93-8067 TCGA-93-A4JQ 
       16.93        18.15        20.58        19.59         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 
       16.54         2.86        15.68        15.65        21.40        17.92 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4389 
       10.09        27.19         5.29         2.43        50.07        45.01 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4430 
       24.03        47.05        14.96        29.98        30.02        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-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       97.74        49.05        44.61        46.98        44.42        44.94 
TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6774 
       38.89        33.30        28.37        23.77        19.56        21.63 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-8117 
       61.28        16.44        19.46         7.17        36.07        12.66 
TCGA-44-8120 TCGA-44-A4SS TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 
        8.55        13.64        28.57        12.66        14.07         8.81 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.89        53.29        22.26        73.12        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       221.33        71.47       101.72 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 
       47.41        49.28        48.46        57.53        53.16        42.35 
TCGA-50-6593 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 
       11.05        10.13        34.29        30.54        35.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6969 TCGA-55-6972 TCGA-55-6975 
       67.89        30.58        42.51        40.73        53.65         3.88 
TCGA-55-6985 TCGA-55-7281 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7907 
       40.54        28.67        27.09        22.03         3.91        11.28 
TCGA-55-7910 TCGA-55-7913 TCGA-55-7994 TCGA-55-8094 TCGA-55-8302 TCGA-55-8505 
       34.19        18.44        19.82        17.79        15.72        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
        0.36        13.74        17.72        17.10        17.62        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 
        1.58        12.33        20.71        19.99        17.95         4.57 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46V TCGA-62-A470 
       39.98        14.60        88.64        49.25        72.30        39.25 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 
       40.96        56.81        39.09        81.80        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        13.41 
TCGA-69-7980 TCGA-69-8255 TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 TCGA-73-A9RS 
       13.51         4.24         8.42        15.35         4.31        11.18 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 
       66.64        77.85        43.82        36.66       100.57         5.69 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7167 
      129.53        21.90        64.90        22.92         9.57        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-8640 TCGA-80-5608 
       26.53        31.20         8.02        53.33       232.18        93.11 
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        38.04        32.78 
TCGA-86-7955 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8279 TCGA-86-8358 
       35.24         4.57        24.33         0.79        31.20        21.47 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 
       14.60        11.61         0.62        41.36        10.19        12.23 
TCGA-91-8499 TCGA-93-7348 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
        1.18        17.46         1.08        41.82        18.67        12.39 
TCGA-95-A4VP TCGA-97-7937 TCGA-97-8175 TCGA-99-8025 TCGA-J2-A4AD TCGA-L4-A4E5 
       19.89        18.54        18.12        34.85        18.08        19.00 
TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T6 
       14.53        18.58        38.63        86.14        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF 
        5.49        29.46        19.13        73.91        71.05 

$`DEL PEAK 12(5Q31.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4418 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-6178 
       14.01         9.01        15.02        15.02        28.41        14.73 
TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 
       43.53        38.10        42.08        86.01        18.31        29.23 
TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
        9.37        11.08        46.72        17.16        11.64       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 
       37.32        40.60        21.47        41.69        48.62         5.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 TCGA-55-8090 TCGA-55-8091 TCGA-55-8205 
        7.99        16.01        14.53        19.66        19.73        19.69 
TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A4DF TCGA-64-1677 
       32.12        13.68        16.93        22.65        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-95-A4VN 
       10.55        85.32        13.71        16.18         1.45        18.18 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A743 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4390 
        6.35        21.83        31.23        10.09         3.98        37.02 
TCGA-05-4395 TCGA-05-4403 TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
        0.00        19.00         2.99        12.00        21.99        26.01 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5429 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 
       24.00         4.96         9.04         0.46         8.68       120.79 
TCGA-38-4627 TCGA-38-A44F TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       37.71         4.37        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6148 
       38.24        34.06        33.73        26.56        28.01        23.15 
TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 
       23.18        32.45        22.72        18.87        23.64        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-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 TCGA-49-AAQV 
       35.54        32.84        29.46        29.75        55.33        22.26 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 
      164.12         9.86        20.52        15.72        60.16         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
        9.27        14.27        78.67         8.45        15.12        60.72 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 
        3.91        25.55        12.16         6.21         0.72        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       36.79        27.25        13.94        14.30        80.52         5.62 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       15.25        46.03        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7283 TCGA-55-7574 TCGA-55-7728 
       24.99       107.21        70.26        20.02        32.71        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       25.41        18.64        17.65        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       23.08         5.06        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-A48Z 
       15.42        17.56        20.28        19.96        26.01        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46P 
        3.25         0.92        15.81        42.38        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A472 TCGA-64-1680 
       56.71        54.35        67.96        13.61        29.92        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        20.05        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       12.66        14.73         5.72         4.64         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         4.41        14.01        13.45 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 
       26.73        19.43        23.38        26.30        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-78-7143 
        1.25        50.33        85.15        49.84       108.66       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        39.95       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7163 TCGA-78-7539 
       38.50        32.09         5.88       104.19       238.29        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-7701 
       39.35        10.55        39.75        77.59       110.50        31.13 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8076 
       20.55        19.89        37.74         4.08        22.82        32.65 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
       31.04        23.05        13.91        30.84        27.58        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       26.50        29.46         3.81        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       10.62         1.97         2.60        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JP 
       16.60        14.27        19.82        22.45        23.61        19.00 
TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       27.29         2.76        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 
       25.48         0.59        15.91        18.67         5.39        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-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.84        18.67        24.56        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A8F4 
       21.63        35.47        32.48        14.30         1.91        15.65 
TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TF 
        2.76        58.45        49.35        37.35        41.59        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       24.36        14.10        11.15        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       47.08         0.49         0.43        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE 
                         0.36                          0.00 
  DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE 
                       232.18                        238.29 
  DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE 
                        22.03                         21.44 
[1] "0.4 - 232.2 (22.0)" "0.0 - 238.3 (21.4)"
[1] "hr=" "1.3"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 12(5Q31.1) MUTATED         3       49       59        0        21
  DEL PEAK 12(5Q31.1) WILD-TYPE       2       84       80        1        29
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 12(5Q31.1) MUTATED          32         29          4       10
  DEL PEAK 12(5Q31.1) WILD-TYPE        40         43          7       15
D41V3, multiclass
            clus
vv           DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            49                            84
  STAGE IB                            59                            80
  STAGE II                             0                             1
  STAGE IIA                           21                            29
  STAGE IIB                           32                            40
  STAGE IIIA                          29                            43
  STAGE IIIB                           4                             7
  STAGE IV                            10                            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 12(5Q31.1) MUTATED    69 118  17   7
  DEL PEAK 12(5Q31.1) WILD-TYPE 102 160  29  12
D41V4, multiclass
    clus
vv   DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE
  T1                          69                           102
  T2                         118                           160
  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 12(5Q31.1) MUTATED   134  43    30
  DEL PEAK 12(5Q31.1) WILD-TYPE 199  53    46
D41V5, multiclass
       clus
vv      DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE
  N0                            134                           199
  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"
D41V6, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q31.1) MUTATED   142  10
  DEL PEAK 12(5Q31.1) WILD-TYPE 207  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q31.1) MUTATED    142   10
  DEL PEAK 12(5Q31.1) WILD-TYPE  207   15
   clus
vv  DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE
  0                         142                           207
  1                          10                            15
[1] 2 2
[1] FALSE
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q31.1) MUTATED   106 105
  DEL PEAK 12(5Q31.1) WILD-TYPE 170 135
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q31.1) MUTATED    106  105
  DEL PEAK 12(5Q31.1) WILD-TYPE  170  135
        clus
vv       DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE
  FEMALE                         106                           170
  MALE                           105                           135
[1] 2 2
[1] FALSE
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q31.1) MUTATED   170  24
  DEL PEAK 12(5Q31.1) WILD-TYPE 240  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q31.1) MUTATED    170   24
  DEL PEAK 12(5Q31.1) WILD-TYPE  240   36
     clus
vv    DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE
  NO                          170                           240
  YES                          24                            36
[1] 2 2
[1] FALSE
D41V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 12(5Q31.1) MUTATED                            9
  DEL PEAK 12(5Q31.1) WILD-TYPE                          9
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 12(5Q31.1) MUTATED                                  46
  DEL PEAK 12(5Q31.1) WILD-TYPE                                61
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 12(5Q31.1) MUTATED                                                  138
  DEL PEAK 12(5Q31.1) WILD-TYPE                                                183
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 12(5Q31.1) MUTATED                                            0
  DEL PEAK 12(5Q31.1) WILD-TYPE                                          5
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 12(5Q31.1) MUTATED                                               3
  DEL PEAK 12(5Q31.1) WILD-TYPE                                            16
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 12(5Q31.1) MUTATED                                1
  DEL PEAK 12(5Q31.1) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 12(5Q31.1) MUTATED                                    2
  DEL PEAK 12(5Q31.1) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 12(5Q31.1) MUTATED                              1
  DEL PEAK 12(5Q31.1) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 12(5Q31.1) MUTATED                               7
  DEL PEAK 12(5Q31.1) WILD-TYPE                            16
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 12(5Q31.1) MUTATED                                 0
  DEL PEAK 12(5Q31.1) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 12(5Q31.1) MUTATED                                               3
  DEL PEAK 12(5Q31.1) WILD-TYPE                                             2
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 12(5Q31.1) MUTATED                              1
  DEL PEAK 12(5Q31.1) WILD-TYPE                            9
D41V10, multiclass
                                                    clus
vv                                                   DEL PEAK 12(5Q31.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         138
  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 12(5Q31.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           183
  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"
D41V11, continuous
D41V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(5Q31.1) MUTATED   148   3   1  13
  DEL PEAK 12(5Q31.1) WILD-TYPE 196  10   3  13
D41V13, multiclass
    clus
vv   DEL PEAK 12(5Q31.1) MUTATED DEL PEAK 12(5Q31.1) WILD-TYPE
  R0                         148                           196
  R1                           3                            10
  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 12(5Q31.1) MUTATED                                  1     3
  DEL PEAK 12(5Q31.1) WILD-TYPE                                0     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(5Q31.1) MUTATED                          28   148
  DEL PEAK 12(5Q31.1) WILD-TYPE                        24   242
D41V14, multiclass
                                  clus
vv                                 DEL PEAK 12(5Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 28
  WHITE                                                    148
                                  clus
vv                                 DEL PEAK 12(5Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      242
[1] 4 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 12(5Q31.1) MUTATED     5 150
  DEL PEAK 12(5Q31.1) WILD-TYPE   2 234
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q31.1) MUTATED      5  150
  DEL PEAK 12(5Q31.1) WILD-TYPE    2  234
                        clus
vv                       DEL PEAK 12(5Q31.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         150
                        clus
vv                       DEL PEAK 12(5Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           234
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 13(6Q14.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(6Q14.3) MUTATED   154  94
  DEL PEAK 13(6Q14.3) WILD-TYPE 169  87
  DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE 
                          248                           256 
  DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE 
                           94                            87 
$`DEL PEAK 13(6Q14.3) MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4405 TCGA-05-4434 TCGA-38-6178 TCGA-44-6147 
       19.96         9.96        20.05        15.02        14.73        27.78 
TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 
       86.01        29.00        29.23        11.08        46.72        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-55-1595 
       11.64       156.66        37.32        40.60        21.47        48.62 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 
       23.18        14.53         6.15        19.66        19.73        17.98 
TCGA-55-8207 TCGA-55-8511 TCGA-55-A48X TCGA-64-1677 TCGA-73-7498 TCGA-78-7633 
       32.12        18.15        22.65        20.65        39.09        50.24 
TCGA-80-5611 TCGA-91-7771 TCGA-93-8067 TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VN 
       85.32        16.18         6.12        16.54        15.65        18.18 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 
       10.09        27.19         2.43        10.09         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4415 TCGA-05-4425 TCGA-05-4430 TCGA-05-5428 
       37.02         0.00         2.99        21.99        25.02        22.03 
TCGA-05-5429 TCGA-35-3615 TCGA-35-4123 TCGA-38-4632 TCGA-44-2656 TCGA-44-2659 
        9.04         0.46         5.98        44.61        46.98        44.94 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 TCGA-44-4112 TCGA-44-5644 TCGA-44-6774 
        3.19        25.02        38.89        26.56        28.37        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7667 
       23.18        32.45        61.28        16.44        22.72        36.07 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4494 
       12.66         8.55        13.45        76.21        28.57        35.54 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 
       14.07         8.81        29.46        29.75        55.89        55.33 
TCGA-49-AAQV TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-50-5051 TCGA-50-5066 
       22.26         8.55        40.41       123.58        15.72        47.41 
TCGA-50-5068 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       49.28        78.67         8.45        15.12        48.46        60.72 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6593 TCGA-50-6594 TCGA-50-7109 TCGA-53-7624 
       53.16        42.35        11.05        12.16        10.13        34.29 
TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 
       30.54        13.94        35.21        67.89        14.30        80.52 
TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 
       42.51        46.03        53.65        45.34        92.81        24.99 
TCGA-55-6985 TCGA-55-7283 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 
       40.54        20.02        22.03         3.91        25.41        18.64 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 TCGA-55-8094 
       17.65        18.44        19.82        29.72        23.08        17.79 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8615 
       15.72         0.36        13.74        20.28        19.96        14.66 
TCGA-55-8616 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-62-8395 
        1.58        20.71         3.25         0.92        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-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-5774 
       72.30        39.25        29.92        56.81        39.09        87.98 
TCGA-64-5779 TCGA-64-5781 TCGA-67-3773 TCGA-67-4679 TCGA-67-6216 TCGA-69-7763 
       28.41        51.25        14.04        14.73         4.64        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       13.61         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
       14.01        13.45        26.73        19.43         8.42        23.38 
TCGA-73-4666 TCGA-73-4675 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6206 
       26.30        30.31         1.25        50.33        11.18        85.15 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7149 TCGA-78-7152 
       36.66       108.66       100.57         5.69       129.53        39.95 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7535 
      119.51        32.09         5.88        64.90       104.19        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 TCGA-78-8655 TCGA-80-5608 
        8.02        53.33        39.35        10.55        77.59        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
       27.09        12.36        31.13        38.04        20.55        32.78 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8074 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
       35.24        37.74         0.79        31.20        23.05        21.47 
TCGA-86-8359 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-91-6831 TCGA-91-6849 
       14.60         0.62        26.50        29.46        10.19         1.15 
TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7567 TCGA-95-7944 
        1.18        19.82        22.45        17.46        18.67        12.39 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
        2.76        19.89        64.60        25.48        18.54         0.59 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M0 TCGA-99-7458 
        5.39        15.39        16.41        21.60        21.44        24.56 
TCGA-99-8025 TCGA-99-8033 TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N4 
       34.85        21.57        19.00        14.53        18.58        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-A4TE TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YP 
       29.46        11.05        11.15        73.91         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A 
       47.08         0.49 

$`DEL PEAK 13(6Q14.3) WILD-TYPE`
TCGA-05-4384 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 TCGA-05-5420 TCGA-38-4629 
       14.01         8.02         9.01        26.01        15.02        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 
       35.28        11.64        26.30        43.53        38.10        42.08 
TCGA-44-6146 TCGA-44-7661 TCGA-44-8119 TCGA-49-6742 TCGA-50-6597 TCGA-55-1592 
       23.93        18.31         9.37        16.04        41.69        23.05 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7726 TCGA-55-8204 
        5.79         7.79         7.99        16.01        21.44        16.93 
TCGA-55-8205 TCGA-55-8619 TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
       19.69        13.68        16.93        20.58        19.59        20.19 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-78-7166 TCGA-78-8660 TCGA-91-6836 
       13.87        52.60        82.68         8.48        10.55        13.71 
TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-97-8172 
        1.45        17.29         2.86        15.68        21.40        17.92 
TCGA-97-A4LX TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-05-4249 TCGA-05-4397 
       20.19        21.83         5.29        31.23        50.07        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       47.05        19.00        14.96        29.98        12.00        30.02 
TCGA-05-4426 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5715 
       26.01        25.02        24.00         4.96        29.00         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-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 
        4.37        44.42        42.77        37.15        38.24        34.06 
TCGA-44-3919 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       33.73        33.30        28.01        23.77        19.56        23.15 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A 
       19.46         7.17        18.87        23.64        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4487 TCGA-49-4490 TCGA-49-4506 
        9.44        11.54        13.64        28.11        12.66        32.84 
TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARQ 
       53.29        22.26        73.12        62.24        28.90       221.33 
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       101.72        60.16 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 
        8.22         9.27        14.27        57.53         3.91        25.55 
TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-55-1594 
        6.21         0.72        36.99        36.79        27.25        38.73 
TCGA-55-5899 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6975 TCGA-55-6980 
       30.58         5.62        40.73        15.25         3.88        69.34 
TCGA-55-6982 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 
       32.71       107.21        70.26        28.67        27.09        32.71 
TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7995 TCGA-55-8087 TCGA-55-8092 
       23.15        11.28        34.19        29.23        15.19         5.06 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8505 TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8620 
       14.47        17.72        26.01        17.10        17.62        12.33 
TCGA-55-A48Z TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8397 TCGA-62-8399 
       21.40        19.99        17.95         4.57        42.38        88.64 
TCGA-62-A46O TCGA-62-A46Y TCGA-62-A471 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
       47.80        13.61        40.96        81.80        37.02        38.37 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        2.04        42.90        28.47        20.05        20.05        18.84 
TCGA-67-3774 TCGA-67-6215 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-8255 
       12.66         5.72         6.64         6.12         5.42         4.24 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
       15.35         4.31         9.24        66.64        77.85        43.82 
TCGA-75-6212 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7150 
       49.84       163.10        27.16        19.27        20.58        21.90 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7167 
       19.50        38.50        22.92         9.57       238.29        88.14 
TCGA-78-7220 TCGA-78-7539 TCGA-78-8640 TCGA-78-8648 TCGA-78-8662 TCGA-86-6851 
       26.53        26.01       232.18        39.75       110.50         5.88 
TCGA-86-7711 TCGA-86-7954 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
       34.39        19.89         4.08         4.57        24.33        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 
       32.65        31.04        11.61        13.91        30.84        27.58 
TCGA-86-8673 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       28.34         3.81        24.23        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       41.36         1.97         2.60        12.23        27.68         7.36 
TCGA-91-8496 TCGA-91-8497 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       16.60        14.27        23.61         1.08        19.00        41.82 
TCGA-95-8039 TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 
       27.29        42.25        63.52        61.48        15.91        18.67 
TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       18.12        14.30        20.58        19.76        20.84        18.67 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
       36.76         1.45        21.63        18.08        35.47        32.48 
TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 
       14.30         1.91        15.65        86.04         5.49        41.59 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A55O 
       24.36        14.10        19.13        71.05        74.33         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        20.28        59.11        16.87 

  DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE 
                         0.00                          0.43 
  DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE 
                       156.66                        238.29 
  DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE 
                        22.03                         21.12 
[1] "0.0 - 156.7 (22.0)" "0.4 - 238.3 (21.1)"
[1] "hr=" "1.1"
D42V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 13(6Q14.3) MUTATED         2       58       71        1        27
  DEL PEAK 13(6Q14.3) WILD-TYPE       3       75       68        0        23
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 13(6Q14.3) MUTATED          29         42          7       12
  DEL PEAK 13(6Q14.3) WILD-TYPE        43         30          4       13
D42V3, multiclass
            clus
vv           DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            58                            75
  STAGE IB                            71                            68
  STAGE II                             1                             0
  STAGE IIA                           27                            23
  STAGE IIB                           29                            43
  STAGE IIIA                          42                            30
  STAGE IIIB                           7                             4
  STAGE IV                            12                            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(6Q14.3) MUTATED    82 136  24  10
  DEL PEAK 13(6Q14.3) WILD-TYPE  89 142  22   9
D42V4, multiclass
    clus
vv   DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE
  T1                          82                            89
  T2                         136                           142
  T3                          24                            22
  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 13(6Q14.3) MUTATED   158  47    42
  DEL PEAK 13(6Q14.3) WILD-TYPE 175  49    34
D42V5, multiclass
       clus
vv      DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE
  N0                            158                           175
  N1                             47                            49
  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"
D42V6, binary
                               cls
clus                              0   1
  DEL PEAK 13(6Q14.3) MUTATED   168  12
  DEL PEAK 13(6Q14.3) WILD-TYPE 181  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6Q14.3) MUTATED    168   12
  DEL PEAK 13(6Q14.3) WILD-TYPE  181   13
   clus
vv  DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE
  0                         168                           181
  1                          12                            13
[1] 2 2
[1] FALSE
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(6Q14.3) MUTATED   131 122
  DEL PEAK 13(6Q14.3) WILD-TYPE 145 118
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6Q14.3) MUTATED    131  122
  DEL PEAK 13(6Q14.3) WILD-TYPE  145  118
        clus
vv       DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE
  FEMALE                         131                           145
  MALE                           122                           118
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(6Q14.3) MUTATED   205  26
  DEL PEAK 13(6Q14.3) WILD-TYPE 205  34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6Q14.3) MUTATED    205   26
  DEL PEAK 13(6Q14.3) WILD-TYPE  205   34
     clus
vv    DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE
  NO                          205                           205
  YES                          26                            34
[1] 2 2
[1] FALSE
D42V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 13(6Q14.3) MUTATED                            8
  DEL PEAK 13(6Q14.3) WILD-TYPE                         10
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 13(6Q14.3) MUTATED                                  59
  DEL PEAK 13(6Q14.3) WILD-TYPE                                48
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 13(6Q14.3) MUTATED                                                  155
  DEL PEAK 13(6Q14.3) WILD-TYPE                                                166
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 13(6Q14.3) MUTATED                                            2
  DEL PEAK 13(6Q14.3) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 13(6Q14.3) MUTATED                                               7
  DEL PEAK 13(6Q14.3) WILD-TYPE                                            12
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 13(6Q14.3) MUTATED                                1
  DEL PEAK 13(6Q14.3) WILD-TYPE                              1
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 13(6Q14.3) MUTATED                                    1
  DEL PEAK 13(6Q14.3) WILD-TYPE                                  2
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 13(6Q14.3) MUTATED                              0
  DEL PEAK 13(6Q14.3) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 13(6Q14.3) MUTATED                              13
  DEL PEAK 13(6Q14.3) WILD-TYPE                            10
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 13(6Q14.3) MUTATED                                 1
  DEL PEAK 13(6Q14.3) WILD-TYPE                               0
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 13(6Q14.3) MUTATED                                               2
  DEL PEAK 13(6Q14.3) WILD-TYPE                                             3
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 13(6Q14.3) MUTATED                              4
  DEL PEAK 13(6Q14.3) WILD-TYPE                            6
D42V10, multiclass
                                                    clus
vv                                                   DEL PEAK 13(6Q14.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           59
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         155
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                7
  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                                                 4
                                                    clus
vv                                                   DEL PEAK 13(6Q14.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           166
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 12
  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                                                   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"
D42V11, continuous
D42V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(6Q14.3) MUTATED   170   4   2  12
  DEL PEAK 13(6Q14.3) WILD-TYPE 174   9   2  14
D42V13, multiclass
    clus
vv   DEL PEAK 13(6Q14.3) MUTATED DEL PEAK 13(6Q14.3) WILD-TYPE
  R0                         170                           174
  R1                           4                             9
  R2                           2                             2
  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 13(6Q14.3) MUTATED                                  0     5
  DEL PEAK 13(6Q14.3) WILD-TYPE                                1     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(6Q14.3) MUTATED                          25   194
  DEL PEAK 13(6Q14.3) WILD-TYPE                        27   196
D42V14, multiclass
                                  clus
vv                                 DEL PEAK 13(6Q14.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 25
  WHITE                                                    194
                                  clus
vv                                 DEL PEAK 13(6Q14.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   27
  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"
D42V15, binary
                               cls
clus                              0   1
  DEL PEAK 13(6Q14.3) MUTATED     5 188
  DEL PEAK 13(6Q14.3) WILD-TYPE   2 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(6Q14.3) MUTATED      5  188
  DEL PEAK 13(6Q14.3) WILD-TYPE    2  196
                        clus
vv                       DEL PEAK 13(6Q14.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         188
                        clus
vv                       DEL PEAK 13(6Q14.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           196
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 14(6Q26) MUTATION ANALYSIS
D43V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 14(6Q26) MUTATED   157  96
  DEL PEAK 14(6Q26) WILD-TYPE 166  85
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                        253                         251 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                         96                          85 
$`DEL PEAK 14(6Q26) MUTATED`
TCGA-05-4382 TCGA-05-4405 TCGA-05-4434 TCGA-38-4631 TCGA-38-6178 TCGA-44-2662 
       19.96        20.05        15.02        11.64        14.73        42.08 
TCGA-44-6147 TCGA-44-7670 TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
       27.78        29.00        11.08        17.16        11.64       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 TCGA-55-1595 TCGA-55-7724 
       37.32        40.60        21.47        23.05        48.62        23.18 
TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8207 
       14.53         6.15        19.66        19.73        17.98        32.12 
TCGA-55-8511 TCGA-55-A48X TCGA-64-1677 TCGA-73-4658 TCGA-73-7498 TCGA-78-7633 
       18.15        22.65        20.65        52.60        39.09        50.24 
TCGA-80-5611 TCGA-91-7771 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VN 
       85.32        16.18        17.29        16.54        15.65        18.18 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       20.19        20.52        17.75        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        6.35        10.09         2.43         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4415 TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 
        0.00         2.99        29.98        21.99        26.01        25.02 
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-38-4632 TCGA-44-2656 TCGA-44-2659 TCGA-44-2666 TCGA-44-2668 TCGA-44-3917 
       44.61        46.98        44.94         3.19        25.02        38.89 
TCGA-44-3918 TCGA-44-5644 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
       34.06        28.37        21.63        23.18        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4486 
       16.44        22.72        12.66         8.55        13.45        76.21 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       28.57        35.54        14.07         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6744 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-50-5051 
       55.89        55.33         8.55        40.41       123.58        15.72 
TCGA-50-5068 TCGA-50-5933 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 
       49.28        78.67        48.46        60.72        53.16        42.35 
TCGA-50-6594 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       12.16        10.13        34.29        30.54        13.94        35.21 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 
       67.89        14.30        80.52        42.51        46.03        53.65 
TCGA-55-6981 TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 TCGA-55-7576 TCGA-55-7815 
       45.34        92.81        40.54        20.02        22.03        25.41 
TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       18.64        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 TCGA-55-8302 TCGA-55-8506 
       23.08         5.06        17.79        15.65        15.72         0.36 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8615 TCGA-55-A48Y TCGA-55-A494 TCGA-62-8395 
       20.28        19.96        14.66        20.71        15.81        39.98 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       14.60        49.25        47.80        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
       72.30        13.61        39.25        29.92        56.81        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-67-4679 TCGA-67-6216 TCGA-69-7760 TCGA-69-7763 
       20.05        14.04        14.73         4.64         6.64        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
       13.61         7.56         6.05         4.41        13.41        14.01 
TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 
       13.45        26.73        19.43         8.42        23.38        26.30 
TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6206 TCGA-75-6214 
        4.31        30.31        50.33        11.18        85.15        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
      108.66       100.57         5.69       129.53        39.95       119.51 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7162 TCGA-78-7167 
       19.50        32.09         5.88        64.90       104.19        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 
       26.53        31.20         8.02        53.33        39.35        10.55 
TCGA-78-8655 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       77.59        27.09        12.36        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8075 TCGA-86-8278 
       20.55        32.78        35.24        37.74        22.82        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
       31.20        23.05        14.60        27.58         0.62        26.50 
TCGA-86-A456 TCGA-91-6831 TCGA-91-6849 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
       29.46        10.19         1.15         1.18        19.82        22.45 
TCGA-93-7348 TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 
       17.46        18.67        12.39         2.76        19.89        64.60 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8174 TCGA-97-8176 TCGA-97-8547 
       25.48        18.54         0.59         5.39        15.39        21.60 
TCGA-97-A4M0 TCGA-97-A4M5 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-L4-A4E5 
       21.44        20.84        34.85        36.76        21.57        19.00 
TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       14.53        18.58        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
       49.35        37.35        58.85        29.46        11.05        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YP 
       11.15        19.13        73.91        71.05         0.13         1.64 
TCGA-NJ-A55A 
        0.49 

$`DEL PEAK 14(6Q26) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 TCGA-05-5420 
       14.01         9.96         8.02         9.01        26.01        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 
       28.41        35.28        26.30        43.53        38.10        23.93 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 
       86.01        18.31        29.23         9.37        46.72        16.04 
TCGA-50-6597 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7726 
       41.69         5.79         7.79         7.99        16.01        21.44 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8619 TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 
       16.93        19.69        13.68        16.93        20.58        19.59 
TCGA-55-A4DF TCGA-67-6217 TCGA-73-4662 TCGA-78-7166 TCGA-78-8660 TCGA-91-6836 
       20.19        13.87        82.68         8.48        10.55        13.71 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-97-8172 
        1.45         6.12         2.86        15.68        21.40        17.92 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 
       21.83        27.19         5.29        31.23        10.09        50.07 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 
       24.03        47.05        19.00        14.96        12.00        30.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5715 TCGA-35-4122 TCGA-35-5375 
       25.02        24.00         4.96         2.04         7.40         8.68 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 
      120.79        37.71        49.05         4.37        44.42        42.77 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
       37.15        38.24        33.73        26.56        33.30        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       23.77        19.56        23.15        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       18.87        23.64        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-49-4487 TCGA-49-4490 TCGA-49-4506 TCGA-49-6743 TCGA-49-6767 
       13.64        28.11        12.66        32.84        53.29        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARQ TCGA-49-AARR 
       22.26        73.12        62.24        28.90       221.33       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       101.72        60.16        47.41 
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        57.53 
TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 
        3.91        25.55        11.05         6.21         0.72        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-55-1594 TCGA-55-5899 TCGA-55-6712 TCGA-55-6969 
       36.79        27.25        38.73        30.58         5.62        40.73 
TCGA-55-6970 TCGA-55-6975 TCGA-55-6980 TCGA-55-6982 TCGA-55-6984 TCGA-55-6986 
       15.25         3.88        69.34        32.71        24.99       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 
       70.26        28.67        27.09        32.71         3.91        23.15 
TCGA-55-7907 TCGA-55-7910 TCGA-55-8087 TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 
       11.28        34.19        15.19        23.64        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 TCGA-55-8513 
       15.42        17.56        14.47        13.74        17.72        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
       17.10        17.62         1.58        12.33        21.40         3.25 
TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8397 TCGA-62-8399 
        0.92        19.99        17.95         4.57        42.38        88.64 
TCGA-62-A46P TCGA-62-A471 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 
       19.53        40.96        81.80        38.37        42.90        20.05 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6215 TCGA-69-7761 TCGA-69-7765 TCGA-69-7980 
       18.84        12.66         5.72         6.12         5.42        13.51 
TCGA-69-8255 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-75-5125 TCGA-75-5146 
        4.24        15.35         9.24         1.25        66.64        77.85 
TCGA-75-5147 TCGA-75-6212 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
       43.82        49.84       163.10        27.16        19.27        20.58 
TCGA-78-7150 TCGA-78-7155 TCGA-78-7160 TCGA-78-7161 TCGA-78-7163 TCGA-78-7539 
       21.90        38.50        22.92         9.57       238.29        26.01 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 TCGA-86-6851 TCGA-86-7954 
      232.18        39.75       110.50        93.11         5.88        19.89 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8358 
        4.08         4.57        24.33         0.79        32.65        21.47 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 TCGA-86-A4JF 
       11.61        13.91        30.84        28.34         3.81        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
       13.64        26.47        10.62        41.36         1.97         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 TCGA-93-A4JN 
       12.23        27.68         7.36        16.60        14.27        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-8039 TCGA-97-7546 TCGA-97-7552 
        1.08        19.00        41.82        27.29        42.25        63.52 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 
       61.48        15.91        18.67        18.12        16.41        14.30 
TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8032 TCGA-99-AA5R 
       20.58        19.76        18.67        24.56         1.45        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A8F4 
       18.08        35.47        32.48        14.30         1.91        15.65 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-NJ-A4YG TCGA-NJ-A4YQ 
       86.04         5.49        41.59        24.36        74.33        47.08 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.43        19.82        20.28        59.11        16.87 

  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                       0.00                        0.43 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                     156.66                      238.29 
  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE 
                      22.82                       20.28 
[1] "0.0 - 156.7 (22.8)" "0.4 - 238.3 (20.3)"
[1] "hr=" "1"  
D43V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 14(6Q26) MUTATED         1       63       69        0        26
  DEL PEAK 14(6Q26) WILD-TYPE       4       70       70        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        38         31          5       10
D43V3, multiclass
            clus
vv           DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  STAGE I                            1                           4
  STAGE IA                          63                          70
  STAGE IB                          69                          70
  STAGE II                           0                           1
  STAGE IIA                         26                          24
  STAGE IIB                         34                          38
  STAGE IIIA                        41                          31
  STAGE IIIB                         6                           5
  STAGE IV                          15                          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 14(6Q26) MUTATED    81 141  26   9
  DEL PEAK 14(6Q26) WILD-TYPE  90 137  20  10
D43V4, multiclass
    clus
vv   DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  T1                        81                          90
  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 14(6Q26) MUTATED   161  49    42
  DEL PEAK 14(6Q26) WILD-TYPE 172  47    34
D43V5, multiclass
       clus
vv      DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  N0                          161                         172
  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"
D43V6, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q26) MUTATED   173  15
  DEL PEAK 14(6Q26) WILD-TYPE 176  10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED    173   15
  DEL PEAK 14(6Q26) WILD-TYPE  176   10
   clus
vv  DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  0                       173                         176
  1                        15                          10
[1] 2 2
[1] FALSE
D43V7, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q26) MUTATED   133 125
  DEL PEAK 14(6Q26) WILD-TYPE 143 115
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED    133  125
  DEL PEAK 14(6Q26) WILD-TYPE  143  115
        clus
vv       DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  FEMALE                       133                         143
  MALE                         125                         115
[1] 2 2
[1] FALSE
D43V8, binary
                             cls
clus                            0   1
  DEL PEAK 14(6Q26) MUTATED   207  29
  DEL PEAK 14(6Q26) WILD-TYPE 203  31
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED    207   29
  DEL PEAK 14(6Q26) WILD-TYPE  203   31
     clus
vv    DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  NO                        207                         203
  YES                        29                          31
[1] 2 2
[1] FALSE
D43V9, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 14(6Q26) MUTATED                            9
  DEL PEAK 14(6Q26) WILD-TYPE                          9
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 14(6Q26) MUTATED                                  62
  DEL PEAK 14(6Q26) WILD-TYPE                                45
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 14(6Q26) MUTATED                                                  156
  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
D43V10, multiclass
                                                    clus
vv                                                   DEL PEAK 14(6Q26) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       156
  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                                           45
  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"
D43V11, continuous
D43V12, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 14(6Q26) MUTATED   181   4   2  10
  DEL PEAK 14(6Q26) WILD-TYPE 163   9   2  16
D43V13, multiclass
    clus
vv   DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  R0                       181                         163
  R1                         4                           9
  R2                         2                           2
  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 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   199
  DEL PEAK 14(6Q26) WILD-TYPE                        28   191
D43V14, multiclass
                                  clus
vv                                 DEL PEAK 14(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               24
  WHITE                                                  199
                                  clus
vv                                 DEL PEAK 14(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 28
  WHITE                                                    191
[1] 4 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 14(6Q26) MUTATED     6 189
  DEL PEAK 14(6Q26) WILD-TYPE   1 195
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 14(6Q26) MUTATED      6  189
  DEL PEAK 14(6Q26) WILD-TYPE    1  195
                        clus
vv                       DEL PEAK 14(6Q26) MUTATED DEL PEAK 14(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             6                           1
  NOT HISPANIC OR LATINO                       189                         195
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 15(8P23.2) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(8P23.2) MUTATED   157  91
  DEL PEAK 15(8P23.2) WILD-TYPE 166  90
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          248                           256 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                           91                            90 
$`DEL PEAK 15(8P23.2) MUTATED`
TCGA-05-4402 TCGA-05-4427 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
        8.02        26.01        28.41        35.28        11.64        14.73 
TCGA-44-2662 TCGA-44-6147 TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 TCGA-49-6761 
       42.08        27.78        29.00         9.37        46.72        11.64 
TCGA-49-AARN TCGA-50-5932 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6979 
       37.32        40.60        41.69        23.05        48.62         7.79 
TCGA-55-7573 TCGA-55-7726 TCGA-55-7914 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       16.01        21.44         6.15        16.93        19.69        32.12 
TCGA-55-A491 TCGA-64-1677 TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 TCGA-78-8660 
       20.58        20.65        13.87        82.68        39.09        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       85.32        13.71         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4M3 TCGA-97-A4M7 
       15.68        15.65        21.40        18.18        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4249 
       24.30        23.80        10.09        31.23         2.43        50.07 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4420 TCGA-05-4425 
       45.01        37.02         0.00        47.05        29.98        21.99 
TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 
       24.00        29.00        22.03         7.40         5.98        97.74 
TCGA-38-4627 TCGA-38-4628 TCGA-44-2656 TCGA-44-2657 TCGA-44-2668 TCGA-44-3917 
       37.71        49.05        46.98        44.42        25.02        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
       34.06        33.73        33.30        28.37        23.77        19.56 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 
       21.63        23.18        32.45        16.44        19.46         7.17 
TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-49-4487 TCGA-49-4488 
       23.64        12.66         8.55        15.98        28.11        28.57 
TCGA-49-4490 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6767 
       12.66        14.07        29.46        29.75        53.29        22.26 
TCGA-49-AAQV TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-50-5045 TCGA-50-5049 
       22.26        28.90         8.55       123.58        71.47       101.72 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       47.41        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5939 TCGA-50-5941 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 
       15.12        48.46         3.91        11.05        12.16         0.72 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 
       10.13        34.29        30.54        35.21        38.73        67.89 
TCGA-55-5899 TCGA-55-6968 TCGA-55-6969 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       30.58        42.51        40.73         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6985 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       32.71        40.54        20.02        27.09        32.71        22.03 
TCGA-55-7727 TCGA-55-7903 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
        3.91        18.64        18.44        19.82        29.23        29.72 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
        5.06        23.64        15.65        17.56        15.72         0.36 
TCGA-55-8510 TCGA-55-8614 TCGA-55-8616 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 
       17.72        17.62         1.58        20.71         3.25         0.92 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8402 
       19.99        17.95         4.57        39.98        42.38        49.25 
TCGA-62-A46O TCGA-62-A46R TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
       47.80        56.71        67.96        29.92        56.81        39.09 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 
       81.80        38.37         2.04        42.90        28.47        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-69-7760 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       20.05        18.84         6.64         6.05         4.41        13.41 
TCGA-69-7980 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4668 
       13.51         4.24        26.73        19.43         8.42        15.35 
TCGA-73-4670 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5147 TCGA-75-6212 
        4.31        50.33        11.18        66.64        43.82        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 
       36.66       108.66        21.90        39.95       119.51        38.50 
TCGA-78-7159 TCGA-78-7167 TCGA-78-7536 TCGA-78-7542 TCGA-78-8640 TCGA-78-8662 
       64.90        88.14         8.02        10.55       232.18       110.50 
TCGA-86-6851 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 
        5.88        38.04        32.78        19.89        37.74         4.08 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 TCGA-86-8668 
        0.79        22.82        31.20        23.05        11.61        13.91 
TCGA-86-8669 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-91-6847 
       30.84        29.46         3.81        24.23        13.64        27.68 
TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BD TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
        7.36         1.18        19.82        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       27.29         2.76        42.25        25.48        18.54         0.59 
TCGA-97-8171 TCGA-97-8547 TCGA-97-A4M0 TCGA-99-7458 TCGA-99-8032 TCGA-J2-A4AD 
       18.67        21.60        21.44        24.56         1.45        18.08 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
       35.47        19.00        14.53         1.91        18.58        15.65 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 
       38.63         2.76        86.14        58.45        86.04         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ 
       41.59        11.05        11.15        71.05         0.13        47.08 
TCGA-NJ-A55O TCGA-O1-A52J 
        0.43        59.11 

$`DEL PEAK 15(8P23.2) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 
       19.96        14.01         9.96        20.05         9.01        15.02 
TCGA-05-5420 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 
       15.02        26.30        43.53        38.10        23.93        86.01 
TCGA-44-7661 TCGA-44-7671 TCGA-44-A47F TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 
       18.31        29.23        11.08        16.04        17.16       156.66 
TCGA-50-5935 TCGA-55-6978 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-8090 
       21.47         5.79         7.99        23.18        14.53        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
       19.73        17.98        18.15        13.68        16.93        22.65 
TCGA-55-A492 TCGA-55-A4DF TCGA-73-4658 TCGA-78-7166 TCGA-78-7633 TCGA-91-7771 
       19.59        20.19        52.60         8.48        50.24        16.18 
TCGA-91-A4BC TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-L9-A443 TCGA-L9-A743 
        1.45        17.92        20.19        20.52         6.35        21.83 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4397 TCGA-05-4403 
       27.19         5.29        10.09         3.98        24.03        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 
        2.99        14.96        12.00        30.02        26.01        25.02 
TCGA-05-4432 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 
       25.02         4.96         9.04         2.04         0.46         8.68 
TCGA-38-4626 TCGA-38-4632 TCGA-38-A44F TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 
      120.79        44.61         4.37        44.94        42.77         3.19 
TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 TCGA-44-5645 TCGA-44-6148 TCGA-44-6778 
       37.15        38.24        26.56        28.01        23.15        61.28 
TCGA-44-7659 TCGA-44-7667 TCGA-44-7669 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       22.72        36.07        18.87        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 
       13.64        13.45        76.21        35.54        32.84         8.81 
TCGA-49-4514 TCGA-49-6744 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARE TCGA-49-AARQ 
       55.89        55.33        73.12        62.24        40.41       221.33 
TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5051 TCGA-50-5055 TCGA-50-5936 
      164.12         9.86        20.52        15.72        60.16         8.45 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 
       60.72        57.53        53.16        42.35        25.55         6.21 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-55-6543 TCGA-55-6642 
       36.99        36.79        27.25        13.94        14.30        80.52 
TCGA-55-6712 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6983 TCGA-55-6984 
        5.62        15.25        46.03        53.65        92.81        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
      107.21        70.26        28.67        23.15        25.41        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 TCGA-55-8206 
       34.19        17.65        15.19        23.08        17.79        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 
       22.16        15.42        14.47        13.74        20.28        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A494 
       26.01        17.10        14.66        12.33        21.40        15.81 
TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y 
       14.60        88.64        19.53        54.35        72.30        13.61 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 TCGA-64-5781 
       39.25        40.96        37.02        87.98        28.41        51.25 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 
       14.04        12.66        14.73         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-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-75-5146 
       23.38        26.30        30.31         9.24         1.25        77.85 
TCGA-75-6206 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       85.15       100.57       163.10        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 
       20.58       129.53        19.50        32.09         5.88        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 
        9.57       104.19       238.29        26.53        31.20        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-83-5908 
       26.01        39.35        39.75        77.59        93.11        27.09 
TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7955 TCGA-86-8056 
       12.36        31.13        34.39        20.55        35.24         4.57 
TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 TCGA-86-8359 TCGA-86-8671 
       24.33        32.65        31.04        21.47        14.60        27.58 
TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
        0.62        28.34        26.50        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6849 TCGA-91-8496 
        1.97        10.19         2.60        12.23         1.15        16.60 
TCGA-91-8497 TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP 
       14.27        22.45        17.46        23.61         1.08        19.00 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8174 
       19.89        64.60        63.52        61.48        15.91         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 
       18.12        15.39        16.41        14.30        20.58        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-99-AA5R 
       20.84        18.67        34.85        36.76        21.57        21.63 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4TE 
       32.48        14.30        49.35        37.35        58.85        29.46 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP 
       24.36        14.10        19.13        73.91        74.33         1.64 
TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.49        19.82        20.28        16.87 

  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                         0.00                          0.46 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                       232.18                        238.29 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                       22.145                        20.710 
[1] "0.0 - 232.2 (22.1)" "0.5 - 238.3 (20.7)"
[1] "hr=" "1.1"
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 15(8P23.2) MUTATED         3       62       68        1        27
  DEL PEAK 15(8P23.2) WILD-TYPE       2       71       71        0        23
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 15(8P23.2) MUTATED          41         34          4       11
  DEL PEAK 15(8P23.2) WILD-TYPE        31         38          7       14
D44V3, multiclass
            clus
vv           DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            62                            71
  STAGE IB                            68                            71
  STAGE II                             1                             0
  STAGE IIA                           27                            23
  STAGE IIB                           41                            31
  STAGE IIIA                          34                            38
  STAGE IIIB                           4                             7
  STAGE IV                            11                            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 15(8P23.2) MUTATED    85 141  22   6
  DEL PEAK 15(8P23.2) WILD-TYPE  86 137  24  13
D44V4, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  T1                          85                            86
  T2                         141                           137
  T3                          22                            24
  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   163  47    39
  DEL PEAK 15(8P23.2) WILD-TYPE 170  49    37
D44V5, multiclass
       clus
vv      DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  N0                            163                           170
  N1                             47                            49
  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"
D44V6, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.2) MUTATED   173  11
  DEL PEAK 15(8P23.2) WILD-TYPE 176  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED    173   11
  DEL PEAK 15(8P23.2) WILD-TYPE  176   14
   clus
vv  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  0                         173                           176
  1                          11                            14
[1] 2 2
[1] FALSE
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.2) MUTATED   148 106
  DEL PEAK 15(8P23.2) WILD-TYPE 128 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED    148  106
  DEL PEAK 15(8P23.2) WILD-TYPE  128  134
        clus
vv       DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  FEMALE                         148                           128
  MALE                           106                           134
[1] 2 2
[1] FALSE
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.2) MUTATED   203  32
  DEL PEAK 15(8P23.2) WILD-TYPE 207  28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED    203   32
  DEL PEAK 15(8P23.2) WILD-TYPE  207   28
     clus
vv    DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  NO                          203                           207
  YES                          32                            28
[1] 2 2
[1] FALSE
D44V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                            7
  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                                                  169
  DEL PEAK 15(8P23.2) WILD-TYPE                                                152
                               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                              0
  DEL PEAK 15(8P23.2) WILD-TYPE                            2
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 15(8P23.2) MUTATED                              10
  DEL PEAK 15(8P23.2) WILD-TYPE                            13
                               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
D44V10, multiclass
                                                    clus
vv                                                   DEL PEAK 15(8P23.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           47
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         169
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                8
  LUNG CLEAR CELL ADENOCARCINOMA                                               2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           3
  LUNG MUCINOUS ADENOCARCINOMA                                                 0
  LUNG PAPILLARY ADENOCARCINOMA                                               10
  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)                           152
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 11
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             0
  LUNG MUCINOUS ADENOCARCINOMA                                                   2
  LUNG PAPILLARY ADENOCARCINOMA                                                 13
  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"
D44V11, continuous
D44V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(8P23.2) MUTATED   163   6   2  16
  DEL PEAK 15(8P23.2) WILD-TYPE 181   7   2  10
D44V13, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  R0                         163                           181
  R1                           6                             7
  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     6
  DEL PEAK 15(8P23.2) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(8P23.2) MUTATED                          25   191
  DEL PEAK 15(8P23.2) WILD-TYPE                        27   199
D44V14, multiclass
                                  clus
vv                                 DEL PEAK 15(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      6
  BLACK OR AFRICAN AMERICAN                                 25
  WHITE                                                    191
                                  clus
vv                                 DEL PEAK 15(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   27
  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"
D44V15, binary
                               cls
clus                              0   1
  DEL PEAK 15(8P23.2) MUTATED     5 195
  DEL PEAK 15(8P23.2) WILD-TYPE   2 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED      5  195
  DEL PEAK 15(8P23.2) WILD-TYPE    2  189
                        clus
vv                       DEL PEAK 15(8P23.2) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                         195
                        clus
vv                       DEL PEAK 15(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           189
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 16(8P11.21) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(8P11.21) MUTATED    77  46
  DEL PEAK 16(8P11.21) WILD-TYPE 246 135
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                           123                            381 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                            46                            135 
$`DEL PEAK 16(8P11.21) MUTATED`
TCGA-05-4402 TCGA-38-4631 TCGA-38-6178 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 
        8.02        11.64        14.73        46.72        16.04        17.16 
TCGA-49-6761 TCGA-49-AARN TCGA-50-5932 TCGA-50-6597 TCGA-55-1595 TCGA-55-6979 
       11.64        37.32        40.60        41.69        48.62         7.79 
TCGA-55-7573 TCGA-55-7726 TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 TCGA-91-7771 
       16.01        21.44        13.87        82.68        39.09        16.18 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-97-A4M3 TCGA-97-A4M7 
       17.29         2.86        15.68        21.40        17.75        20.68 
TCGA-J2-8192 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4420 TCGA-05-4425 
       24.30         5.29         2.43        50.07        29.98        21.99 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2668 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 
       46.98        44.42        25.02        28.37        23.77        19.56 
TCGA-44-6775 TCGA-44-6777 TCGA-44-7662 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 
       23.18        32.45         7.17        23.64         8.55        15.98 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-6743 
       13.45        28.11        12.66        14.07         8.81        53.29 
TCGA-49-6744 TCGA-49-AARQ TCGA-50-5049 TCGA-50-5933 TCGA-50-5939 TCGA-50-6591 
       55.33       221.33       101.72        78.67        15.12         3.91 
TCGA-53-7813 TCGA-55-1596 TCGA-55-6972 TCGA-55-6975 TCGA-55-6985 TCGA-55-7283 
       13.94        67.89        53.65         3.88        40.54        20.02 
TCGA-55-7913 TCGA-55-7994 TCGA-55-8097 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 
       18.44        19.82        15.65        15.72         0.36        17.72 
TCGA-55-8615 TCGA-55-A490 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8402 TCGA-62-A46O 
       14.66         3.25        19.99         4.57        49.25        47.80 
TCGA-62-A46R TCGA-62-A46U TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-67-3770 
       56.71        67.96        29.92        39.09        81.80        20.05 
TCGA-69-7978 TCGA-69-7980 TCGA-69-A59K TCGA-71-6725 TCGA-73-4668 TCGA-73-4670 
        4.41        13.51        19.43         8.42        15.35         4.31 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-6212 TCGA-75-7025 TCGA-78-7146 
       50.33        11.18        66.64        49.84       108.66         5.69 
TCGA-78-7161 TCGA-78-8640 TCGA-86-7711 TCGA-86-7953 TCGA-86-8054 TCGA-86-8074 
        9.57       232.18        34.39        32.78        37.74         0.79 
TCGA-86-8280 TCGA-86-8359 TCGA-86-8668 TCGA-86-A456 TCGA-86-A4JF TCGA-91-6847 
       23.05        14.60        13.91        29.46        24.23        27.68 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 
       41.82        18.67        12.39        27.29         2.76        42.25 
TCGA-97-7938 TCGA-97-8547 TCGA-97-A4M0 TCGA-99-8025 TCGA-L4-A4E5 TCGA-L9-A50W 
        0.59        21.60        21.44        34.85        19.00        14.53 
TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T7 
        1.91        15.65        38.63        58.45        86.04         5.49 
TCGA-MP-A4T9 TCGA-NJ-A4YQ TCGA-O1-A52J 
       41.59        47.08        59.11 

$`DEL PEAK 16(8P11.21) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 
       15.02        15.02        28.41        35.28        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       38.10        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-AAR0 TCGA-50-5935 
       29.00        29.23         9.37        11.08       156.66        21.47 
TCGA-55-1592 TCGA-55-6978 TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-7914 
       23.05         5.79         7.99        23.18        14.53         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       19.66        19.73        17.98        16.93        19.69        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
       18.15        13.68        16.93        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       20.19        20.65        52.60         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7043 TCGA-95-7948 
       85.32        13.71         1.45         6.12        16.54        15.65 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-J2-8194 TCGA-L9-A443 
       18.18        17.92        20.19        20.52        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4250 
       10.09        21.83        27.19        31.23        10.09         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       45.01        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4426 TCGA-05-4430 
        2.99        14.96        12.00        30.02        26.01        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        2.04         0.46         7.40         5.98         8.68        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2659 
      120.79        37.71        49.05        44.61         4.37        44.94 
TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 
       42.77         3.19        37.15        38.24        38.89        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6148 TCGA-44-6774 
       33.73        26.56        33.30        28.01        23.15        21.63 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       61.28        16.44        22.72        19.46        36.07        18.87 
TCGA-44-8117 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 
       12.66        15.32         9.44        11.54        13.64        76.21 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       28.57        35.54        32.84        29.46        29.75        55.89 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26        22.26        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
       40.41       123.58       164.12         9.86        20.52        71.47 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5931 TCGA-50-5936 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
       14.27         8.45        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
       42.35        25.55        11.05        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
       10.13        36.99        36.79        27.25        34.29        30.54 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       35.21        38.73        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6980 TCGA-55-6981 
       42.51        40.73        15.25        46.03        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       32.71        92.81        24.99       107.21        70.26        28.67 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7995 TCGA-55-8085 
       18.64        11.28        34.19        17.65        29.23        29.72 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 
       15.19        23.08         5.06        17.79        23.64        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
       22.16        15.42        17.56        14.47        13.74        20.28 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 
       19.96        26.01        17.10        17.62         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 
       20.71        21.40         0.92        15.81        17.95        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P TCGA-62-A46S TCGA-62-A46V 
       42.38        14.60        88.64        19.53        54.35        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1680 TCGA-64-1681 
       13.61        39.25        40.96        56.81        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-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       20.05        18.84        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        7.56         6.05        13.41        14.01        13.45         4.24 
TCGA-69-8453 TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       26.73        23.38        26.30        30.31         9.24         1.25 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 
       77.85        43.82        85.15        36.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
      119.51        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 
       22.92       104.19       238.29        88.14        26.53        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
        8.02        53.33        26.01        39.35        10.55        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 
       77.59       110.50        93.11        27.09        12.36         5.88 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
       31.13        38.04        20.55        19.89        35.24         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 
        4.57        24.33        22.82        32.65        31.04        31.20 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       21.47        11.61        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
       26.50         3.81        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 
        1.97        10.19         2.60        12.23         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
       23.61         1.08        19.00        19.89        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       61.48        25.48        18.54        15.91        18.67         5.39 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 
       18.12        15.39        16.41        14.30        20.58        19.76 
TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       20.84        18.67        24.56        36.76         1.45        21.57 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A7SV 
       21.63        18.08        35.47        32.48        14.30        18.58 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4TE 
        2.76        86.14        49.35        37.35        58.85        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
       11.05        24.36        14.10        11.15        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       71.05        74.33         0.13         1.64         0.49         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       19.82        20.28        16.87 

  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                          0.36                           0.00 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                        232.18                         238.29 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                         20.68                          22.03 
[1] "0.4 - 232.2 (20.7)" "0.0 - 238.3 (22.0)"
[1] "hr=" "1"  
D45V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 16(8P11.21) MUTATED         3       30       29        0        12
  DEL PEAK 16(8P11.21) WILD-TYPE       2      103      110        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        49         54          8       19
D45V3, multiclass
            clus
vv           DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             30                            103
  STAGE IB                             29                            110
  STAGE II                              0                              1
  STAGE IIA                            12                             38
  STAGE IIB                            23                             49
  STAGE IIIA                           18                             54
  STAGE IIIB                            3                              8
  STAGE IV                              6                             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 16(8P11.21) MUTATED    38  68  16   3
  DEL PEAK 16(8P11.21) WILD-TYPE 133 210  30  16
D45V4, multiclass
    clus
vv   DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  T1                           38                            133
  T2                           68                            210
  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    77  25    20
  DEL PEAK 16(8P11.21) WILD-TYPE 256  71    56
D45V5, multiclass
       clus
vv      DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  N0                              77                            256
  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"
D45V6, binary
                                cls
clus                               0   1
  DEL PEAK 16(8P11.21) MUTATED    80   6
  DEL PEAK 16(8P11.21) WILD-TYPE 269  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED     80    6
  DEL PEAK 16(8P11.21) WILD-TYPE  269   19
   clus
vv  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  0                           80                            269
  1                            6                             19
[1] 2 2
[1] FALSE
D45V7, binary
                                cls
clus                               0   1
  DEL PEAK 16(8P11.21) MUTATED    79  46
  DEL PEAK 16(8P11.21) WILD-TYPE 197 194
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED     79   46
  DEL PEAK 16(8P11.21) WILD-TYPE  197  194
        clus
vv       DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  FEMALE                           79                            197
  MALE                             46                            194
[1] 2 2
[1] FALSE
D45V8, binary
                                cls
clus                               0   1
  DEL PEAK 16(8P11.21) MUTATED   107  12
  DEL PEAK 16(8P11.21) WILD-TYPE 303  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED    107   12
  DEL PEAK 16(8P11.21) WILD-TYPE  303   48
     clus
vv    DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  NO                           107                            303
  YES                           12                             48
[1] 2 2
[1] FALSE
D45V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 16(8P11.21) MUTATED                            4
  DEL PEAK 16(8P11.21) WILD-TYPE                         14
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 16(8P11.21) MUTATED                                  24
  DEL PEAK 16(8P11.21) WILD-TYPE                                83
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 16(8P11.21) MUTATED                                                   83
  DEL PEAK 16(8P11.21) WILD-TYPE                                                238
                                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
D45V10, multiclass
                                                    clus
vv                                                   DEL PEAK 16(8P11.21) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           83
  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                                                     14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            238
  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"
D45V11, continuous
D45V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 16(8P11.21) MUTATED    75   4   1  11
  DEL PEAK 16(8P11.21) WILD-TYPE 269   9   3  15
D45V13, multiclass
    clus
vv   DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  R0                           75                            269
  R1                            4                              9
  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                          12    95
  DEL PEAK 16(8P11.21) WILD-TYPE                        40   295
D45V14, multiclass
                                  clus
vv                                 DEL PEAK 16(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      95
                                  clus
vv                                 DEL PEAK 16(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    40
  WHITE                                                       295
[1] 4 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 16(8P11.21) MUTATED     2  99
  DEL PEAK 16(8P11.21) WILD-TYPE   5 285
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED      2   99
  DEL PEAK 16(8P11.21) WILD-TYPE    5  285
                        clus
vv                       DEL PEAK 16(8P11.21) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           99
                        clus
vv                       DEL PEAK 16(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            285
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 17(9P23) MUTATION ANALYSIS
D46V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 17(9P23) MUTATED   171 111
  DEL PEAK 17(9P23) WILD-TYPE 152  70
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                        282                         222 
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                        111                          70 
$`DEL PEAK 17(9P23) MUTATED`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-5420 
       14.01         9.96         8.02        20.05         9.01        15.02 
TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 
       35.28        11.64        14.73        43.53        38.10        42.08 
TCGA-44-6146 TCGA-44-7670 TCGA-44-7671 TCGA-49-4501 TCGA-49-6742 TCGA-49-AAR0 
       23.93        29.00        29.23        46.72        16.04       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-7573 
       37.32        40.60        21.47        41.69        23.05        16.01 
TCGA-55-7724 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       23.18        21.44        19.66        19.73        17.98        16.93 
TCGA-55-8207 TCGA-55-A48X TCGA-55-A492 TCGA-67-6217 TCGA-73-4662 TCGA-78-7166 
       32.12        22.65        19.59        13.87        82.68         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-91-6836 TCGA-93-8067 TCGA-95-7562 TCGA-95-A4VK 
       50.24        10.55        13.71         6.12         2.86        21.40 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       20.68        24.30        21.83        27.19         5.29        31.23 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 
       10.09        50.07         3.98        45.01        37.02         0.00 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
        2.99        29.98        30.02        25.02        24.00         4.96 
TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-4122 TCGA-38-4627 TCGA-38-4628 
       29.00         9.04         2.04         7.40        37.71        49.05 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2668 
       44.61         4.37        44.42        44.94        42.77        25.02 
TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6777 TCGA-44-6778 
       38.89        33.30        28.37        23.77        32.45        61.28 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 
       16.44         7.17        36.07        18.87        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-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 TCGA-49-6767 
       14.07         8.81        29.46        55.89        53.29        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO 
       22.26        73.12        62.24        28.90         8.55       123.58 
TCGA-50-5044 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       20.52        60.16        49.28         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 
       78.67         8.45        15.12        57.53        53.16        25.55 
TCGA-50-6593 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
       11.05         0.72        10.13        36.79        27.25        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 
       13.94        35.21        38.73        67.89        30.58        80.52 
TCGA-55-6712 TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
        5.62        46.03         3.88        69.34        45.34        32.71 
TCGA-55-6985 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 
       40.54       107.21        28.67        20.02        27.09        22.03 
TCGA-55-7907 TCGA-55-7913 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
       11.28        18.44        23.08         5.06        17.79        15.65 
TCGA-55-8206 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 
       29.19        14.47         0.36        13.74        17.72        19.96 
TCGA-55-8614 TCGA-55-8615 TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B 
       17.62        14.66         3.25         0.92        19.99        17.95 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O 
       39.98        42.38        14.60        88.64        49.25        47.80 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 
       72.30        13.61        40.96        29.92        39.09        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       37.02        38.37        51.25        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       18.84        12.66         4.64         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7974 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-73-4666 
       13.61         6.05        13.45         4.24        26.73        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5147 
       15.35         4.31        30.31        50.33        11.18        43.82 
TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       49.84       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7156 TCGA-78-7160 
       19.27        20.58       129.53        21.90        32.09        22.92 
TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        9.57        88.14        26.53        39.35        10.55       232.18 
TCGA-78-8655 TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
       77.59       110.50         5.88        34.39        38.04        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 
       19.89        35.24        37.74         4.08         4.57         0.79 
TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 
       22.82        31.20        23.05        21.47        11.61        13.91 
TCGA-86-8672 TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 
        0.62        29.46        41.36         1.97         2.60        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        17.46 
TCGA-93-A4JN TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7937 
       23.61        18.67        27.29         2.76        19.89        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.59        15.91         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M6 
       14.30        21.60        20.58        21.44        19.76        18.67 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A50W TCGA-L9-A7SV 
        1.45        21.57        18.08        32.48        14.53        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       15.65        38.63         2.76        86.14        58.45        49.35 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TK TCGA-MP-A5C7 
       58.85         5.49        41.59        29.46        19.13        73.91 
TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
       71.05         0.13        47.08         0.43        20.28        59.11 

$`DEL PEAK 17(9P23) WILD-TYPE`
TCGA-05-4382 TCGA-05-4427 TCGA-05-4434 TCGA-38-4629 TCGA-38-7271 TCGA-44-6147 
       19.96        26.01        15.02        28.41        26.30        27.78 
TCGA-44-6776 TCGA-44-7661 TCGA-44-8119 TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 
       86.01        18.31         9.37        11.08        17.16        11.64 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7725 TCGA-55-7914 
       48.62         5.79         7.79         7.99        14.53         6.15 
TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A491 TCGA-55-A4DF 
       19.69        18.15        13.68        16.93        20.58        20.19 
TCGA-64-1677 TCGA-73-4658 TCGA-73-7498 TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC 
       20.65        52.60        39.09        85.32        16.18         1.45 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VN TCGA-97-8172 
       17.29        16.54        15.68        15.65        18.18        17.92 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 
       20.19        20.52        17.75        23.80         6.35        10.09 
TCGA-MP-A4TC TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 
        2.43        24.03        47.05        19.00        14.96        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-5428 TCGA-35-3615 TCGA-35-4123 
       21.99        26.01        25.02        22.03         0.46         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-44-2656 TCGA-44-2666 TCGA-44-3396 
        8.68        97.74       120.79        46.98         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        33.73        26.56        28.01        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-7659 TCGA-44-7660 TCGA-44-7672 
       23.15        21.63        23.18        22.72        19.46        23.64 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4488 TCGA-49-4506 
       15.98        15.32         9.44        11.54        28.57        32.84 
TCGA-49-4512 TCGA-49-6744 TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       29.75        55.33        40.41       221.33       164.12         9.86 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5941 TCGA-50-5942 
       71.47       101.72        15.72        47.41        48.46        60.72 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6594 TCGA-50-6595 TCGA-50-8457 TCGA-53-7624 
       42.35         3.91        12.16         6.21        36.99        34.29 
TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6983 
       14.30        42.51        40.73        15.25        53.65        92.81 
TCGA-55-6984 TCGA-55-6987 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       24.99        70.26        32.71         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       18.64        34.19        17.65        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8096 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.19        23.64        22.16        15.42        17.56        15.72 
TCGA-55-8508 TCGA-55-8513 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y 
       20.28        26.01        17.10         1.58        12.33        20.71 
TCGA-55-A48Z TCGA-55-A494 TCGA-62-8394 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       21.40        15.81         4.57        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A470 TCGA-64-1676 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       67.96        39.25        56.81        87.98         2.04        42.90 
TCGA-64-5779 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-69-7765 TCGA-69-7973 
       28.41        14.04        14.73         5.72         5.42         7.56 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-A59K TCGA-71-6725 
        4.41        13.41        13.51        14.01        19.43         8.42 
TCGA-73-4659 TCGA-73-4676 TCGA-73-4677 TCGA-75-5125 TCGA-75-5146 TCGA-75-6206 
       23.38         9.24         1.25        66.64        77.85        85.15 
TCGA-75-6214 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 
       36.66        39.95       119.51        19.50        38.50         5.88 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
       64.90       104.19       238.29        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-8648 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-7701 
       26.01        39.75        93.11        27.09        12.36        31.13 
TCGA-86-7714 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 TCGA-86-8669 
       20.55        24.33        32.65        31.04        14.60        30.84 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
       27.58        28.34        26.50         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6831 TCGA-91-8496 TCGA-91-A4BD TCGA-93-7347 
       26.47        10.62        10.19        16.60        19.82        22.45 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-97-7546 TCGA-97-7547 
        1.08        19.00        41.82        12.39        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-8171 TCGA-97-A4M5 TCGA-99-7458 
       63.52        61.48        25.48        18.67        20.84        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 
       34.85        36.76        21.63        35.47        19.00        14.30 
TCGA-L9-A5IP TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
        1.91        37.35        86.04        11.05        24.36        14.10 
TCGA-MP-A4TJ TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55R TCGA-S2-AA1A 
       11.15        74.33         1.64         0.49        19.82        16.87 

  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                       0.00                        0.46 
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                     232.18                      238.29 
  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE 
                     21.715                      21.515 
[1] "0.0 - 232.2 (21.7)" "0.5 - 238.3 (21.5)"
[1] "hr=" "1.3"
D46V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 17(9P23) MUTATED         2       68       72        1        31
  DEL PEAK 17(9P23) WILD-TYPE       3       65       67        0        19
                             vv
clus                          STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 17(9P23) MUTATED          45         43          7       15
  DEL PEAK 17(9P23) WILD-TYPE        27         29          4       10
D46V3, multiclass
            clus
vv           DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  STAGE I                            2                           3
  STAGE IA                          68                          65
  STAGE IB                          72                          67
  STAGE II                           1                           0
  STAGE IIA                         31                          19
  STAGE IIB                         45                          27
  STAGE IIIA                        43                          29
  STAGE IIIB                         7                           4
  STAGE IV                          15                          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 17(9P23) MUTATED    92 156  26  12
  DEL PEAK 17(9P23) WILD-TYPE  79 122  20   7
D46V4, multiclass
    clus
vv   DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  T1                        92                          79
  T2                       156                         122
  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   171  68    43
  DEL PEAK 17(9P23) WILD-TYPE 162  28    33
D46V5, multiclass
       clus
vv      DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  N0                          171                         162
  N1                           68                          28
  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"
D46V6, binary
                             cls
clus                            0   1
  DEL PEAK 17(9P23) MUTATED   195  15
  DEL PEAK 17(9P23) WILD-TYPE 154  10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(9P23) MUTATED    195   15
  DEL PEAK 17(9P23) WILD-TYPE  154   10
   clus
vv  DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  0                       195                         154
  1                        15                          10
[1] 2 2
[1] FALSE
D46V7, binary
                             cls
clus                            0   1
  DEL PEAK 17(9P23) MUTATED   148 139
  DEL PEAK 17(9P23) WILD-TYPE 128 101
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(9P23) MUTATED    148  139
  DEL PEAK 17(9P23) WILD-TYPE  128  101
        clus
vv       DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  FEMALE                       148                         128
  MALE                         139                         101
[1] 2 2
[1] FALSE
D46V8, binary
                             cls
clus                            0   1
  DEL PEAK 17(9P23) MUTATED   223  39
  DEL PEAK 17(9P23) WILD-TYPE 187  21
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(9P23) MUTATED    223   39
  DEL PEAK 17(9P23) WILD-TYPE  187   21
     clus
vv    DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  NO                        223                         187
  YES                        39                          21
[1] 2 2
[1] FALSE
D46V9, continuous
                             vv
clus                          LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 17(9P23) MUTATED                           12
  DEL PEAK 17(9P23) WILD-TYPE                          6
                             vv
clus                          LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 17(9P23) MUTATED                                  62
  DEL PEAK 17(9P23) WILD-TYPE                                45
                             vv
clus                          LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 17(9P23) MUTATED                                                  178
  DEL PEAK 17(9P23) WILD-TYPE                                                143
                             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
D46V10, multiclass
                                                    clus
vv                                                   DEL PEAK 17(9P23) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                         62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                       178
  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                                           45
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         143
  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"
D46V11, continuous
D46V12, continuous
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 17(9P23) MUTATED   190   6   2  18
  DEL PEAK 17(9P23) WILD-TYPE 154   7   2   8
D46V13, multiclass
    clus
vv   DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  R0                       190                         154
  R1                         6                           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                          30   215
  DEL PEAK 17(9P23) WILD-TYPE                        22   175
D46V14, multiclass
                                  clus
vv                                 DEL PEAK 17(9P23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               30
  WHITE                                                  215
                                  clus
vv                                 DEL PEAK 17(9P23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                    175
[1] 4 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 17(9P23) MUTATED     4 208
  DEL PEAK 17(9P23) WILD-TYPE   3 176
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(9P23) MUTATED      4  208
  DEL PEAK 17(9P23) WILD-TYPE    3  176
                        clus
vv                       DEL PEAK 17(9P23) MUTATED DEL PEAK 17(9P23) WILD-TYPE
  HISPANIC OR LATINO                             4                           3
  NOT HISPANIC OR LATINO                       208                         176
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 18(9P21.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(9P21.3) MUTATED   172 116
  DEL PEAK 18(9P21.3) WILD-TYPE 151  65
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          288                           216 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                          116                            65 
$`DEL PEAK 18(9P21.3) MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-44-2655 TCGA-44-2661 
       15.02        28.41        11.64        14.73        43.53        38.10 
TCGA-44-2662 TCGA-44-6146 TCGA-44-7670 TCGA-44-7671 TCGA-49-4501 TCGA-49-6742 
       42.08        23.93        29.00        29.23        46.72        16.04 
TCGA-49-6745 TCGA-49-AAR0 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       17.16       156.66        40.60        21.47        41.69        23.05 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
        7.99        16.01        23.18        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-A48X TCGA-55-A492 
       19.73        17.98        16.93        32.12        22.65        19.59 
TCGA-67-6217 TCGA-73-4662 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       13.87        82.68         8.48        50.24        10.55        85.32 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-A4VK TCGA-97-A4M7 TCGA-J2-8192 
        6.12        17.29         2.86        21.40        20.68        24.30 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 
       21.83        27.19         5.29        31.23        10.09        50.07 
TCGA-05-4250 TCGA-05-4389 TCGA-05-4395 TCGA-05-4403 TCGA-05-4415 TCGA-05-4420 
        3.98        45.01         0.00        19.00         2.99        29.98 
TCGA-05-4424 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
       30.02        25.02        24.00         4.96        29.00         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 
        2.04         7.40        97.74        37.71        49.05        44.61 
TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2668 TCGA-44-3917 
        4.37        44.42        44.94        42.77        25.02        38.89 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       33.30        28.37        23.77        32.45        61.28        16.44 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS 
        7.17        36.07        18.87        12.66         8.55        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 
       13.45        76.21        28.11        12.66        35.54        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 TCGA-49-6767 
       32.84         8.81        29.46        55.89        53.29        22.26 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO 
       22.26        73.12        62.24        28.90         8.55       123.58 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       60.16        49.28         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 TCGA-50-6593 
        8.45        15.12        57.53        53.16        25.55        11.05 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
        0.72        10.13        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 
       13.94        38.73        67.89        30.58        80.52         5.62 
TCGA-55-6971 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 
       46.03         3.88        69.34        45.34        32.71        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7576 
      107.21        70.26        28.67        20.02        27.09        22.03 
TCGA-55-7907 TCGA-55-7913 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8097 
       11.28        18.44        23.08         5.06        17.79        15.65 
TCGA-55-8206 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 
       29.19        14.47         0.36        13.74        17.72        19.96 
TCGA-55-8614 TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 
       17.62         3.25         0.92        19.99        17.95        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46V 
       42.38        14.60        88.64        49.25        47.80        72.30 
TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       13.61        40.96        29.92        56.81        39.09        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       37.02        38.37        51.25        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-3774 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
       18.84        12.66         4.64         6.64         6.12        22.68 
TCGA-69-7764 TCGA-69-7974 TCGA-69-7980 TCGA-69-8255 TCGA-69-8453 TCGA-73-4668 
       13.61         6.05        13.51         4.24        26.73        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-6212 
        4.31        30.31        50.33        11.18        66.64        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 
       36.66       108.66       100.57       163.10        27.16         5.69 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7156 TCGA-78-7160 
       19.27        20.58       129.53        21.90        32.09        22.92 
TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        9.57        88.14        26.53        39.35        10.55       232.18 
TCGA-78-8655 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 
       77.59        12.36         5.88        34.39        38.04        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 
       35.24        37.74         4.08         4.57         0.79        22.82 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8672 
       31.20        23.05        21.47        11.61        13.91         0.62 
TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       29.46        41.36         1.97        10.19         2.60        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        17.46 
TCGA-93-A4JN TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 
       23.61        18.67        27.29         2.76        19.89        64.60 
TCGA-97-7552 TCGA-97-7937 TCGA-97-7938 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 
       63.52        18.54         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-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A50W 
       18.67         1.45        21.57        18.08        32.48        14.53 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       18.58        15.65        38.63         2.76        86.14        58.45 
TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       49.35        58.85         5.49        41.59        29.46        11.05 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A7XG TCGA-O1-A52J 
       19.13        73.91         0.13        47.08        20.28        59.11 

$`DEL PEAK 18(9P21.3) WILD-TYPE`
TCGA-05-4427 TCGA-05-4434 TCGA-38-4630 TCGA-38-7271 TCGA-44-6147 TCGA-44-6776 
       26.01        15.02        35.28        26.30        27.78        86.01 
TCGA-44-7661 TCGA-44-8119 TCGA-44-A47F TCGA-49-6761 TCGA-49-AARN TCGA-55-1595 
       18.31         9.37        11.08        11.64        37.32        48.62 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7725 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 
        5.79         7.79        14.53        19.69        18.15        13.68 
TCGA-55-8621 TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-7498 
       16.93        20.58        20.19        20.65        52.60        39.09 
TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 
       13.71        16.18         1.45        16.54        15.68        15.65 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8194 
       18.18        17.92        20.19        20.52        17.75        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4TC TCGA-05-4390 TCGA-05-4397 TCGA-05-4398 
        6.35        10.09         2.43        37.02        24.03        47.05 
TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-5428 
       14.96        12.00        21.99        26.01        25.02        22.03 
TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 TCGA-38-4626 TCGA-44-2656 TCGA-44-2666 
        0.46         5.98         8.68       120.79        46.98         3.19 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       37.15        38.24        34.06        33.73        26.56        28.01 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-7659 TCGA-44-7660 
       19.56        23.15        21.63        23.18        22.72        19.46 
TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4488 
       23.64        15.98        15.32         9.44        11.54        28.57 
TCGA-49-4512 TCGA-49-6744 TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       29.75        55.33        40.41       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5941 
       20.52        71.47       101.72        15.72        47.41        48.46 
TCGA-50-5942 TCGA-50-6590 TCGA-50-6591 TCGA-50-6594 TCGA-50-6595 TCGA-50-8457 
       60.72        42.35         3.91        12.16         6.21        36.99 
TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 
       35.21        14.30        42.51        40.73        15.25        53.65 
TCGA-55-6983 TCGA-55-6984 TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       92.81        24.99        32.71         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       18.64        34.19        17.65        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8096 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       15.19        23.64        22.16        15.42        17.56        15.72 
TCGA-55-8508 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       20.28        26.01        17.10        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A494 TCGA-62-8394 TCGA-62-A46P TCGA-62-A46R 
       20.71        21.40        15.81         4.57        19.53        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 
       54.35        67.96        39.25        87.98         2.04        42.90 
TCGA-64-5779 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-69-7765 TCGA-69-7973 
       28.41        14.04        14.73         5.72         5.42         7.56 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-A59K TCGA-71-6725 
        4.41        13.41        14.01        13.45        19.43         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4676 TCGA-73-4677 TCGA-75-5146 TCGA-75-5147 
       23.38        26.30         9.24         1.25        77.85        43.82 
TCGA-75-6206 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 
       85.15        39.95       119.51        19.50        38.50         5.88 
TCGA-78-7159 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
       64.90       104.19       238.29        31.20         8.02        53.33 
TCGA-78-7539 TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 
       26.01        39.75       110.50        93.11        27.09        31.13 
TCGA-86-7714 TCGA-86-7953 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 
       20.55        32.78        24.33        32.65        31.04        14.60 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF 
       30.84        27.58        28.34        26.50         3.81        24.23 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-8496 TCGA-91-A4BD TCGA-93-7347 
       13.64        26.47        10.62        16.60        19.82        22.45 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-97-7546 TCGA-97-7553 
        1.08        19.00        41.82        12.39        42.25        61.48 
TCGA-97-7554 TCGA-97-7941 TCGA-97-8171 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 
       25.48        15.91        18.67        20.84        24.56        34.85 
TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A5IP 
       36.76        21.63        35.47        19.00        14.30         1.91 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-NJ-A4YF 
       37.35        86.04        24.36        14.10        11.15        71.05 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
       74.33         1.64         0.49         0.43        19.82        16.87 

  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                         0.00                          0.43 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                       232.18                        238.29 
  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE 
                       21.585                        21.630 
[1] "0.0 - 232.2 (21.6)" "0.4 - 238.3 (21.6)"
[1] "hr=" "1.3"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 18(9P21.3) MUTATED         3       67       74        1        32
  DEL PEAK 18(9P21.3) WILD-TYPE       2       66       65        0        18
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 18(9P21.3) MUTATED          49         45          6       15
  DEL PEAK 18(9P21.3) WILD-TYPE        23         27          5       10
D47V3, multiclass
            clus
vv           DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  STAGE I                              3                             2
  STAGE IA                            67                            66
  STAGE IB                            74                            65
  STAGE II                             1                             0
  STAGE IIA                           32                            18
  STAGE IIB                           49                            23
  STAGE IIIA                          45                            27
  STAGE IIIB                           6                             5
  STAGE IV                            15                            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 18(9P21.3) MUTATED    91 164  27  11
  DEL PEAK 18(9P21.3) WILD-TYPE  80 114  19   8
D47V4, multiclass
    clus
vv   DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  T1                          91                            80
  T2                         164                           114
  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   176  69    45
  DEL PEAK 18(9P21.3) WILD-TYPE 157  27    31
D47V5, multiclass
       clus
vv      DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  N0                            176                           157
  N1                             69                            27
  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"
D47V6, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED   202  15
  DEL PEAK 18(9P21.3) WILD-TYPE 147  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED    202   15
  DEL PEAK 18(9P21.3) WILD-TYPE  147   10
   clus
vv  DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  0                         202                           147
  1                          15                            10
[1] 2 2
[1] FALSE
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED   144 150
  DEL PEAK 18(9P21.3) WILD-TYPE 132  90
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED    144  150
  DEL PEAK 18(9P21.3) WILD-TYPE  132   90
        clus
vv       DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  FEMALE                         144                           132
  MALE                           150                            90
[1] 2 2
[1] FALSE
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(9P21.3) MUTATED   230  38
  DEL PEAK 18(9P21.3) WILD-TYPE 180  22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED    230   38
  DEL PEAK 18(9P21.3) WILD-TYPE  180   22
     clus
vv    DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  NO                          230                           180
  YES                          38                            22
[1] 2 2
[1] FALSE
D47V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 18(9P21.3) MUTATED                           11
  DEL PEAK 18(9P21.3) WILD-TYPE                          7
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 18(9P21.3) MUTATED                                  61
  DEL PEAK 18(9P21.3) WILD-TYPE                                46
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 18(9P21.3) MUTATED                                                  185
  DEL PEAK 18(9P21.3) WILD-TYPE                                                136
                               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
D47V10, multiclass
                                                    clus
vv                                                   DEL PEAK 18(9P21.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         185
  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                                             46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           136
  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"
D47V11, continuous
D47V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(9P21.3) MUTATED   197   6   2  17
  DEL PEAK 18(9P21.3) WILD-TYPE 147   7   2   9
D47V13, multiclass
    clus
vv   DEL PEAK 18(9P21.3) MUTATED DEL PEAK 18(9P21.3) WILD-TYPE
  R0                         197                           147
  R1                           6                             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                          28   221
  DEL PEAK 18(9P21.3) WILD-TYPE                        24   169
D47V14, multiclass
                                  clus
vv                                 DEL PEAK 18(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 28
  WHITE                                                    221
                                  clus
vv                                 DEL PEAK 18(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      169
[1] 4 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 18(9P21.3) MUTATED     4 211
  DEL PEAK 18(9P21.3) WILD-TYPE   3 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(9P21.3) MUTATED      4  211
  DEL PEAK 18(9P21.3) WILD-TYPE    3  173
                        clus
vv                       DEL PEAK 18(9P21.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         211
                        clus
vv                       DEL PEAK 18(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           173
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 19(9Q21.11) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(9Q21.11) MUTATED   159  96
  DEL PEAK 19(9Q21.11) WILD-TYPE 164  85
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                           255                            249 
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                            96                             85 
$`DEL PEAK 19(9Q21.11) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4418 TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 
       19.96         8.02         9.01        15.02        35.28        11.64 
TCGA-38-6178 TCGA-44-2661 TCGA-44-2662 TCGA-44-6147 TCGA-44-7670 TCGA-44-7671 
       14.73        38.10        42.08        27.78        29.00        29.23 
TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-AAR0 TCGA-50-5932 TCGA-50-5935 
        9.37        46.72        16.04       156.66        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 
       41.69        23.05        16.01        23.18        21.44         6.15 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 TCGA-55-A48X 
       19.66        19.73        17.98        16.93        32.12        22.65 
TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 
       19.59        20.19        13.87        50.24        10.55        85.32 
TCGA-91-7771 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7948 TCGA-97-A4M7 TCGA-J2-8192 
       16.18        17.29        16.54        15.65        20.68        24.30 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
       27.19         5.29        31.23        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 
       45.01        37.02         2.99        29.98        30.02        25.02 
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-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-3917 
       49.05        44.61         4.37        44.42        44.94        38.89 
TCGA-44-3918 TCGA-44-5644 TCGA-44-6144 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 
       34.06        28.37        23.77        21.63        32.45        61.28 
TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 
       16.44        19.46         7.17        36.07        18.87        12.66 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 
        8.55        15.98        13.64        13.45        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 
       12.66        35.54        14.07        32.84        29.46        55.89 
TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       53.29        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AARO TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5933 
      123.58        60.16        49.28         8.22        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 
        8.45        15.12        57.53        11.05        12.16         0.72 
TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 
       10.13        36.79        27.25        34.29        13.94        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6975 
       67.89        30.58        80.52         5.62        46.03         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 
       69.34        45.34        32.71        40.54       107.21        20.02 
TCGA-55-7570 TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-8085 TCGA-55-8089 
       27.09        11.28        17.65        19.82        29.72        23.08 
TCGA-55-8094 TCGA-55-8097 TCGA-55-8206 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 
       17.79        15.65        29.19        17.56        14.47        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
       20.28        17.72        19.96        17.10        17.62        14.66 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8397 TCGA-62-8398 
        0.92        15.81        19.99        17.95        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y 
       88.64        49.25        47.80        56.71        72.30        13.61 
TCGA-62-A470 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 
       39.25        56.81        39.09        81.80        38.37        87.98 
TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3774 TCGA-67-6216 
       28.41        20.05        20.05        18.84        12.66         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 
        6.64         6.12        22.68         7.56         6.05        13.51 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 
        4.24        26.73        19.43        23.38        15.35         4.31 
TCGA-73-4675 TCGA-73-A9RS TCGA-75-5146 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 
       30.31        11.18        77.85        49.84       108.66       100.57 
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       129.53 
TCGA-78-7150 TCGA-78-7161 TCGA-78-7167 TCGA-78-7536 TCGA-78-8640 TCGA-80-5608 
       21.90         9.57        88.14         8.02       232.18        93.11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8075 
       34.39        38.04        19.89        35.24         4.08        22.82 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       31.20        23.05        21.47        11.61        13.91        30.84 
TCGA-86-8672 TCGA-86-A456 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 
        0.62        29.46        41.36         1.97        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-93-7348 TCGA-95-7039 
       12.23        27.68         7.36         1.18        17.46        41.82 
TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7937 TCGA-97-8174 
       18.67        27.29         2.76        19.89        18.54         5.39 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M6 TCGA-99-8032 
       15.39        16.41        21.60        20.58        18.67         1.45 
TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       21.57        18.08        32.48        18.58        15.65        38.63 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       86.14        58.45        49.35        58.85         5.49        41.59 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YI 
       29.46        11.05        11.15        73.91        71.05         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A7XG TCGA-O1-A52J 
       47.08        20.28        59.11 

$`DEL PEAK 19(9Q21.11) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4427 TCGA-05-4434 TCGA-38-4629 
       14.01         9.96        20.05        26.01        15.02        28.41 
TCGA-38-7271 TCGA-44-2655 TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-A47F 
       26.30        43.53        23.93        86.01        18.31        11.08 
TCGA-49-6745 TCGA-49-6761 TCGA-49-AARN TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       17.16        11.64        37.32        48.62         5.79         7.79 
TCGA-55-7284 TCGA-55-7725 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
        7.99        14.53        19.69        18.15        13.68        16.93 
TCGA-55-A491 TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.58        20.65        52.60        82.68        39.09         8.48 
TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK 
       13.71         1.45         6.12         2.86        15.68        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8194 
       18.18        17.92        20.19        20.52        17.75        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4TC TCGA-05-4395 TCGA-05-4397 
        6.35        10.09        21.83         2.43         0.00        24.03 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
       47.05        19.00        14.96        12.00        21.99        26.01 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 
       25.02        24.00         4.96        22.03         9.04         0.46 
TCGA-35-4123 TCGA-38-4626 TCGA-44-2656 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
        5.98       120.79        46.98        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
       37.15        38.24        33.73        26.56        33.30        28.01 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 TCGA-44-7659 TCGA-44-7672 TCGA-44-A47A 
       19.56        23.15        23.18        22.72        23.64        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 TCGA-49-4507 TCGA-49-4512 TCGA-49-6744 
        9.44        11.54        76.21         8.81        29.75        55.33 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
        8.55        40.41       221.33       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5930 TCGA-50-5941 
       71.47       101.72        15.72        47.41         9.27        48.46 
TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 
       60.72        53.16        42.35         3.91        25.55         6.21 
TCGA-50-8457 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6968 TCGA-55-6969 
       36.99        30.54        35.21        14.30        42.51        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6983 TCGA-55-6984 TCGA-55-6987 TCGA-55-7281 
       15.25        53.65        92.81        24.99        70.26        28.67 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       32.71        22.03         3.91        23.15        25.41        18.64 
TCGA-55-7910 TCGA-55-7913 TCGA-55-7995 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 
       34.19        18.44        29.23        15.19         5.06        23.64 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 TCGA-55-8513 TCGA-55-8616 
       22.16        15.42        15.72         0.36        26.01         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-62-8394 TCGA-62-8395 
       12.33        20.71        21.40         3.25         4.57        39.98 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1680 
       19.53        54.35        67.96        40.96        29.92        37.02 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-4679 
        2.04        42.90        51.25        28.47        14.04        14.73 
TCGA-67-6215 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 
        5.72        13.61         5.42         4.41        13.41        14.01 
TCGA-69-8254 TCGA-71-6725 TCGA-73-4666 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       13.45         8.42        26.30         9.24         1.25        50.33 
TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 TCGA-75-6214 TCGA-78-7152 TCGA-78-7153 
       66.64        43.82        85.15        36.66        39.95       119.51 
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        22.92 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
      104.19       238.29        26.53        31.20        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 
       39.35        10.55        39.75        77.59       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 
       12.36         5.88        31.13        20.55        32.78        37.74 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 
        4.57        24.33         0.79        32.65        31.04        14.60 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 
       27.58        28.34        26.50         3.81        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
       26.47        10.62         1.15        16.60        14.27        19.82 
TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 TCGA-97-7546 
       22.45        23.61         1.08        19.00        12.39        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 
       64.60        63.52        61.48        25.48         0.59        15.91 
TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 
       18.67        18.12        14.30        21.44        19.76        20.84 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E5 
       24.56        34.85        36.76        21.63        35.47        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4T4 
       14.30        14.53         1.91         2.76        37.35        86.04 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TK TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A 
       24.36        14.10        19.13        74.33         1.64         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-S2-AA1A 
        0.43        19.82        16.87 

  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                        232.18                         238.29 
  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE 
                         21.57                          21.83 
[1] "0.1 - 232.2 (21.6)" "0.0 - 238.3 (21.8)"
[1] "hr=" "1"  
D48V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 19(9Q21.11) MUTATED         3       64       71        1        25
  DEL PEAK 19(9Q21.11) WILD-TYPE       2       69       68        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        34         32          7       15
D48V3, multiclass
            clus
vv           DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             64                             69
  STAGE IB                             71                             68
  STAGE II                              1                              0
  STAGE IIA                            25                             25
  STAGE IIB                            38                             34
  STAGE IIIA                           40                             32
  STAGE IIIB                            4                              7
  STAGE IV                             10                             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 19(9Q21.11) MUTATED    85 142  24   6
  DEL PEAK 19(9Q21.11) WILD-TYPE  86 136  22  13
D48V4, multiclass
    clus
vv   DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  T1                           85                             86
  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   163  52    38
  DEL PEAK 19(9Q21.11) WILD-TYPE 170  44    38
D48V5, multiclass
       clus
vv      DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  N0                             163                            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"
D48V6, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q21.11) MUTATED   172  10
  DEL PEAK 19(9Q21.11) WILD-TYPE 177  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q21.11) MUTATED    172   10
  DEL PEAK 19(9Q21.11) WILD-TYPE  177   15
   clus
vv  DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  0                          172                            177
  1                           10                             15
[1] 2 2
[1] FALSE
D48V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q21.11) MUTATED   135 123
  DEL PEAK 19(9Q21.11) WILD-TYPE 141 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q21.11) MUTATED    135  123
  DEL PEAK 19(9Q21.11) WILD-TYPE  141  117
        clus
vv       DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  FEMALE                          135                            141
  MALE                            123                            117
[1] 2 2
[1] FALSE
D48V8, binary
                                cls
clus                               0   1
  DEL PEAK 19(9Q21.11) MUTATED   211  32
  DEL PEAK 19(9Q21.11) WILD-TYPE 199  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q21.11) MUTATED    211   32
  DEL PEAK 19(9Q21.11) WILD-TYPE  199   28
     clus
vv    DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  NO                           211                            199
  YES                           32                             28
[1] 2 2
[1] FALSE
D48V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 19(9Q21.11) MUTATED                           10
  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                                                  171
  DEL PEAK 19(9Q21.11) WILD-TYPE                                                150
                                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
D48V10, multiclass
                                                    clus
vv                                                   DEL PEAK 19(9Q21.11) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            43
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          171
  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)                            150
  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"
D48V11, continuous
D48V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 19(9Q21.11) MUTATED   172   7   2  11
  DEL PEAK 19(9Q21.11) WILD-TYPE 172   6   2  15
D48V13, multiclass
    clus
vv   DEL PEAK 19(9Q21.11) MUTATED DEL PEAK 19(9Q21.11) WILD-TYPE
  R0                          172                            172
  R1                            7                              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   199
  DEL PEAK 19(9Q21.11) WILD-TYPE                        26   191
D48V14, multiclass
                                  clus
vv                                 DEL PEAK 19(9Q21.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     199
                                  clus
vv                                 DEL PEAK 19(9Q21.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       191
[1] 4 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 19(9Q21.11) MUTATED     4 194
  DEL PEAK 19(9Q21.11) WILD-TYPE   3 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(9Q21.11) MUTATED      4  194
  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                          194
                        clus
vv                       DEL PEAK 19(9Q21.11) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            190
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 20(10P15.3) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(10P15.3) MUTATED    72  58
  DEL PEAK 20(10P15.3) WILD-TYPE 251 123
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                           130                            374 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                            58                            123 
$`DEL PEAK 20(10P15.3) MUTATED`
TCGA-05-4402 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-44-2662 TCGA-44-6776 
        8.02        35.28        11.64        14.73        42.08        86.01 
TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-50-6597 TCGA-55-7726 
       29.00         9.37        46.72        16.04        41.69        21.44 
TCGA-55-8091 TCGA-55-A48X TCGA-55-A4DF TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       19.73        22.65        20.19        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-97-A4M7 TCGA-J2-8192 TCGA-05-4420 TCGA-05-5429 
       15.68        15.65        20.68        24.30        29.98         9.04 
TCGA-05-5715 TCGA-38-4627 TCGA-38-4628 TCGA-44-2656 TCGA-44-2657 TCGA-44-3398 
        2.04        37.71        49.05        46.98        44.42        38.24 
TCGA-44-3919 TCGA-44-5644 TCGA-44-6775 TCGA-44-6779 TCGA-44-7660 TCGA-44-7669 
       33.73        28.37        23.18        16.44        19.46        18.87 
TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 
       13.45        28.57        12.66        14.07        29.46        29.75 
TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARQ TCGA-50-5931 TCGA-50-6591 TCGA-50-6593 
       73.12         8.55       221.33        14.27         3.91        11.05 
TCGA-50-6594 TCGA-53-7624 TCGA-53-7626 TCGA-55-1596 TCGA-55-6642 TCGA-55-6968 
       12.16        34.29        30.54        67.89        80.52        42.51 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6986 TCGA-55-7281 TCGA-55-7283 
       69.34        45.34        32.71       107.21        28.67        20.02 
TCGA-55-7994 TCGA-55-8094 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8514 
       19.82        17.79        14.47         0.36        13.74        17.10 
TCGA-55-8614 TCGA-55-A490 TCGA-62-8394 TCGA-62-8402 TCGA-62-A46Y TCGA-64-1679 
       17.62         3.25         4.57        49.25        13.61        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 TCGA-67-3772 
       38.37        87.98         2.04        28.41        20.05        18.84 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 
        5.42         7.56         6.05        26.73        19.43        23.38 
TCGA-73-4666 TCGA-73-4675 TCGA-75-5147 TCGA-75-6212 TCGA-78-7150 TCGA-78-7155 
       26.30        30.31        43.82        49.84        21.90        38.50 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-8640 TCGA-78-8655 
       88.14        26.53         8.02        39.35       232.18        77.59 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 
       27.09         5.88        19.89        37.74         4.08         0.79 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8669 TCGA-91-6828 
       22.82        31.04        23.05        14.60        30.84        10.62 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-93-7348 TCGA-93-A4JN 
       10.19         2.60        12.23         7.36        17.46        23.61 
TCGA-95-8494 TCGA-97-7546 TCGA-97-8547 TCGA-97-A4M1 TCGA-J2-A4AD TCGA-J2-A4AG 
        2.76        42.25        21.60        19.76        18.08        32.48 
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 TCGA-O1-A52J 
       73.91         0.13         0.49        59.11 

$`DEL PEAK 20(10P15.3) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       15.02        15.02        28.41        26.30        43.53        38.10 
TCGA-44-6146 TCGA-44-6147 TCGA-44-7661 TCGA-44-7671 TCGA-44-A47F TCGA-49-6745 
       23.93        27.78        18.31        29.23        11.08        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 
       11.64       156.66        37.32        40.60        21.47        23.05 
TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       48.62         5.79         7.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
       14.53         6.15        19.66        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 
       32.12        18.15        13.68        16.93        20.58        19.59 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 
       20.65        13.87        52.60        82.68        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       50.24        10.55        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
        6.12        21.40        18.18        17.92        20.19        20.52 
TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 
       17.75        23.80         6.35        10.09        21.83        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       45.01        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
        2.99        14.96        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       25.02        25.02        24.00         4.96        29.00        22.03 
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-38-4632 TCGA-38-A44F TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       44.61         4.37        44.94        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
       37.15        38.89        34.06        26.56        33.30        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 
       23.77        19.56        23.15        21.63        32.45        61.28 
TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       22.72         7.17        36.07        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-49-4487 TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 
       28.11        35.54        32.84         8.81        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE 
       55.33        22.26        22.26        62.24        28.90        40.41 
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       101.72 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
       15.72        60.16        47.41        49.28         8.22         9.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       78.67         8.45        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       53.16        42.35        25.55         6.21         0.72        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       36.99        36.79        27.25        13.94        35.21        38.73 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       30.58        14.30         5.62        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 
       53.65         3.88        92.81        24.99        40.54        70.26 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
       27.09        32.71        22.03         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 
       18.64        11.28        34.19        17.65        18.44        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
       29.72        15.19        23.08         5.06        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 
       29.19        22.16        15.42        17.56        15.72        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       17.72        19.96        26.01        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B 
       20.71        21.40         0.92        15.81        19.99        17.95 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P 
       39.98        42.38        14.60        88.64        47.80        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 
       56.71        54.35        67.96        72.30        39.25        40.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-5778 TCGA-64-5781 
       29.92        56.81        39.09        37.02        42.90        51.25 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       28.47        20.05        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7978 
        4.64         6.64         6.12        22.68        13.61         4.41 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 
       13.41        13.51        14.01        13.45         4.24         8.42 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS 
       15.35         4.31         9.24         1.25        50.33        11.18 
TCGA-75-5125 TCGA-75-5146 TCGA-75-6206 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       66.64        77.85        85.15        36.66       108.66       100.57 
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       129.53 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.95       119.51        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7537 
       22.92         9.57       104.19       238.29        31.20        53.33 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 
       26.01        10.55        39.75       110.50        93.11        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 
       31.13        34.39        38.04        20.55        32.78        35.24 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8279 TCGA-86-8358 TCGA-86-8585 
        4.57        24.33        32.65        31.20        21.47        11.61 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 
        3.81        24.23        13.64        26.47        41.36         1.97 
TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
       27.68         1.15        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       22.45         1.08        19.00        41.82        18.67        12.39 
TCGA-95-8039 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       27.29        19.89        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 
       18.54         0.59        15.91        18.67         5.39        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 
       15.39        16.41        14.30        20.58        21.44        20.84 
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        21.57 
TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       21.63        35.47        19.00        14.30        14.53         1.91 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
       18.58        15.65        38.63         2.76        86.14        58.45 
TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       86.04         5.49        29.46        11.05        24.36        14.10 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R 
       71.05        74.33         1.64        47.08         0.43        19.82 
TCGA-NJ-A7XG TCGA-S2-AA1A 
       20.28        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 
                        232.18                         238.29 
  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE 
                         21.75                          21.60 
[1] "0.1 - 232.2 (21.8)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1.4"
D49V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 20(10P15.3) MUTATED         1       30       32        0        15
  DEL PEAK 20(10P15.3) WILD-TYPE       4      103      107        1        35
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 20(10P15.3) MUTATED          18         25          1        8
  DEL PEAK 20(10P15.3) WILD-TYPE        54         47         10       17
D49V3, multiclass
            clus
vv           DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             30                            103
  STAGE IB                             32                            107
  STAGE II                              0                              1
  STAGE IIA                            15                             35
  STAGE IIB                            18                             54
  STAGE IIIA                           25                             47
  STAGE IIIB                            1                             10
  STAGE IV                              8                             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 20(10P15.3) MUTATED    45  71  12   3
  DEL PEAK 20(10P15.3) WILD-TYPE 126 207  34  16
D49V4, multiclass
    clus
vv   DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  T1                           45                            126
  T2                           71                            207
  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 20(10P15.3) MUTATED    79  26    24
  DEL PEAK 20(10P15.3) WILD-TYPE 254  70    52
D49V5, multiclass
       clus
vv      DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  N0                              79                            254
  N1                              26                             70
  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"
D49V6, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED    81   8
  DEL PEAK 20(10P15.3) WILD-TYPE 268  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED     81    8
  DEL PEAK 20(10P15.3) WILD-TYPE  268   17
   clus
vv  DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  0                           81                            268
  1                            8                             17
[1] 2 2
[1] FALSE
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED    81  50
  DEL PEAK 20(10P15.3) WILD-TYPE 195 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED     81   50
  DEL PEAK 20(10P15.3) WILD-TYPE  195  190
        clus
vv       DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  FEMALE                           81                            195
  MALE                             50                            190
[1] 2 2
[1] FALSE
D49V8, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED   109  14
  DEL PEAK 20(10P15.3) WILD-TYPE 301  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED    109   14
  DEL PEAK 20(10P15.3) WILD-TYPE  301   46
     clus
vv    DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  NO                           109                            301
  YES                           14                             46
[1] 2 2
[1] FALSE
D49V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 20(10P15.3) MUTATED                            6
  DEL PEAK 20(10P15.3) WILD-TYPE                         12
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 20(10P15.3) MUTATED                                  20
  DEL PEAK 20(10P15.3) WILD-TYPE                                87
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 20(10P15.3) MUTATED                                                   92
  DEL PEAK 20(10P15.3) WILD-TYPE                                                229
                                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
D49V10, multiclass
                                                    clus
vv                                                   DEL PEAK 20(10P15.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            20
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           92
  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                                                     12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              87
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            229
  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"
D49V11, continuous
D49V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 20(10P15.3) MUTATED    88   3   1   7
  DEL PEAK 20(10P15.3) WILD-TYPE 256  10   3  19
D49V13, multiclass
    clus
vv   DEL PEAK 20(10P15.3) MUTATED DEL PEAK 20(10P15.3) WILD-TYPE
  R0                           88                            256
  R1                            3                             10
  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     1
  DEL PEAK 20(10P15.3) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10P15.3) MUTATED                          11   107
  DEL PEAK 20(10P15.3) WILD-TYPE                        41   283
D49V14, multiclass
                                  clus
vv                                 DEL PEAK 20(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                     107
                                  clus
vv                                 DEL PEAK 20(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  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"
D49V15, binary
                                cls
clus                               0   1
  DEL PEAK 20(10P15.3) MUTATED     3 102
  DEL PEAK 20(10P15.3) WILD-TYPE   4 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10P15.3) MUTATED      3  102
  DEL PEAK 20(10P15.3) WILD-TYPE    4  282
                        clus
vv                       DEL PEAK 20(10P15.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          102
                        clus
vv                       DEL PEAK 20(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            282
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 21(10Q26.3) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 21(10Q26.3) MUTATED    85  59
  DEL PEAK 21(10Q26.3) WILD-TYPE 238 122
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                           144                            360 
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                            59                            122 
$`DEL PEAK 21(10Q26.3) MUTATED`
TCGA-05-4402 TCGA-38-4631 TCGA-44-2662 TCGA-44-7670 TCGA-49-6742 TCGA-49-AAR0 
        8.02        11.64        42.08        29.00        16.04       156.66 
TCGA-50-6597 TCGA-55-1592 TCGA-55-6979 TCGA-55-8091 TCGA-55-8207 TCGA-55-A48X 
       41.69        23.05         7.79        19.73        32.12        22.65 
TCGA-55-A4DF TCGA-78-8660 TCGA-91-6836 TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 
       20.19        10.55        13.71        16.54         2.86        15.68 
TCGA-95-7948 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 TCGA-05-4389 TCGA-05-4390 
       15.65        20.68        24.30         6.35        45.01        37.02 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4420 TCGA-05-4424 TCGA-05-4430 TCGA-05-5429 
       24.03        47.05        29.98        30.02        25.02         9.04 
TCGA-05-5715 TCGA-38-4628 TCGA-44-2657 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 
        2.04        49.05        44.42        37.15        38.24        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-6775 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 
       34.06        33.73        23.18        19.46         7.17        18.87 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4494 TCGA-49-4505 TCGA-49-AARE TCGA-49-AARQ 
       13.45        28.11        35.54        14.07        40.41       221.33 
TCGA-50-5049 TCGA-50-5931 TCGA-50-5941 TCGA-50-5944 TCGA-50-6591 TCGA-50-6673 
      101.72        14.27        48.46        57.53         3.91         0.72 
TCGA-50-7109 TCGA-55-5899 TCGA-55-6971 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       10.13        30.58        46.03        69.34        45.34        32.71 
TCGA-55-6986 TCGA-55-7281 TCGA-55-7994 TCGA-55-8092 TCGA-55-8094 TCGA-55-8206 
      107.21        28.67        19.82         5.06        17.79        29.19 
TCGA-55-8505 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-A4DG TCGA-55-A57B 
       14.47        20.28        17.10        17.62        19.99        17.95 
TCGA-62-8394 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46U TCGA-62-A46Y TCGA-64-1676 
        4.57        49.25        19.53        67.96        13.61        56.81 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-67-3770 TCGA-67-3772 
       81.80        38.37        87.98        42.90        20.05        18.84 
TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 
        4.41        13.41         4.24        19.43         8.42        26.30 
TCGA-73-4668 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5147 TCGA-75-6212 TCGA-78-7147 
       15.35        11.18        66.64        43.82        49.84        19.27 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7220 TCGA-78-7535 TCGA-78-7540 TCGA-78-7542 
       19.50        38.50        26.53        31.20        39.35        10.55 
TCGA-78-8640 TCGA-78-8655 TCGA-83-5908 TCGA-86-6851 TCGA-86-7954 TCGA-86-7955 
      232.18        77.59        27.09         5.88        19.89        35.24 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 
        4.08         0.79        22.82        31.04        23.05        21.47 
TCGA-86-8359 TCGA-86-8669 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 
       14.60        30.84        24.23        10.62        41.36         2.60 
TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-93-7348 TCGA-95-7944 TCGA-97-7546 
       12.23         7.36         1.18        17.46        12.39        42.25 
TCGA-97-7554 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M1 TCGA-J2-A4AD TCGA-J2-A4AG 
       25.48        18.12        21.60        19.76        18.08        32.48 
TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 
        2.76        49.35        37.35        86.04        58.85        41.59 
TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-O1-A52J 
       11.05        11.15        19.13         0.13        47.08        59.11 

$`DEL PEAK 21(10Q26.3) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96        20.05         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 
       15.02        15.02        28.41        35.28        14.73        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       43.53        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 
       29.23         9.37        11.08        46.72        17.16        11.64 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 
       37.32        40.60        21.47        48.62         5.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       17.98        16.93        19.69        18.15        13.68        16.93 
TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       20.58        19.59        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC 
       39.09         8.48        50.24        85.32        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
        6.12        17.29        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 
       20.52        17.75        23.80        10.09        21.83        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
        5.29        31.23         2.43        10.09        50.07         3.98 
TCGA-05-4395 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 
        0.00        19.00         2.99        14.96        12.00        21.99 
TCGA-05-4426 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 
       26.01        25.02        24.00         4.96        29.00        22.03 
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-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2659 TCGA-44-2665 
       37.71        44.61         4.37        46.98        44.94        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 
        3.19        25.02        26.56        33.30        28.37        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 
       23.77        19.56        23.15        21.63        32.45        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
       16.44        22.72        36.07        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-49-4488 TCGA-49-4490 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
       28.57        12.66        32.84         8.81        29.46        29.75 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 
       55.89        53.29        55.33        22.26        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V 
       62.24        28.90         8.55       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        47.41        49.28 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5942 
        8.22         9.27        78.67         8.45        15.12        60.72 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 
       53.16        42.35        25.55        11.05        12.16         6.21 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 
       36.99        36.79        27.25        34.29        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       35.21        38.73        67.89        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6983 
       42.51        40.73        15.25        53.65         3.88        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       24.99        40.54        70.26        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
       22.03         3.91        23.15        25.41        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       34.19        17.65        18.44        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8096 TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.08        23.64        15.65        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
       15.72         0.36        13.74        17.72        19.96        26.01 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
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-64-1678 TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 
       29.92        39.09        37.02         2.04        28.41        51.25 
TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       28.47        20.05        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
        4.64         6.64         6.12        22.68        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 
        7.56         6.05        13.51        14.01        13.45        26.73 
TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       23.38         4.31        30.31         9.24         1.25        50.33 
TCGA-75-5146 TCGA-75-6206 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       77.85        85.15        36.66       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       27.16         5.69        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
      119.51        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
      104.19       238.29        88.14         8.02        53.33        26.01 
TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 TCGA-86-7701 TCGA-86-7711 
       39.75       110.50        93.11        12.36        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8054 TCGA-86-8056 TCGA-86-8073 
       38.04        20.55        32.78        37.74         4.57        24.33 
TCGA-86-8076 TCGA-86-8279 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 
       32.65        31.20        11.61        13.91        27.58         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
       28.34        26.50        29.46         3.81        13.64        26.47 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
        1.97        10.19        27.68         1.15        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 
       19.82        22.45        23.61         1.08        19.00        41.82 
TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 
       18.67        27.29         2.76        19.89        64.60        63.52 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 
       61.48        18.54         0.59        15.91        18.67         5.39 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 
       15.39        16.41        14.30        20.58        21.44        20.84 
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        21.57 
TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       21.63        35.47        19.00        14.30        14.53         1.91 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T7 
       18.58        15.65        38.63        86.14        58.45         5.49 
TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       29.46        24.36        14.10        73.91        71.05        74.33 
TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        1.64         0.49         0.43        19.82        20.28        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 
                        232.18                         238.29 
  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE 
                        22.735                         21.520 
[1] "0.1 - 232.2 (22.7)" "0.0 - 238.3 (21.5)"
[1] "hr=" "1.2"
D50V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 21(10Q26.3) MUTATED         2       44       41        0        13
  DEL PEAK 21(10Q26.3) WILD-TYPE       3       89       98        1        37
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 21(10Q26.3) MUTATED          22         18          2        5
  DEL PEAK 21(10Q26.3) WILD-TYPE        50         54          9       20
D50V3, multiclass
            clus
vv           DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             44                             89
  STAGE IB                             41                             98
  STAGE II                              0                              1
  STAGE IIA                            13                             37
  STAGE IIB                            22                             50
  STAGE IIIA                           18                             54
  STAGE IIIB                            2                              9
  STAGE IV                              5                             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 21(10Q26.3) MUTATED    55  81  10   2
  DEL PEAK 21(10Q26.3) WILD-TYPE 116 197  36  17
D50V4, multiclass
    clus
vv   DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  T1                           55                            116
  T2                           81                            197
  T3                           10                             36
  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    97  28    21
  DEL PEAK 21(10Q26.3) WILD-TYPE 236  68    55
D50V5, multiclass
       clus
vv      DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  N0                              97                            236
  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"
D50V6, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q26.3) MUTATED   106   5
  DEL PEAK 21(10Q26.3) WILD-TYPE 243  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q26.3) MUTATED    106    5
  DEL PEAK 21(10Q26.3) WILD-TYPE  243   20
   clus
vv  DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  0                          106                            243
  1                            5                             20
[1] 2 2
[1] FALSE
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q26.3) MUTATED    88  60
  DEL PEAK 21(10Q26.3) WILD-TYPE 188 180
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q26.3) MUTATED     88   60
  DEL PEAK 21(10Q26.3) WILD-TYPE  188  180
        clus
vv       DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  FEMALE                           88                            188
  MALE                             60                            180
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q26.3) MUTATED   120  14
  DEL PEAK 21(10Q26.3) WILD-TYPE 290  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q26.3) MUTATED    120   14
  DEL PEAK 21(10Q26.3) WILD-TYPE  290   46
     clus
vv    DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  NO                           120                            290
  YES                           14                             46
[1] 2 2
[1] FALSE
D50V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 21(10Q26.3) MUTATED                            4
  DEL PEAK 21(10Q26.3) WILD-TYPE                         14
                                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                                                  100
  DEL PEAK 21(10Q26.3) WILD-TYPE                                                221
                                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                              0
  DEL PEAK 21(10Q26.3) WILD-TYPE                            2
                                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
D50V10, multiclass
                                                    clus
vv                                                   DEL PEAK 21(10Q26.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          100
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 6
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            2
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  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                                                     14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              80
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            221
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  13
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              1
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  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"
D50V11, continuous
D50V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 21(10Q26.3) MUTATED   110   1   1   9
  DEL PEAK 21(10Q26.3) WILD-TYPE 234  12   3  17
D50V13, multiclass
    clus
vv   DEL PEAK 21(10Q26.3) MUTATED DEL PEAK 21(10Q26.3) WILD-TYPE
  R0                          110                            234
  R1                            1                             12
  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                          10   113
  DEL PEAK 21(10Q26.3) WILD-TYPE                        42   277
D50V14, multiclass
                                  clus
vv                                 DEL PEAK 21(10Q26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                     113
                                  clus
vv                                 DEL PEAK 21(10Q26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    42
  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"
D50V15, binary
                                cls
clus                               0   1
  DEL PEAK 21(10Q26.3) MUTATED     3 104
  DEL PEAK 21(10Q26.3) WILD-TYPE   4 280
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(10Q26.3) MUTATED      3  104
  DEL PEAK 21(10Q26.3) WILD-TYPE    4  280
                        clus
vv                       DEL PEAK 21(10Q26.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          104
                        clus
vv                       DEL PEAK 21(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            280
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 22(11P15.5) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(11P15.5) MUTATED    87  55
  DEL PEAK 22(11P15.5) WILD-TYPE 236 126
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                           142                            362 
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                            55                            126 
$`DEL PEAK 22(11P15.5) MUTATED`
TCGA-05-4382 TCGA-05-4427 TCGA-05-4434 TCGA-44-2662 TCGA-44-7671 TCGA-44-A47F 
       19.96        26.01        15.02        42.08        29.23        11.08 
TCGA-49-4501 TCGA-55-1595 TCGA-55-7573 TCGA-55-8511 TCGA-64-1677 TCGA-91-6836 
       46.72        48.62        16.01        18.15        20.65        13.71 
TCGA-95-7043 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-05-4389 TCGA-05-4390 TCGA-05-5425 
       16.54        27.19         5.29        45.01        37.02        29.00 
TCGA-05-5428 TCGA-35-5375 TCGA-38-4632 TCGA-44-3917 TCGA-44-5644 TCGA-44-7660 
       22.03         8.68        44.61        38.89        28.37        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-8117 TCGA-44-A4SS TCGA-49-4490 TCGA-49-4505 
        7.17        36.07        12.66        13.64        12.66        14.07 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAQV 
       32.84         8.81        29.46        53.29        22.26        22.26 
TCGA-49-AAR3 TCGA-49-AAR9 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       62.24         8.55         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5939 TCGA-50-5946 TCGA-50-6592 TCGA-50-6593 TCGA-50-6594 
        8.45        15.12        53.16        25.55        11.05        12.16 
TCGA-50-6673 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1596 
        0.72        27.25        34.29        30.54        35.21        67.89 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6968 TCGA-55-6972 TCGA-55-6975 TCGA-55-7570 
       30.58        80.52        42.51        53.65         3.88        27.09 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7994 TCGA-55-7995 
       22.03         3.91        25.41        18.64        19.82        29.23 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8302 TCGA-55-8507 TCGA-55-8510 TCGA-55-8614 
       23.08         5.06        15.72        13.74        17.72        17.62 
TCGA-55-A490 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 
        3.25        19.99        17.95        42.38        14.60        88.64 
TCGA-62-A46O TCGA-62-A46S TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 
       47.80        54.35        40.96        29.92        56.81        81.80 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       87.98        42.90        51.25        28.47        20.05        20.05 
TCGA-69-7763 TCGA-69-7974 TCGA-69-7979 TCGA-69-A59K TCGA-73-4659 TCGA-73-4670 
       22.68         6.05        13.41        19.43        23.38         4.31 
TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-7025 TCGA-78-7145 
       30.31        50.33        11.18        66.64       108.66        27.16 
TCGA-78-7147 TCGA-78-7154 TCGA-78-7160 TCGA-78-7535 TCGA-78-8640 TCGA-86-7701 
       19.27        19.50        22.92        31.20       232.18        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8280 TCGA-86-8358 
       34.39        38.04        32.78        35.24        23.05        21.47 
TCGA-86-8669 TCGA-86-8673 TCGA-86-A4JF TCGA-91-6840 TCGA-91-6847 TCGA-95-7039 
       30.84        28.34        24.23        12.23        27.68        41.82 
TCGA-95-8039 TCGA-95-8494 TCGA-97-7553 TCGA-97-8174 TCGA-97-A4M1 TCGA-97-A4M5 
       27.29         2.76        61.48         5.39        19.76        20.84 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV 
       34.85        36.76        21.57        18.08        19.00        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TE 
       15.65        38.63        37.35        86.04        41.59        29.46 
TCGA-MP-A4TF TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YQ 
       11.05        19.13        71.05        47.08 

$`DEL PEAK 22(11P15.5) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-5420 
       14.01         9.96         8.02        20.05         9.01        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       28.41        35.28        11.64        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       38.10        23.93        27.78        86.01        18.31        29.00 
TCGA-44-8119 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN 
        9.37        16.04        17.16        11.64       156.66        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 
       40.60        21.47        41.69        23.05         5.79         7.79 
TCGA-55-7284 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
        7.99        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 
       19.73        17.98        16.93        19.69        32.12        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 
       16.93        22.65        20.58        19.59        20.19        13.87 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       52.60        82.68        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 
       85.32        16.18         1.45         6.12        17.29         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
       15.68        15.65        21.40        18.18        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
       10.09        21.83        31.23         2.43        10.09        50.07 
TCGA-05-4250 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
        3.98         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 
       14.96        29.98        12.00        30.02        21.99        26.01 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 
       25.02        25.02        24.00         4.96         9.04         2.04 
TCGA-35-3615 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        0.46         7.40         5.98        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 
       49.05         4.37        46.98        44.42        44.94        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        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 
       26.56        33.30        28.01        23.77        19.56        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       21.63        23.18        32.45        61.28        16.44        22.72 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       18.87        23.64         8.55        15.98        15.32         9.44 
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-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AARE 
       29.75        55.89        55.33        73.12        28.90        40.41 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
      123.58       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5941 
      101.72        15.72        60.16        47.41        49.28        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6595 TCGA-50-7109 
       60.72        57.53        42.35         3.91         6.21        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-53-7813 TCGA-55-1594 TCGA-55-6543 TCGA-55-6712 
       36.99        36.79        13.94        38.73        14.30         5.62 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       40.73        15.25        46.03        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       92.81        24.99        40.54       107.21        70.26        28.67 
TCGA-55-7283 TCGA-55-7574 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       20.02        32.71        23.15        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-8085 TCGA-55-8087 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
       18.44        29.72        15.19        17.79        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 
       29.19        22.16        15.42        17.56        14.47         0.36 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 
       20.28        19.96        26.01        17.10        14.66         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 TCGA-62-8394 
       12.33        20.71        21.40         0.92        15.81         4.57 
TCGA-62-8395 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V 
       39.98        49.25        19.53        56.71        67.96        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 
       13.61        39.25        39.09        37.02        38.37         2.04 
TCGA-64-5779 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       28.41        18.84        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 
        4.64         6.64         6.12        13.61         5.42         7.56 
TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        4.41        13.51        14.01        13.45         4.24        26.73 
TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-73-4677 TCGA-75-5146 
        8.42        26.30        15.35         9.24         1.25        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 
       43.82        85.15        49.84        36.66       100.57       163.10 
TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        20.58       129.53        21.90        39.95       119.51 
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         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
      238.29        88.14        26.53         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       39.35        10.55        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
       27.09        12.36         5.88        20.55        19.89        37.74 
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        22.82        32.65 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
       31.04        31.20        14.60        11.61        13.91        27.58 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 
        0.62        26.50        29.46         3.81        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6848 
       10.62        41.36         1.97        10.19         2.60         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 
        1.15        16.60        14.27         1.18        19.82        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 
       17.46        23.61         1.08        19.00        18.67        12.39 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 
       19.89        42.25        64.60        63.52        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.59        15.91        18.67        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M6 TCGA-99-7458 
       14.30        21.60        20.58        21.44        18.67        24.56 
TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W 
        1.45        21.63        35.47        32.48        14.30        14.53 
TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T6 
        1.91         2.76        86.14        58.45        49.35        58.85 
TCGA-MP-A4T7 TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YG 
        5.49        24.36        14.10        11.15        73.91        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.13         1.64         0.49         0.43        19.82        20.28 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                          0.72                           0.00 
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                        232.18                         238.29 
  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE 
                         24.82                          20.58 
[1] "0.7 - 232.2 (24.8)" "0.0 - 238.3 (20.6)"
[1] "hr=" "1"  
D51V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 22(11P15.5) MUTATED         2       31       37        1        14
  DEL PEAK 22(11P15.5) WILD-TYPE       3      102      102        0        36
                                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        46         51         10       16
D51V3, multiclass
            clus
vv           DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             31                            102
  STAGE IB                             37                            102
  STAGE II                              1                              0
  STAGE IIA                            14                             36
  STAGE IIB                            26                             46
  STAGE IIIA                           21                             51
  STAGE IIIB                            1                             10
  STAGE IV                              9                             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 22(11P15.5) MUTATED    43  78  17   4
  DEL PEAK 22(11P15.5) WILD-TYPE 128 200  29  15
D51V4, multiclass
    clus
vv   DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  T1                           43                            128
  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 242  66    55
D51V5, multiclass
       clus
vv      DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  N0                              91                            242
  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"
D51V6, binary
                                cls
clus                               0   1
  DEL PEAK 22(11P15.5) MUTATED    95   9
  DEL PEAK 22(11P15.5) WILD-TYPE 254  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11P15.5) MUTATED     95    9
  DEL PEAK 22(11P15.5) WILD-TYPE  254   16
   clus
vv  DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  0                           95                            254
  1                            9                             16
[1] 2 2
[1] FALSE
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 22(11P15.5) MUTATED    64  79
  DEL PEAK 22(11P15.5) WILD-TYPE 212 161
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11P15.5) MUTATED     64   79
  DEL PEAK 22(11P15.5) WILD-TYPE  212  161
        clus
vv       DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  FEMALE                           64                            212
  MALE                             79                            161
[1] 2 2
[1] FALSE
D51V8, binary
                                cls
clus                               0   1
  DEL PEAK 22(11P15.5) MUTATED   113  23
  DEL PEAK 22(11P15.5) WILD-TYPE 297  37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11P15.5) MUTATED    113   23
  DEL PEAK 22(11P15.5) WILD-TYPE  297   37
     clus
vv    DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  NO                           113                            297
  YES                           23                             37
[1] 2 2
[1] FALSE
D51V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 22(11P15.5) MUTATED                            3
  DEL PEAK 22(11P15.5) WILD-TYPE                         15
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 22(11P15.5) MUTATED                                  29
  DEL PEAK 22(11P15.5) WILD-TYPE                                78
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 22(11P15.5) MUTATED                                                   99
  DEL PEAK 22(11P15.5) WILD-TYPE                                                222
                                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
D51V10, multiclass
                                                    clus
vv                                                   DEL PEAK 22(11P15.5) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            29
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           99
  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                                                     15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            222
  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"
D51V11, continuous
D51V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 22(11P15.5) MUTATED    94   2   1  10
  DEL PEAK 22(11P15.5) WILD-TYPE 250  11   3  16
D51V13, multiclass
    clus
vv   DEL PEAK 22(11P15.5) MUTATED DEL PEAK 22(11P15.5) WILD-TYPE
  R0                           94                            250
  R1                            2                             11
  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                        33   282
D51V14, 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                                    33
  WHITE                                                       282
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V15, binary
                                cls
clus                               0   1
  DEL PEAK 22(11P15.5) MUTATED     3 114
  DEL PEAK 22(11P15.5) WILD-TYPE   4 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11P15.5) MUTATED      3  114
  DEL PEAK 22(11P15.5) WILD-TYPE    4  270
                        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                            270
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 23(11Q23.1) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(11Q23.1) MUTATED    77  42
  DEL PEAK 23(11Q23.1) WILD-TYPE 246 139
  DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE 
                           119                            385 
  DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE 
                            42                            139 
$`DEL PEAK 23(11Q23.1) MUTATED`
TCGA-05-4427 TCGA-05-5420 TCGA-38-4631 TCGA-44-7671 TCGA-44-A47F TCGA-49-6761 
       26.01        15.02        11.64        29.23        11.08        11.64 
TCGA-55-1595 TCGA-55-8203 TCGA-55-8204 TCGA-55-A4DF TCGA-73-4662 TCGA-91-6836 
       48.62        17.98        16.93        20.19        82.68        13.71 
TCGA-93-8067 TCGA-95-7043 TCGA-95-A4VN TCGA-97-A4M3 TCGA-L9-A443 TCGA-MN-A4N1 
        6.12        16.54        18.18        17.75         6.35        27.19 
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-05-4433 TCGA-05-5425 TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 
       12.00        24.00        29.00         7.40         8.68        97.74 
TCGA-38-4628 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-7667 TCGA-44-A4SS 
       49.05        34.06        26.56        33.30        36.07        13.64 
TCGA-49-4487 TCGA-49-4494 TCGA-49-4506 TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 
       28.11        35.54        32.84        29.46        55.89        55.33 
TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AARE TCGA-4B-A93V TCGA-50-5044 TCGA-50-5066 
       22.26        73.12        40.41         9.86        20.52        47.41 
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        35.21 
TCGA-55-5899 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-7283 TCGA-55-7576 
       30.58        46.03        53.65         3.88        20.02        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7995 TCGA-55-8085 
        3.91        23.15        25.41        18.64        29.23        29.72 
TCGA-55-8094 TCGA-55-8302 TCGA-55-8615 TCGA-55-A490 TCGA-62-8395 TCGA-62-8397 
       17.79        15.72        14.66         3.25        39.98        42.38 
TCGA-62-A46S TCGA-62-A470 TCGA-62-A472 TCGA-64-1678 TCGA-64-1681 TCGA-64-5774 
       54.35        39.25        29.92        39.09        38.37        87.98 
TCGA-64-5778 TCGA-64-5815 TCGA-67-3774 TCGA-69-7763 TCGA-69-7764 TCGA-69-8453 
       42.90        28.47        12.66        22.68        13.61        26.73 
TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 TCGA-78-7145 
       30.31        50.33        11.18        36.66       108.66        27.16 
TCGA-78-7148 TCGA-78-7159 TCGA-78-7160 TCGA-78-7220 TCGA-78-8640 TCGA-80-5608 
       20.58        64.90        22.92        26.53       232.18        93.11 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-8054 TCGA-86-8074 TCGA-86-8358 
       31.13        38.04        32.78        37.74         0.79        21.47 
TCGA-86-8669 TCGA-86-8673 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6835 TCGA-91-6849 
       30.84        28.34         3.81        24.23         2.60         1.15 
TCGA-95-8039 TCGA-95-8494 TCGA-97-8174 TCGA-97-A4M5 TCGA-99-8033 TCGA-L4-A4E5 
       27.29         2.76         5.39        20.84        21.57        19.00 
TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-NJ-A4YF 
        2.76        37.35        29.46        11.05        71.05 

$`DEL PEAK 23(11Q23.1) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       15.02        28.41        35.28        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       38.10        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 
       29.00         9.37        46.72        16.04        17.16       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 
       37.32        40.60        21.47        41.69        23.05         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
        6.15        19.66        19.73        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-64-1677 
       13.68        16.93        22.65        20.58        19.59        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       13.87        52.60        39.09         8.48        50.24        10.55 
TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 
       85.32        16.18         1.45        17.29         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 
       15.65        21.40        17.92        20.19        20.52        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA 
       24.30        23.80        10.09        21.83         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4395 TCGA-05-4403 
        2.43        10.09        50.07         3.98         0.00        19.00 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       29.98        30.02        21.99        26.01        25.02        25.02 
TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 
        4.96        22.03         9.04         2.04         0.46         5.98 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 
      120.79        37.71        44.61         4.37        46.98        44.42 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
       44.94        42.77         3.19        25.02        37.15        38.24 
TCGA-44-3917 TCGA-44-3919 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       38.89        33.73        28.37        28.01        23.77        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       23.15        21.63        23.18        32.45        61.28        16.44 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 
       22.72        19.46         7.17        18.87        23.64        12.66 
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-49-4505 TCGA-49-4507 TCGA-49-4512 
       76.21        28.57        12.66        14.07         8.81        29.75 
TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO 
       53.29        22.26        62.24        28.90         8.55       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
      221.33       164.12        71.47       101.72        15.72        60.16 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 
       49.28         9.27        78.67        15.12        48.46        60.72 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       57.53        53.16        42.35         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6595 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
       12.16         6.21        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 
       34.29        13.94        38.73        67.89        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6980 TCGA-55-6981 
        5.62        42.51        40.73        15.25        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       32.71        92.81        24.99        40.54       107.21        70.26 
TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       28.67        27.09        32.71        11.28        34.19        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 
       18.44        19.82        15.19        23.08         5.06        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 
       15.65        29.19        22.16        15.42        17.56        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
        0.36        13.74        20.28        17.72        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       17.10        17.62         1.58        12.33        20.71        21.40 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 
        0.92        15.81        19.99        17.95         4.57        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U 
       88.64        49.25        47.80        19.53        56.71        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-64-1676 TCGA-64-1679 TCGA-64-1680 
       72.30        13.61        40.96        56.81        81.80        37.02 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 
        2.04        28.41        51.25        20.05        20.05        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
        5.42         7.56         6.05         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 
       14.01        13.45         4.24        19.43         8.42        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-75-5125 
       26.30        15.35         4.31         9.24         1.25        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7027 TCGA-78-7143 
       77.85        43.82        85.15        49.84       100.57       163.10 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
        5.69        19.27       129.53        21.90        39.95       119.51 
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         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
      238.29        88.14        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 
       39.35        10.55        39.75        77.59       110.50        27.09 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 
       12.36         5.88        34.39        20.55        19.89        35.24 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57        24.33        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
       31.20        23.05        14.60        11.61        13.91        27.58 
TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
        0.62        26.50        29.46        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       41.36         1.97        10.19        12.23        27.68         7.36 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 
       23.61         1.08        19.00        41.82        18.67        12.39 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 
       19.89        42.25        64.60        63.52        61.48        25.48 
TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 
       18.54         0.59        15.91        18.67        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-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R 
       18.67        24.56        34.85        36.76         1.45        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       18.08        35.47        32.48        14.30        14.53         1.91 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       18.58        15.65        38.63        86.14        58.45        49.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI 
       86.04        58.85         5.49        41.59        24.36        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       11.15        19.13        73.91        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       47.08         0.49         0.43        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE 
                          0.72                           0.00 
  DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE 
                        232.18                         238.29 
  DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE 
                         26.53                          20.58 
[1] "0.7 - 232.2 (26.5)" "0.0 - 238.3 (20.6)"
[1] "hr=" "1"  
D52V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 23(11Q23.1) MUTATED         2       31       29        1        14
  DEL PEAK 23(11Q23.1) WILD-TYPE       3      102      110        0        36
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 23(11Q23.1) MUTATED          18         14          3        6
  DEL PEAK 23(11Q23.1) WILD-TYPE        54         58          8       19
D52V3, multiclass
            clus
vv           DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             31                            102
  STAGE IB                             29                            110
  STAGE II                              1                              0
  STAGE IIA                            14                             36
  STAGE IIB                            18                             54
  STAGE IIIA                           14                             58
  STAGE IIIB                            3                              8
  STAGE IV                              6                             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(11Q23.1) MUTATED    40  63  11   5
  DEL PEAK 23(11Q23.1) WILD-TYPE 131 215  35  14
D52V4, multiclass
    clus
vv   DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE
  T1                           40                            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(11Q23.1) MUTATED    77  24    17
  DEL PEAK 23(11Q23.1) WILD-TYPE 256  72    59
D52V5, multiclass
       clus
vv      DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE
  N0                              77                            256
  N1                              24                             72
  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"
D52V6, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.1) MUTATED    88   6
  DEL PEAK 23(11Q23.1) WILD-TYPE 261  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.1) MUTATED     88    6
  DEL PEAK 23(11Q23.1) WILD-TYPE  261   19
   clus
vv  DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE
  0                           88                            261
  1                            6                             19
[1] 2 2
[1] FALSE
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.1) MUTATED    55  65
  DEL PEAK 23(11Q23.1) WILD-TYPE 221 175
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.1) MUTATED     55   65
  DEL PEAK 23(11Q23.1) WILD-TYPE  221  175
        clus
vv       DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE
  FEMALE                           55                            221
  MALE                             65                            175
[1] 2 2
[1] FALSE
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.1) MUTATED    95  14
  DEL PEAK 23(11Q23.1) WILD-TYPE 315  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.1) MUTATED     95   14
  DEL PEAK 23(11Q23.1) WILD-TYPE  315   46
     clus
vv    DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE
  NO                            95                            315
  YES                           14                             46
[1] 2 2
[1] FALSE
D52V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 23(11Q23.1) MUTATED                            5
  DEL PEAK 23(11Q23.1) WILD-TYPE                         13
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 23(11Q23.1) MUTATED                                  30
  DEL PEAK 23(11Q23.1) WILD-TYPE                                77
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 23(11Q23.1) MUTATED                                                   72
  DEL PEAK 23(11Q23.1) WILD-TYPE                                                249
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 23(11Q23.1) MUTATED                                            0
  DEL PEAK 23(11Q23.1) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 23(11Q23.1) MUTATED                                               3
  DEL PEAK 23(11Q23.1) WILD-TYPE                                            16
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 23(11Q23.1) MUTATED                                1
  DEL PEAK 23(11Q23.1) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 23(11Q23.1) MUTATED                                    0
  DEL PEAK 23(11Q23.1) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(11Q23.1) MUTATED                              0
  DEL PEAK 23(11Q23.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 23(11Q23.1) MUTATED                               5
  DEL PEAK 23(11Q23.1) WILD-TYPE                            18
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 23(11Q23.1) MUTATED                                 0
  DEL PEAK 23(11Q23.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 23(11Q23.1) MUTATED                                               1
  DEL PEAK 23(11Q23.1) WILD-TYPE                                             4
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 23(11Q23.1) MUTATED                              3
  DEL PEAK 23(11Q23.1) WILD-TYPE                            7
D52V10, multiclass
                                                    clus
vv                                                   DEL PEAK 23(11Q23.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            30
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           72
  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(11Q23.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              77
  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"
D52V11, continuous
D52V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(11Q23.1) MUTATED    88   2   0   8
  DEL PEAK 23(11Q23.1) WILD-TYPE 256  11   4  18
D52V13, multiclass
    clus
vv   DEL PEAK 23(11Q23.1) MUTATED DEL PEAK 23(11Q23.1) WILD-TYPE
  R0                           88                            256
  R1                            2                             11
  R2                            0                              4
  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 23(11Q23.1) MUTATED                                  0     2
  DEL PEAK 23(11Q23.1) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(11Q23.1) MUTATED                          13    88
  DEL PEAK 23(11Q23.1) WILD-TYPE                        39   302
D52V14, multiclass
                                  clus
vv                                 DEL PEAK 23(11Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      88
                                  clus
vv                                 DEL PEAK 23(11Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       302
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V15, binary
                                cls
clus                               0   1
  DEL PEAK 23(11Q23.1) MUTATED     1  92
  DEL PEAK 23(11Q23.1) WILD-TYPE   6 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(11Q23.1) MUTATED      1   92
  DEL PEAK 23(11Q23.1) WILD-TYPE    6  292
                        clus
vv                       DEL PEAK 23(11Q23.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           92
                        clus
vv                       DEL PEAK 23(11Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            292
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 24(11Q25) MUTATION ANALYSIS
D53V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 24(11Q25) MUTATED    70  44
  DEL PEAK 24(11Q25) WILD-TYPE 253 137
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                         114                          390 
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                          44                          137 
$`DEL PEAK 24(11Q25) MUTATED`
TCGA-05-4427 TCGA-05-5420 TCGA-38-4631 TCGA-44-7671 TCGA-44-A47F TCGA-49-6761 
       26.01        15.02        11.64        29.23        11.08        11.64 
TCGA-55-1595 TCGA-55-8203 TCGA-55-8204 TCGA-73-4662 TCGA-80-5611 TCGA-93-8067 
       48.62        17.98        16.93        82.68        85.32         6.12 
TCGA-95-7043 TCGA-95-A4VN TCGA-97-A4M3 TCGA-L9-A443 TCGA-MN-A4N1 TCGA-MP-A4T8 
       16.54        18.18        17.75         6.35        27.19         5.29 
TCGA-05-4390 TCGA-05-4397 TCGA-05-4415 TCGA-05-4422 TCGA-05-4433 TCGA-05-5425 
       37.02        24.03         2.99        12.00        24.00        29.00 
TCGA-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 TCGA-44-3918 
        7.40         8.68        97.74        49.05        44.61        34.06 
TCGA-44-5643 TCGA-44-6779 TCGA-44-7667 TCGA-44-7672 TCGA-49-4487 TCGA-49-4506 
       33.30        16.44        36.07        23.64        28.11        32.84 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AARE TCGA-4B-A93V 
       29.46        55.89        55.33        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        47.41         8.22        14.27         8.45        12.16 
TCGA-50-6673 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6971 TCGA-55-6972 
        0.72        30.54        35.21        30.58        46.03        53.65 
TCGA-55-6975 TCGA-55-7283 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 
        3.88        20.02        22.03         3.91        23.15        25.41 
TCGA-55-7903 TCGA-55-7913 TCGA-55-8085 TCGA-55-8094 TCGA-55-8302 TCGA-55-8615 
       18.64        18.44        29.72        17.79        15.72        14.66 
TCGA-55-A490 TCGA-62-8395 TCGA-62-8397 TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 
        3.25        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-69-8453 TCGA-73-4675 TCGA-73-7499 TCGA-75-6214 
       22.68        13.61        26.73        30.31        50.33        36.66 
TCGA-75-7025 TCGA-78-7145 TCGA-78-7148 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 
      108.66        27.16        20.58        19.50        64.90        22.92 
TCGA-78-7220 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-86-7701 TCGA-86-7713 
       26.53        26.01        10.55       232.18        31.13        38.04 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8074 TCGA-86-8358 TCGA-86-8669 TCGA-86-A4JF 
       32.78        37.74         0.79        21.47        30.84        24.23 
TCGA-91-6849 TCGA-95-8039 TCGA-95-8494 TCGA-97-8174 TCGA-97-A4M5 TCGA-L4-A4E5 
        1.15        27.29         2.76         5.39        20.84        19.00 
TCGA-MN-A4N5 TCGA-MP-A4T2 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-NJ-A4YF 
        2.76        37.35        29.46        11.05        14.10        71.05 

$`DEL PEAK 24(11Q25) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       15.02        28.41        35.28        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       38.10        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 
       29.00         9.37        46.72        16.04        17.16       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 
       37.32        40.60        21.47        41.69        23.05         5.79 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
        6.15        19.66        19.73        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DF 
       13.68        16.93        22.65        20.58        19.59        20.19 
TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       20.65        13.87        52.60        39.09         8.48        50.24 
TCGA-78-8660 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7562 
       10.55        13.71        16.18         1.45        17.29         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 
       15.68        15.65        21.40        17.92        20.19        20.52 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4TA 
       20.68        24.30        23.80        10.09        21.83        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4395 
        2.43        10.09        50.07         3.98        45.01         0.00 
TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 
       47.05        19.00        14.96        29.98        30.02        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5428 TCGA-05-5429 
       26.01        25.02        25.02         4.96        22.03         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F 
        2.04         0.46         5.98       120.79        37.71         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       46.98        44.42        44.94        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        33.73        26.56        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7669 
       32.45        61.28        22.72        19.46         7.17        18.87 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       12.66         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-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR2 
       14.07         8.81        29.75        53.29        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       62.24        28.90         8.55       123.58       221.33       164.12 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 
       71.47       101.72        15.72        60.16        49.28         9.27 
TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 
       78.67        15.12        48.46        60.72        57.53        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6595 TCGA-50-7109 
       42.35         3.91        25.55        11.05         6.21        10.13 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 
       36.99        36.79        27.25        34.29        13.94        38.73 
TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 
       67.89        14.30        80.52         5.62        42.51        40.73 
TCGA-55-6970 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
       15.25        69.34        45.34        32.71        92.81        24.99 
TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 
       40.54       107.21        70.26        28.67        27.09        32.71 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 
       11.28        34.19        17.65        19.82        29.23        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       23.08         5.06        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42        17.56        14.47         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
       17.72        19.96        26.01        17.10        17.62         1.58 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       12.33        20.71        21.40         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-64-1679 TCGA-64-1680 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 
       81.80        37.02         2.04        28.41        51.25        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 
       20.05        18.84        14.04        12.66        14.73         5.72 
TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 
        4.64         6.64         6.12         5.42         7.56         6.05 
TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        4.41        13.41        13.51        14.01        13.45         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       19.43         8.42        23.38        26.30        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 
        9.24         1.25        11.18        66.64        77.85        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-7027 TCGA-78-7143 TCGA-78-7146 TCGA-78-7147 
       85.15        49.84       100.57       163.10         5.69        19.27 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 
      129.53        21.90        39.95       119.51        38.50        32.09 
TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 
        5.88         9.57       104.19       238.29        88.14        31.20 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
        8.02        53.33        39.35        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 
       93.11        27.09        12.36         5.88        34.39        20.55 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
       19.89        35.24         4.08         4.57        24.33        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
       32.65        31.04        31.20        23.05        14.60        11.61 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        27.58         0.62        28.34        26.50        29.46 
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-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 
       10.19         2.60        12.23        27.68         7.36        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VP 
        1.08        19.00        41.82        18.67        12.39        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
       42.25        64.60        63.52        61.48        25.48        18.54 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
        0.59        15.91        18.67        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M6 
       14.30        21.60        20.58        21.44        19.76        18.67 
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        21.57        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       18.08        35.47        32.48        14.30        14.53         1.91 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
       18.58        15.65        38.63        86.14        58.45        49.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TJ 
       86.04        58.85         5.49        41.59        24.36        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        73.91        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.49         0.43        19.82        20.28        59.11        16.87 

  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                        0.72                         0.00 
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                      232.18                       238.29 
  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE 
                      25.710                       20.615 
[1] "0.7 - 232.2 (25.7)" "0.0 - 238.3 (20.6)"
[1] "hr=" "1.1"
D53V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 24(11Q25) MUTATED         2       27       25        1        15
  DEL PEAK 24(11Q25) WILD-TYPE       3      106      114        0        35
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 24(11Q25) MUTATED          19         16          2        6
  DEL PEAK 24(11Q25) WILD-TYPE        53         56          9       19
D53V3, multiclass
            clus
vv           DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  STAGE I                             2                            3
  STAGE IA                           27                          106
  STAGE IB                           25                          114
  STAGE II                            1                            0
  STAGE IIA                          15                           35
  STAGE IIB                          19                           53
  STAGE IIIA                         16                           56
  STAGE IIIB                          2                            9
  STAGE IV                            6                           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 24(11Q25) MUTATED    36  64  11   4
  DEL PEAK 24(11Q25) WILD-TYPE 135 214  35  15
D53V4, multiclass
    clus
vv   DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  T1                         36                          135
  T2                         64                          214
  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    68  28    18
  DEL PEAK 24(11Q25) WILD-TYPE 265  68    58
D53V5, multiclass
       clus
vv      DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  N0                            68                          265
  N1                            28                           68
  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"
D53V6, binary
                              cls
clus                             0   1
  DEL PEAK 24(11Q25) MUTATED    84   6
  DEL PEAK 24(11Q25) WILD-TYPE 265  19
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(11Q25) MUTATED     84    6
  DEL PEAK 24(11Q25) WILD-TYPE  265   19
   clus
vv  DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  0                         84                          265
  1                          6                           19
[1] 2 2
[1] FALSE
D53V7, binary
                              cls
clus                             0   1
  DEL PEAK 24(11Q25) MUTATED    52  63
  DEL PEAK 24(11Q25) WILD-TYPE 224 177
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(11Q25) MUTATED     52   63
  DEL PEAK 24(11Q25) WILD-TYPE  224  177
        clus
vv       DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  FEMALE                         52                          224
  MALE                           63                          177
[1] 2 2
[1] FALSE
D53V8, binary
                              cls
clus                             0   1
  DEL PEAK 24(11Q25) MUTATED    91  12
  DEL PEAK 24(11Q25) WILD-TYPE 319  48
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(11Q25) MUTATED     91   12
  DEL PEAK 24(11Q25) WILD-TYPE  319   48
     clus
vv    DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  NO                          91                          319
  YES                         12                           48
[1] 2 2
[1] FALSE
D53V9, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 24(11Q25) MUTATED                            4
  DEL PEAK 24(11Q25) WILD-TYPE                         14
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 24(11Q25) MUTATED                                  29
  DEL PEAK 24(11Q25) WILD-TYPE                                78
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 24(11Q25) MUTATED                                                   69
  DEL PEAK 24(11Q25) WILD-TYPE                                                252
                              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
D53V10, multiclass
                                                    clus
vv                                                   DEL PEAK 24(11Q25) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          29
  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                                                   14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          252
  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"
D53V11, continuous
D53V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 24(11Q25) MUTATED    83   2   0   7
  DEL PEAK 24(11Q25) WILD-TYPE 261  11   4  19
D53V13, multiclass
    clus
vv   DEL PEAK 24(11Q25) MUTATED DEL PEAK 24(11Q25) WILD-TYPE
  R0                         83                          261
  R1                          2                           11
  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    84
  DEL PEAK 24(11Q25) WILD-TYPE                        38   306
D53V14, multiclass
                                  clus
vv                                 DEL PEAK 24(11Q25) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                14
  WHITE                                                    84
                                  clus
vv                                 DEL PEAK 24(11Q25) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  38
  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"
D53V15, binary
                              cls
clus                             0   1
  DEL PEAK 24(11Q25) MUTATED     1  85
  DEL PEAK 24(11Q25) WILD-TYPE   6 299
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(11Q25) MUTATED      1   85
  DEL PEAK 24(11Q25) WILD-TYPE    6  299
                        clus
vv                       DEL PEAK 24(11Q25) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         85
                        clus
vv                       DEL PEAK 24(11Q25) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          299
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 25(12P13.2) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(12P13.2) MUTATED    99  41
  DEL PEAK 25(12P13.2) WILD-TYPE 224 140
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                           140                            364 
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                            41                            140 
$`DEL PEAK 25(12P13.2) MUTATED`
TCGA-05-4405 TCGA-05-4427 TCGA-05-4434 TCGA-38-6178 TCGA-44-2661 TCGA-44-6147 
       20.05        26.01        15.02        14.73        38.10        27.78 
TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
       29.23        11.08        46.72        17.16        11.64       156.66 
TCGA-49-AARN TCGA-50-5935 TCGA-55-1592 TCGA-55-6979 TCGA-55-7573 TCGA-55-7914 
       37.32        21.47        23.05         7.79        16.01         6.15 
TCGA-55-8511 TCGA-55-8619 TCGA-55-A48X TCGA-55-A491 TCGA-67-6217 TCGA-73-4662 
       18.15        13.68        22.65        20.58        13.87        82.68 
TCGA-73-7498 TCGA-80-5611 TCGA-91-6836 TCGA-95-7947 TCGA-95-7948 TCGA-97-A4M3 
       39.09        85.32        13.71        15.68        15.65        17.75 
TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4397 TCGA-05-4425 
        2.43        50.07         3.98        37.02        24.03        21.99 
TCGA-05-4426 TCGA-05-4432 TCGA-44-2656 TCGA-44-2657 TCGA-44-2666 TCGA-44-3396 
       26.01        25.02        46.98        44.42         3.19        37.15 
TCGA-44-3918 TCGA-44-6775 TCGA-44-6778 TCGA-44-7662 TCGA-44-8117 TCGA-44-8120 
       34.06        23.18        61.28         7.17        12.66         8.55 
TCGA-44-A47B TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-6743 TCGA-49-AAQV 
        9.44        13.45        28.57        12.66        53.29        22.26 
TCGA-49-AAR9 TCGA-49-AARE TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 TCGA-50-5939 
        8.55        40.41       101.72        15.72        49.28        15.12 
TCGA-50-5942 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 
       60.72        53.16         3.91        11.05        12.16        36.99 
TCGA-55-5899 TCGA-55-6968 TCGA-55-6975 TCGA-55-6986 TCGA-55-7283 TCGA-55-7727 
       30.58        42.51         3.88       107.21        20.02         3.91 
TCGA-55-7728 TCGA-55-7910 TCGA-55-8087 TCGA-55-8092 TCGA-55-8507 TCGA-55-8510 
       23.15        34.19        15.19         5.06        13.74        17.72 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-A48Z TCGA-55-A4DG TCGA-62-A46R 
       17.10        17.62         1.58        21.40        19.99        56.71 
TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-64-1676 TCGA-64-1681 TCGA-64-5778 
       54.35        72.30        13.61        56.81        38.37        42.90 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3774 TCGA-69-7763 TCGA-69-7765 TCGA-69-7974 
       20.05        20.05        12.66        22.68         5.42         6.05 
TCGA-69-7979 TCGA-69-8253 TCGA-71-6725 TCGA-73-4668 TCGA-73-4677 TCGA-73-7499 
       13.41        14.01         8.42        15.35         1.25        50.33 
TCGA-75-5147 TCGA-78-7145 TCGA-78-7147 TCGA-78-7153 TCGA-78-7161 TCGA-78-7535 
       43.82        27.16        19.27       119.51         9.57        31.20 
TCGA-83-5908 TCGA-86-7955 TCGA-86-8073 TCGA-86-8074 TCGA-86-8279 TCGA-86-8358 
       27.09        35.24        24.33         0.79        31.20        21.47 
TCGA-86-8672 TCGA-91-6828 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 
        0.62        10.62         2.60        12.23        27.68         1.15 
TCGA-95-7567 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-7938 
       18.67         2.76        42.25        64.60        25.48         0.59 
TCGA-97-8177 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-J2-A4AD 
       16.41        19.76        18.67        24.56        34.85        18.08 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4TH TCGA-NJ-A4YF TCGA-NJ-A4YI 
       18.58        15.65         2.76        24.36        71.05         0.13 
TCGA-NJ-A4YQ TCGA-O1-A52J 
       47.08        59.11 

$`DEL PEAK 25(12P13.2) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-5420 
       19.96        14.01         9.96         8.02         9.01        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2662 
       28.41        35.28        11.64        26.30        43.53        42.08 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-49-6742 
       23.93        86.01        18.31        29.00         9.37        16.04 
TCGA-50-5932 TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7724 
       40.60        41.69        48.62         5.79         7.99        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       14.53        21.44        19.66        19.73        17.98        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8621 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 
       19.69        32.12        16.93        19.59        20.19        20.65 
TCGA-73-4658 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-7771 TCGA-91-A4BC 
       52.60         8.48        50.24        10.55        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-A4VK TCGA-95-A4VN 
        6.12        17.29        16.54         2.86        21.40        18.18 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 
       17.92        20.19        20.52        20.68        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
        6.35        10.09        21.83        27.19         5.29        31.23 
TCGA-MP-A4TD TCGA-05-4389 TCGA-05-4395 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       10.09        45.01         0.00        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4430 TCGA-05-4433 
       14.96        29.98        12.00        30.02        25.02        24.00 
TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
        4.96        29.00        22.03         9.04         2.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2659 TCGA-44-2665 TCGA-44-2668 
       49.05        44.61         4.37        44.94        42.77        25.02 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       38.24        38.89        33.73        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6777 
       28.01        23.77        19.56        23.15        21.63        32.45 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 
       16.44        22.72        19.46        36.07        18.87        23.64 
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-49-6744 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.89        55.33        22.26        73.12        62.24        28.90 
TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 
      123.58       221.33       164.12         9.86        20.52        71.47 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
       60.16        47.41         8.22         9.27        14.27        78.67 
TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 
        8.45        48.46        57.53        42.35        25.55         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 
        0.72        10.13        36.79        27.25        34.29        30.54 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 
       13.94        35.21        38.73        67.89        14.30        80.52 
TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
        5.62        40.73        15.25        46.03        53.65        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 
       45.34        32.71        92.81        24.99        40.54        70.26 
TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7815 TCGA-55-7903 
       28.67        27.09        32.71        22.03        25.41        18.64 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       11.28        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       23.08        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 
       15.42        17.56        15.72        14.47         0.36        20.28 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 
       19.96        26.01        14.66        12.33        20.71         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
        0.92        15.81        17.95         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U 
       14.60        88.64        49.25        47.80        19.53        67.96 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
       39.25        40.96        29.92        39.09        81.80        37.02 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 
       87.98         2.04        28.41        51.25        28.47        18.84 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       14.04        14.73         5.72         4.64         6.64         6.12 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 
       13.61         7.56         4.41        13.51        13.45         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4675 
       26.73        19.43        23.38        26.30         4.31        30.31 
TCGA-73-4676 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-6206 TCGA-75-6212 
        9.24        11.18        66.64        77.85        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7146 TCGA-78-7148 
       36.66       108.66       100.57       163.10         5.69        20.58 
TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
      129.53        21.90        39.95        19.50        38.50        32.09 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
        5.88        64.90        22.92       104.19       238.29        88.14 
TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
       26.53         8.02        53.33        26.01        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 
      232.18        39.75        77.59       110.50        93.11        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        38.04        20.55        32.78 
TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8075 TCGA-86-8076 
       19.89        37.74         4.08         4.57        22.82        32.65 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
       31.04        23.05        14.60        11.61        13.91        30.84 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF 
       27.58        28.34        26.50        29.46         3.81        24.23 
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-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 
       16.60        14.27         1.18        19.82        22.45        17.46 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 
       23.61         1.08        19.00        41.82        12.39        27.29 
TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 
       19.89        63.52        61.48        18.54        15.91        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 
        5.39        18.12        15.39        14.30        21.60        20.58 
TCGA-97-A4M0 TCGA-97-A4M5 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R 
       21.44        20.84        36.76         1.45        21.57        21.63 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       35.47        32.48        19.00        14.30        14.53         1.91 
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-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI 
       58.85         5.49        41.59        29.46        11.05        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A 
       11.15        19.13        73.91        74.33         1.64         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
        0.43        19.82        20.28        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 
                        156.66                         238.29 
  DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE 
                        20.050                         22.095 
[1] "0.1 - 156.7 (20.1)" "0.0 - 238.3 (22.1)"
[1] "hr=" "1.2"
D54V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 25(12P13.2) MUTATED         0       42       44        1         9
  DEL PEAK 25(12P13.2) WILD-TYPE       5       91       95        0        41
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 25(12P13.2) MUTATED          15         20          1        5
  DEL PEAK 25(12P13.2) WILD-TYPE        57         52         10       20
D54V3, multiclass
            clus
vv           DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  STAGE I                               0                              5
  STAGE IA                             42                             91
  STAGE IB                             44                             95
  STAGE II                              1                              0
  STAGE IIA                             9                             41
  STAGE IIB                            15                             57
  STAGE IIIA                           20                             52
  STAGE IIIB                            1                             10
  STAGE IV                              5                             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    53  73  10   4
  DEL PEAK 25(12P13.2) WILD-TYPE 118 205  36  15
D54V4, multiclass
    clus
vv   DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  T1                           53                            118
  T2                           73                            205
  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    96  23    19
  DEL PEAK 25(12P13.2) WILD-TYPE 237  73    57
D54V5, multiclass
       clus
vv      DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  N0                              96                            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"
D54V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(12P13.2) MUTATED    91   5
  DEL PEAK 25(12P13.2) WILD-TYPE 258  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(12P13.2) MUTATED     91    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                           91                            258
  1                            5                             20
[1] 2 2
[1] FALSE
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 25(12P13.2) MUTATED    93  47
  DEL PEAK 25(12P13.2) WILD-TYPE 183 193
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(12P13.2) MUTATED     93   47
  DEL PEAK 25(12P13.2) WILD-TYPE  183  193
        clus
vv       DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  FEMALE                           93                            183
  MALE                             47                            193
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(12P13.2) MUTATED   114  15
  DEL PEAK 25(12P13.2) WILD-TYPE 296  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(12P13.2) MUTATED    114   15
  DEL PEAK 25(12P13.2) WILD-TYPE  296   45
     clus
vv    DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  NO                           114                            296
  YES                           15                             45
[1] 2 2
[1] FALSE
D54V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 25(12P13.2) MUTATED                            2
  DEL PEAK 25(12P13.2) WILD-TYPE                         16
                                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                                                   87
  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
D54V10, multiclass
                                                    clus
vv                                                   DEL PEAK 25(12P13.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            34
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           87
  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                                                     16
  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"
D54V11, continuous
D54V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(12P13.2) MUTATED    85   4   2   6
  DEL PEAK 25(12P13.2) WILD-TYPE 259   9   2  20
D54V13, multiclass
    clus
vv   DEL PEAK 25(12P13.2) MUTATED DEL PEAK 25(12P13.2) WILD-TYPE
  R0                           85                            259
  R1                            4                              9
  R2                            2                              2
  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 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   106
  DEL PEAK 25(12P13.2) WILD-TYPE                        32   284
D54V14, multiclass
                                  clus
vv                                 DEL PEAK 25(12P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                     106
                                  clus
vv                                 DEL PEAK 25(12P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    32
  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"
D54V15, binary
                                cls
clus                               0   1
  DEL PEAK 25(12P13.2) MUTATED     2 114
  DEL PEAK 25(12P13.2) WILD-TYPE   5 270
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(12P13.2) MUTATED      2  114
  DEL PEAK 25(12P13.2) WILD-TYPE    5  270
                        clus
vv                       DEL PEAK 25(12P13.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          114
                        clus
vv                       DEL PEAK 25(12P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            270
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 26(12Q12) MUTATION ANALYSIS
D55V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 26(12Q12) MUTATED    63  36
  DEL PEAK 26(12Q12) WILD-TYPE 260 145
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                          99                          405 
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                          36                          145 
$`DEL PEAK 26(12Q12) MUTATED`
TCGA-05-4405 TCGA-38-6178 TCGA-44-2661 TCGA-44-6147 TCGA-44-7671 TCGA-44-A47F 
       20.05        14.73        38.10        27.78        29.23        11.08 
TCGA-49-6745 TCGA-49-AAR0 TCGA-49-AARN TCGA-55-1592 TCGA-55-6979 TCGA-55-7914 
       17.16       156.66        37.32        23.05         7.79         6.15 
TCGA-55-8204 TCGA-55-8207 TCGA-55-8619 TCGA-55-A48X TCGA-55-A491 TCGA-67-6217 
       16.93        32.12        13.68        22.65        20.58        13.87 
TCGA-73-7498 TCGA-95-7043 TCGA-95-7948 TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4426 
       39.09        16.54        15.65         2.43         3.98        26.01 
TCGA-35-3615 TCGA-38-4632 TCGA-44-2657 TCGA-44-2666 TCGA-44-6775 TCGA-44-6779 
        0.46        44.61        44.42         3.19        23.18        16.44 
TCGA-44-7662 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-6767 
        7.17         8.55        13.45        28.57        12.66        22.26 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 TCGA-50-5939 TCGA-50-6591 TCGA-50-6593 
      101.72        15.72        49.28        15.12         3.91        11.05 
TCGA-50-8457 TCGA-50-8460 TCGA-55-5899 TCGA-55-6712 TCGA-55-6981 TCGA-55-7283 
       36.99        27.25        30.58         5.62        45.34        20.02 
TCGA-55-7727 TCGA-55-7907 TCGA-55-8089 TCGA-55-8092 TCGA-55-8505 TCGA-55-8510 
        3.91        11.28        23.08         5.06        14.47        17.72 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 TCGA-55-A48Z TCGA-62-A46R TCGA-62-A46S 
       17.10        17.62         1.58        21.40        56.71        54.35 
TCGA-62-A46U TCGA-62-A46Y TCGA-64-1676 TCGA-64-5778 TCGA-69-7763 TCGA-69-7765 
       67.96        13.61        56.81        42.90        22.68         5.42 
TCGA-71-6725 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 TCGA-75-6214 TCGA-78-7153 
        8.42         4.31        30.31         1.25        36.66       119.51 
TCGA-78-7535 TCGA-86-6851 TCGA-86-7955 TCGA-86-8074 TCGA-86-8279 TCGA-86-8280 
       31.20         5.88        35.24         0.79        31.20        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        41.82 
TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 TCGA-97-7554 TCGA-97-8177 TCGA-97-A4M1 
       27.29        42.25        64.60        25.48        16.41        19.76 
TCGA-99-7458 TCGA-99-8025 TCGA-J2-A4AD TCGA-L9-A8F4 TCGA-MP-A4T6 TCGA-MP-A4TK 
       24.56        34.85        18.08        15.65        58.85        19.13 
TCGA-NJ-A55O TCGA-NJ-A7XG TCGA-O1-A52J 
        0.43        20.28        59.11 

$`DEL PEAK 26(12Q12) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96         8.02         9.01        26.01 
TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 
       15.02        15.02        28.41        35.28        11.64        26.30 
TCGA-44-2655 TCGA-44-2662 TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 
       43.53        42.08        23.93        86.01        18.31        29.00 
TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-49-6761 TCGA-50-5932 TCGA-50-5935 
        9.37        46.72        16.04        11.64        40.60        21.47 
TCGA-50-6597 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       41.69        48.62         5.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8205 
       14.53        21.44        19.66        19.73        17.98        19.69 
TCGA-55-8511 TCGA-55-8621 TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 
       18.15        16.93        19.59        20.19        20.65        52.60 
TCGA-73-4662 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       82.68         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 
       16.18         1.45         6.12        17.29         2.86        15.68 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       21.40        18.18        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
       20.68        24.30        23.80         6.35        10.09        21.83 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4389 
       27.19         5.29        31.23        10.09        50.07        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 
       37.02         0.00        24.03        47.05        19.00         2.99 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4430 
       14.96        29.98        12.00        30.02        21.99        25.02 
TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       25.02        24.00         4.96        29.00        22.03         9.04 
TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 
        2.04         7.40         5.98         8.68        97.74       120.79 
TCGA-38-4627 TCGA-38-4628 TCGA-38-A44F TCGA-44-2656 TCGA-44-2659 TCGA-44-2665 
       37.71        49.05         4.37        46.98        44.94        42.77 
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        33.73 
TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       26.56        33.30        28.37        28.01        23.77        19.56 
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        22.72        19.46 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A 
       36.07        18.87        23.64        12.66        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 
        9.44        11.54        13.64        76.21        28.11        35.54 
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-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       53.29        55.33        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
        8.55        40.41       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 
       20.52        71.47        60.16        47.41         8.22         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       14.27        78.67         8.45        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 
       53.16        42.35        25.55        12.16         6.21         0.72 
TCGA-50-7109 TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ 
       10.13        36.79        34.29        30.54        13.94        35.21 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 
       38.73        67.89        14.30        80.52        42.51        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6982 
       15.25        46.03        53.65         3.88        69.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 
       92.81        24.99        40.54       107.21        70.26        28.67 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       27.09        32.71        22.03        23.15        25.41        18.64 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8087 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       15.19        17.79        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42        17.56        15.72         0.36        13.74        20.28 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 
       19.96        26.01        14.66        12.33        20.71         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        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-64-1678 TCGA-64-1679 
       72.30        39.25        40.96        29.92        39.09        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 
       37.02        38.37        87.98         2.04        28.41        51.25 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       28.47        20.05        20.05        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 
       14.73         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         4.41        13.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 
       13.45         4.24        26.73        19.43        23.38        26.30 
TCGA-73-4668 TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 
       15.35         9.24        50.33        11.18        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       43.82        85.15        49.84       108.66       100.57       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       129.53        21.90 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.95        19.50        38.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        27.09        12.36 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       31.13        34.39        38.04        20.55        32.78        19.89 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8076 
       37.74         4.08         4.57        24.33        22.82        32.65 
TCGA-86-8278 TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 
       31.04        21.47        11.61        30.84        27.58        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 
       26.50        29.46         3.81        24.23        13.64        26.47 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       10.62        41.36         1.97        10.19         2.60        12.23 
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        22.45 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 
       17.46        23.61         1.08        19.00        18.67        12.39 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
        2.76        19.89        63.52        61.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 
       15.91        18.67         5.39        18.12        15.39        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-8028 
       21.60        20.58        21.44        20.84        18.67        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        21.63        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MN-A4N5 
       14.30        14.53         1.91        18.58        38.63         2.76 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 
       86.14        58.45        49.35        37.35        86.04         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       41.59        29.46        11.05        24.36        14.10        11.15 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       73.91        71.05        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55R TCGA-S2-AA1A 
        0.49        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 
                      156.66                       238.29 
  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE 
                       20.02                        21.99 
[1] "0.4 - 156.7 (20.0)" "0.0 - 238.3 (22.0)"
[1] "hr=" "1.2"
D55V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 26(12Q12) MUTATED         0       22       28        0        10
  DEL PEAK 26(12Q12) WILD-TYPE       5      111      111        1        40
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 26(12Q12) MUTATED          11         21          1        3
  DEL PEAK 26(12Q12) WILD-TYPE        61         51         10       22
D55V3, multiclass
            clus
vv           DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  STAGE I                             0                            5
  STAGE IA                           22                          111
  STAGE IB                           28                          111
  STAGE II                            0                            1
  STAGE IIA                          10                           40
  STAGE IIB                          11                           61
  STAGE IIIA                         21                           51
  STAGE IIIB                          1                           10
  STAGE IV                            3                           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    33  52  11   3
  DEL PEAK 26(12Q12) WILD-TYPE 138 226  35  16
D55V4, multiclass
    clus
vv   DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  T1                         33                          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 274  76    58
D55V5, multiclass
       clus
vv      DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  N0                            59                          274
  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"
D55V6, binary
                              cls
clus                             0   1
  DEL PEAK 26(12Q12) MUTATED    58   3
  DEL PEAK 26(12Q12) WILD-TYPE 291  22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(12Q12) MUTATED     58    3
  DEL PEAK 26(12Q12) WILD-TYPE  291   22
   clus
vv  DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  0                         58                          291
  1                          3                           22
[1] 2 2
[1] FALSE
D55V7, binary
                              cls
clus                             0   1
  DEL PEAK 26(12Q12) MUTATED    61  38
  DEL PEAK 26(12Q12) WILD-TYPE 215 202
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(12Q12) MUTATED     61   38
  DEL PEAK 26(12Q12) WILD-TYPE  215  202
        clus
vv       DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  FEMALE                         61                          215
  MALE                           38                          202
[1] 2 2
[1] FALSE
D55V8, binary
                              cls
clus                             0   1
  DEL PEAK 26(12Q12) MUTATED    78  13
  DEL PEAK 26(12Q12) WILD-TYPE 332  47
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(12Q12) MUTATED     78   13
  DEL PEAK 26(12Q12) WILD-TYPE  332   47
     clus
vv    DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  NO                          78                          332
  YES                         13                           47
[1] 2 2
[1] FALSE
D55V9, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 26(12Q12) MUTATED                            3
  DEL PEAK 26(12Q12) WILD-TYPE                         15
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 26(12Q12) MUTATED                                  18
  DEL PEAK 26(12Q12) WILD-TYPE                                89
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 26(12Q12) MUTATED                                                   65
  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
D55V10, multiclass
                                                    clus
vv                                                   DEL PEAK 26(12Q12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          18
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                         65
  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                                                   15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            89
  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"
D55V11, continuous
D55V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 26(12Q12) MUTATED    62   2   1   6
  DEL PEAK 26(12Q12) WILD-TYPE 282  11   3  20
D55V13, multiclass
    clus
vv   DEL PEAK 26(12Q12) MUTATED DEL PEAK 26(12Q12) WILD-TYPE
  R0                         62                          282
  R1                          2                           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    81
  DEL PEAK 26(12Q12) WILD-TYPE                        40   309
D55V14, multiclass
                                  clus
vv                                 DEL PEAK 26(12Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                12
  WHITE                                                    81
                                  clus
vv                                 DEL PEAK 26(12Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  40
  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"
D55V15, binary
                              cls
clus                             0   1
  DEL PEAK 26(12Q12) MUTATED     2  85
  DEL PEAK 26(12Q12) WILD-TYPE   5 299
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 26(12Q12) MUTATED      2   85
  DEL PEAK 26(12Q12) WILD-TYPE    5  299
                        clus
vv                       DEL PEAK 26(12Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         85
                        clus
vv                       DEL PEAK 26(12Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          299
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 27(12Q24.33) MUTATION ANALYSIS
D56V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 27(12Q24.33) MUTATED    82  49
  DEL PEAK 27(12Q24.33) WILD-TYPE 241 132
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                            131                             373 
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                             49                             132 
$`DEL PEAK 27(12Q24.33) MUTATED`
TCGA-05-4434 TCGA-38-6178 TCGA-44-2661 TCGA-44-6147 TCGA-44-6776 TCGA-44-7671 
       15.02        14.73        38.10        27.78        86.01        29.23 
TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       11.08        46.72        17.16       156.66        37.32        40.60 
TCGA-50-6597 TCGA-55-1592 TCGA-55-6979 TCGA-55-7914 TCGA-55-8204 TCGA-55-8511 
       41.69        23.05         7.79         6.15        16.93        18.15 
TCGA-55-8619 TCGA-55-A48X TCGA-55-A4DF TCGA-67-6217 TCGA-73-4658 TCGA-80-5611 
       13.68        22.65        20.19        13.87        52.60        85.32 
TCGA-91-7771 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-MN-A4N1 TCGA-MP-A4TC 
       16.18         2.86        15.68        15.65        27.19         2.43 
TCGA-05-4424 TCGA-05-4426 TCGA-35-3615 TCGA-38-4628 TCGA-38-4632 TCGA-44-2657 
       30.02        26.01         0.46        49.05        44.61        44.42 
TCGA-44-6775 TCGA-44-6779 TCGA-44-7662 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4488 
       23.18        16.44         7.17         8.55        13.45        28.57 
TCGA-49-4490 TCGA-49-4510 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR9 TCGA-49-AARE 
       12.66        29.46        55.33        22.26         8.55        40.41 
TCGA-49-AARQ TCGA-50-5049 TCGA-50-5068 TCGA-50-5939 TCGA-50-5946 TCGA-50-6591 
      221.33       101.72        49.28        15.12        53.16         3.91 
TCGA-50-6593 TCGA-50-8457 TCGA-50-8460 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       11.05        36.99        27.25        69.34        45.34        32.71 
TCGA-55-6984 TCGA-55-6986 TCGA-55-7283 TCGA-55-7727 TCGA-55-7911 TCGA-55-8087 
       24.99       107.21        20.02         3.91        17.65        15.19 
TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8616 
        0.36        20.28        17.72        17.10        17.62         1.58 
TCGA-55-A48Z TCGA-55-A4DG TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y 
       21.40        19.99        56.71        54.35        67.96        13.61 
TCGA-64-5778 TCGA-67-3772 TCGA-67-3774 TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 
       42.90        18.84        12.66         6.12        22.68         5.42 
TCGA-69-7974 TCGA-69-7979 TCGA-69-8253 TCGA-71-6725 TCGA-73-4670 TCGA-73-4677 
        6.05        13.41        14.01         8.42         4.31         1.25 
TCGA-75-5147 TCGA-75-7025 TCGA-78-7147 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 
       43.82       108.66        19.27        21.90       119.51        19.50 
TCGA-78-7155 TCGA-78-7167 TCGA-78-7535 TCGA-78-8640 TCGA-86-6562 TCGA-86-8075 
       38.50        88.14        31.20       232.18        12.36        22.82 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-A4D0 TCGA-91-6847 TCGA-91-6849 
       31.04        31.20        23.05         3.81        27.68         1.15 
TCGA-93-7348 TCGA-93-A4JO TCGA-95-7039 TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 
       17.46         1.08        41.82        27.29        42.25        64.60 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8174 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M6 
       25.48        18.54         5.39        20.58        19.76        18.67 
TCGA-99-7458 TCGA-99-8025 TCGA-J2-A4AD TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4T4 
       24.56        34.85        18.08        15.65         2.76        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TK TCGA-NJ-A55O TCGA-NJ-A7XG 
       58.85        41.59        19.13         0.43        20.28 

$`DEL PEAK 27(12Q24.33) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 
       26.01        15.02        28.41        35.28        11.64        26.30 
TCGA-44-2655 TCGA-44-2662 TCGA-44-6146 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 
       43.53        42.08        23.93        18.31        29.00         9.37 
TCGA-49-6742 TCGA-49-6761 TCGA-50-5935 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 
       16.04        11.64        21.47        48.62         5.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 
       16.01        23.18        14.53        21.44        19.66        19.73 
TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8621 TCGA-55-A491 TCGA-55-A492 
       17.98        19.69        32.12        16.93        20.58        19.59 
TCGA-64-1677 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 
       20.65        82.68        39.09         8.48        50.24        10.55 
TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-A4VK 
       13.71         1.45         6.12        17.29        16.54        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       18.18        17.92        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4T8 
       24.30        23.80         6.35        10.09        21.83         5.29 
TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
       31.23        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        0.00        24.03        47.05        19.00         2.99        14.96 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 
       29.98        12.00        21.99        25.02        25.02        24.00 
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-A44F 
        5.98         8.68        97.74       120.79        37.71         4.37 
TCGA-44-2656 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       46.98        44.94        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        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 
       32.45        61.28        22.72        19.46        36.07        18.87 
TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       23.64        12.66        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4494 TCGA-49-4505 TCGA-49-4506 
       13.64        76.21        28.11        35.54        14.07        32.84 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR2 
        8.81        29.75        55.89        53.29        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       62.24        28.90       123.58       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 
       71.47        15.72        60.16        47.41         8.22         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       14.27        78.67         8.45        48.46        60.72        57.53 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       42.35        25.55        12.16         6.21         0.72        10.13 
TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       36.79        34.29        30.54        13.94        35.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       67.89        30.58        14.30        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6983 
       40.73        15.25        46.03        53.65         3.88        92.81 
TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7576 
       40.54        70.26        28.67        27.09        32.71        22.03 
TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 
       23.15        25.41        18.64        11.28        34.19        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       19.82        29.23        29.72        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8512 TCGA-55-8513 TCGA-55-8615 
       15.72        14.47        13.74        19.96        26.01        14.66 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B 
       12.33        20.71         3.25         0.92        15.81        17.95 
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-A46V TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
       47.80        19.53        72.30        39.25        40.96        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       56.81        39.09        81.80        37.02        38.37        87.98 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        2.04        28.41        51.25        28.47        20.05        20.05 
TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7764 
       14.04        14.73         5.72         4.64         6.64        13.61 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        7.56         4.41        13.51        13.45         4.24        26.73 
TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
       19.43        23.38        26.30        15.35        30.31         9.24 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-6206 TCGA-75-6212 
       50.33        11.18        66.64        77.85        85.15        49.84 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7148 
       36.66       100.57       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 
      129.53        39.95        32.09         5.88        64.90        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 
        9.57       104.19       238.29        26.53         8.02        53.33 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       26.01        39.35        10.55        39.75        77.59       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       93.11        27.09         5.88        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       20.55        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8076 TCGA-86-8358 TCGA-86-8359 
        4.57        24.33         0.79        32.65        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       11.61        13.91        30.84        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
       26.50        29.46        24.23        13.64        26.47        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 
       41.36         1.97        10.19         2.60        12.23         7.36 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN 
       16.60        14.27         1.18        19.82        22.45        23.61 
TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7552 
       19.00        18.67        12.39         2.76        19.89        63.52 
TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 TCGA-97-8176 
       61.48         0.59        15.91        18.67        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-99-8028 
       16.41        14.30        21.60        21.44        20.84        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 
        1.45        21.57        21.63        35.47        32.48        19.00 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV 
       14.30        14.53         1.91        18.58        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TF 
       58.45        49.35        37.35         5.49        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        11.15        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64        47.08         0.49        19.82        59.11 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                           0.36                            0.00 
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                         232.18                          238.29 
  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE 
                          20.58                           21.63 
[1] "0.4 - 232.2 (20.6)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1"  
D56V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 27(12Q24.33) MUTATED         2       27       40        1        15
  DEL PEAK 27(12Q24.33) WILD-TYPE       3      106       99        0        35
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 27(12Q24.33) MUTATED          21         19          1        5
  DEL PEAK 27(12Q24.33) WILD-TYPE        51         53         10       20
D56V3, multiclass
            clus
vv           DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  STAGE I                                2                               3
  STAGE IA                              27                             106
  STAGE IB                              40                              99
  STAGE II                               1                               0
  STAGE IIA                             15                              35
  STAGE IIB                             21                              51
  STAGE IIIA                            19                              53
  STAGE IIIB                             1                              10
  STAGE IV                               5                              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  81  10   4
  DEL PEAK 27(12Q24.33) WILD-TYPE 133 197  36  15
D56V4, multiclass
    clus
vv   DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  T1                            38                             133
  T2                            81                             197
  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 27(12Q24.33) MUTATED    82  31    18
  DEL PEAK 27(12Q24.33) WILD-TYPE 251  65    58
D56V5, multiclass
       clus
vv      DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  N0                               82                             251
  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"
D56V6, binary
                                 cls
clus                                0   1
  DEL PEAK 27(12Q24.33) MUTATED    75   5
  DEL PEAK 27(12Q24.33) WILD-TYPE 274  20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(12Q24.33) MUTATED     75    5
  DEL PEAK 27(12Q24.33) WILD-TYPE  274   20
   clus
vv  DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  0                            75                             274
  1                             5                              20
[1] 2 2
[1] FALSE
D56V7, binary
                                 cls
clus                                0   1
  DEL PEAK 27(12Q24.33) MUTATED    82  51
  DEL PEAK 27(12Q24.33) WILD-TYPE 194 189
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(12Q24.33) MUTATED     82   51
  DEL PEAK 27(12Q24.33) WILD-TYPE  194  189
        clus
vv       DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  FEMALE                            82                             194
  MALE                              51                             189
[1] 2 2
[1] FALSE
D56V8, binary
                                 cls
clus                                0   1
  DEL PEAK 27(12Q24.33) MUTATED   108  15
  DEL PEAK 27(12Q24.33) WILD-TYPE 302  45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(12Q24.33) MUTATED    108   15
  DEL PEAK 27(12Q24.33) WILD-TYPE  302   45
     clus
vv    DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  NO                            108                             302
  YES                            15                              45
[1] 2 2
[1] FALSE
D56V9, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 27(12Q24.33) MUTATED                            4
  DEL PEAK 27(12Q24.33) WILD-TYPE                         14
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 27(12Q24.33) MUTATED                                  24
  DEL PEAK 27(12Q24.33) WILD-TYPE                                83
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 27(12Q24.33) MUTATED                                                   86
  DEL PEAK 27(12Q24.33) WILD-TYPE                                                235
                                 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                              0
  DEL PEAK 27(12Q24.33) WILD-TYPE                            2
                                 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
D56V10, multiclass
                                                    clus
vv                                                   DEL PEAK 27(12Q24.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            86
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  7
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             1
  LUNG MUCINOUS ADENOCARCINOMA                                                   0
  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                                                      14
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               83
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             235
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   12
  LUNG CLEAR CELL ADENOCARCINOMA                                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               2
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  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"
D56V11, continuous
D56V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 27(12Q24.33) MUTATED    82   2   1   8
  DEL PEAK 27(12Q24.33) WILD-TYPE 262  11   3  18
D56V13, multiclass
    clus
vv   DEL PEAK 27(12Q24.33) MUTATED DEL PEAK 27(12Q24.33) WILD-TYPE
  R0                            82                             262
  R1                             2                              11
  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                          21   101
  DEL PEAK 27(12Q24.33) WILD-TYPE                        31   289
D56V14, multiclass
                                  clus
vv                                 DEL PEAK 27(12Q24.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      101
                                  clus
vv                                 DEL PEAK 27(12Q24.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     31
  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"
D56V15, binary
                                 cls
clus                                0   1
  DEL PEAK 27(12Q24.33) MUTATED     1 105
  DEL PEAK 27(12Q24.33) WILD-TYPE   6 279
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(12Q24.33) MUTATED      1  105
  DEL PEAK 27(12Q24.33) WILD-TYPE    6  279
                        clus
vv                       DEL PEAK 27(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           105
                        clus
vv                       DEL PEAK 27(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   6
  NOT HISPANIC OR LATINO                             279
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 28(13Q12.11) MUTATION ANALYSIS
D57V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(13Q12.11) MUTATED   186 102
  DEL PEAK 28(13Q12.11) WILD-TYPE 137  79
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                            288                             216 
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                            102                              79 
$`DEL PEAK 28(13Q12.11) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4405 TCGA-38-6178 TCGA-44-2662 TCGA-44-6147 
       19.96         8.02        20.05        14.73        42.08        27.78 
TCGA-44-7670 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 TCGA-49-6761 TCGA-49-AAR0 
       29.00         9.37        11.08        46.72        11.64       156.66 
TCGA-49-AARN TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 
       37.32        21.47        41.69        23.05        48.62         5.79 
TCGA-55-7573 TCGA-55-7724 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 
       16.01        23.18        19.66        19.73        17.98        16.93 
TCGA-55-8207 TCGA-55-8511 TCGA-55-A491 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       32.12        18.15        20.58        20.65        13.87        52.60 
TCGA-73-4662 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 
       82.68        10.55        85.32        13.71        16.18         6.12 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VN TCGA-97-A4LX 
       17.29         2.86        15.68        15.65        18.18        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.52        17.75        20.68        24.30        23.80         6.35 
TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 
       21.83         5.29         2.43        10.09         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 
       37.02         0.00        24.03        47.05         2.99        14.96 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       29.98        30.02        21.99        26.01        25.02        25.02 
TCGA-05-5423 TCGA-05-5425 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 
        4.96        29.00         7.40         5.98         8.68        97.74 
TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2665 TCGA-44-3917 TCGA-44-3919 
       49.05        44.61        46.98        42.77        38.89        33.73 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 
       33.30        28.37        32.45        61.28        16.44        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
        7.17        36.07        18.87        12.66         8.55        15.98 
TCGA-44-A47B TCGA-44-A4SU TCGA-49-4487 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        9.44        13.45        28.11        32.84         8.81        29.46 
TCGA-49-4512 TCGA-49-6743 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AARO TCGA-4B-A93V 
       29.75        53.29        22.26        62.24       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        47.41        49.28         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 
       78.67         8.45        15.12        48.46        57.53        53.16 
TCGA-50-6591 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 
        3.91        10.13        27.25        13.94        38.73        67.89 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 
       30.58        80.52         5.62        42.51        46.03        53.65 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 
        3.88        69.34        45.34        32.71        40.54       107.21 
TCGA-55-6987 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 
       70.26        27.09        22.03         3.91        25.41        18.64 
TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8089 TCGA-55-8092 
       17.65        18.44        19.82        29.23        23.08         5.06 
TCGA-55-8094 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8507 
       17.79        29.19        17.56        15.72         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       20.28        17.72        17.62        14.66         1.58        12.33 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
       21.40         3.25         0.92        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8399 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
       42.38        88.64        47.80        56.71        54.35        67.96 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 
       72.30        13.61        40.96        29.92        56.81        81.80 
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-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 
       20.05         6.64         6.12        13.61         5.42         4.41 
TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4675 
       13.51         4.24        19.43         8.42        23.38        30.31 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6214 
       50.33        66.64        77.85        43.82        85.15        36.66 
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-78-7167 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
       22.92         9.57        88.14        31.20        53.33        26.01 
TCGA-78-8640 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
      232.18        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
       38.04        32.78        19.89        35.24        37.74         4.08 
TCGA-86-8073 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 
       24.33        22.82        31.20        23.05        21.47        14.60 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 
       13.91        30.84        27.58        28.34        29.46         3.81 
TCGA-86-A4JF TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       24.23        10.62        41.36        10.19         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 
       27.68         7.36         1.18         1.08        41.82        18.67 
TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 
       12.39        27.29         2.76        19.89        42.25        25.48 
TCGA-97-7938 TCGA-97-8174 TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
        0.59         5.39        16.41        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       19.76        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 
       18.08        35.47        32.48        19.00        18.58        15.65 
TCGA-MP-A4SV TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TE 
       86.14        37.35        86.04        58.85        41.59        29.46 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI 
       11.05        14.10        11.15        19.13        71.05         0.13 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       47.08         0.49         0.43        19.82        20.28        59.11 

$`DEL PEAK 28(13Q12.11) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 
       14.01         9.96         9.01        26.01        15.02        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       28.41        35.28        11.64        26.30        43.53        38.10 
TCGA-44-6146 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 TCGA-49-6742 TCGA-49-6745 
       23.93        86.01        18.31        29.23        16.04        17.16 
TCGA-50-5932 TCGA-55-6979 TCGA-55-7284 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 
       40.60         7.79         7.99        14.53        21.44         6.15 
TCGA-55-8205 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF 
       19.69        13.68        16.93        22.65        19.59        20.19 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-91-A4BC TCGA-95-7043 TCGA-95-A4VK 
       39.09         8.48        50.24         1.45        16.54        21.40 
TCGA-97-8172 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4TA TCGA-05-4249 TCGA-05-4403 
       17.92        10.09        27.19        31.23        50.07        19.00 
TCGA-05-4422 TCGA-05-4433 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 
       12.00        24.00        22.03         9.04         2.04         0.46 
TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2666 
      120.79        37.71         4.37        44.42        44.94         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5645 
       25.02        37.15        38.24        34.06        26.56        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-7659 
       23.77        19.56        23.15        21.63        23.18        22.72 
TCGA-44-7672 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4488 
       23.64        15.32        11.54        13.64        76.21        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 
       12.66        35.54        14.07        55.89        55.33        22.26 
TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR 
       73.12        28.90         8.55        40.41       221.33       164.12 
TCGA-50-5044 TCGA-50-5049 TCGA-50-5055 TCGA-50-5072 TCGA-50-5942 TCGA-50-6590 
       20.52       101.72        60.16         8.22        60.72        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        36.99 
TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6969 
       36.79        34.29        30.54        35.21        14.30        40.73 
TCGA-55-6970 TCGA-55-6983 TCGA-55-6984 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 
       15.25        92.81        24.99        28.67        20.02        32.71 
TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 
       23.15        11.28        34.19        29.72        15.19        23.64 
TCGA-55-8097 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 
       15.65        22.16        15.42        14.47        19.96        26.01 
TCGA-55-8514 TCGA-55-A48Y TCGA-55-A494 TCGA-55-A57B TCGA-62-8398 TCGA-62-8402 
       17.10        20.71        15.81        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-67-4679 TCGA-67-6215 TCGA-67-6216 
       18.84        14.04        12.66        14.73         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        13.41        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         9.24         1.25 
TCGA-73-A9RS TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 
       11.18        49.84       108.66       100.57        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       21.90        39.95       119.51        32.09         5.88        64.90 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 
      104.19       238.29        26.53         8.02        39.35        10.55 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-7714 TCGA-86-8056 
       39.75        77.59       110.50        93.11        20.55         4.57 
TCGA-86-8074 TCGA-86-8076 TCGA-86-8278 TCGA-86-8585 TCGA-86-8672 TCGA-86-8674 
        0.79        32.65        31.04        11.61         0.62        26.50 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
       13.64        26.47         1.97         1.15        16.60        14.27 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-97-7547 
       19.82        22.45        17.46        23.61        19.00        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 
       63.52        61.48        18.54        15.91        18.67        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-AA5R TCGA-L4-A4E6 
       15.39        14.30        20.84        18.67        21.63        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4SY 
       14.53         1.91        38.63         2.76        58.45        49.35 
TCGA-MP-A4T7 TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-S2-AA1A 
        5.49        24.36        73.91        74.33         1.64        16.87 

  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                           0.00                            0.46 
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                         232.18                          238.29 
  DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE 
                          22.01                           21.12 
[1] "0.0 - 232.2 (22.0)" "0.5 - 238.3 (21.1)"
[1] "hr=" "1.1"
D57V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 28(13Q12.11) MUTATED         3       72       82        1        28
  DEL PEAK 28(13Q12.11) WILD-TYPE       2       61       57        0        22
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 28(13Q12.11) MUTATED          43         41          7       13
  DEL PEAK 28(13Q12.11) WILD-TYPE        29         31          4       12
D57V3, multiclass
            clus
vv           DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  STAGE I                                3                               2
  STAGE IA                              72                              61
  STAGE IB                              82                              57
  STAGE II                               1                               0
  STAGE IIA                             28                              22
  STAGE IIB                             43                              29
  STAGE IIIA                            41                              31
  STAGE IIIB                             7                               4
  STAGE IV                              13                              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    91 167  23  11
  DEL PEAK 28(13Q12.11) WILD-TYPE  80 111  23   8
D57V4, multiclass
    clus
vv   DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  T1                            91                              80
  T2                           167                             111
  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   189  56    44
  DEL PEAK 28(13Q12.11) WILD-TYPE 144  40    32
D57V5, multiclass
       clus
vv      DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  N0                              189                             144
  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"
D57V6, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q12.11) MUTATED   196  13
  DEL PEAK 28(13Q12.11) WILD-TYPE 153  12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q12.11) MUTATED    196   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                           196                             153
  1                            13                              12
[1] 2 2
[1] FALSE
D57V7, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q12.11) MUTATED   146 147
  DEL PEAK 28(13Q12.11) WILD-TYPE 130  93
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q12.11) MUTATED    146  147
  DEL PEAK 28(13Q12.11) WILD-TYPE  130   93
        clus
vv       DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  FEMALE                           146                             130
  MALE                             147                              93
[1] 2 2
[1] FALSE
D57V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q12.11) MUTATED   239  33
  DEL PEAK 28(13Q12.11) WILD-TYPE 171  27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q12.11) MUTATED    239   33
  DEL PEAK 28(13Q12.11) WILD-TYPE  171   27
     clus
vv    DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  NO                            239                             171
  YES                            33                              27
[1] 2 2
[1] FALSE
D57V9, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 28(13Q12.11) MUTATED                            9
  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                                                  187
  DEL PEAK 28(13Q12.11) WILD-TYPE                                                134
                                 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
D57V10, multiclass
                                                    clus
vv                                                   DEL PEAK 28(13Q12.11) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             62
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           187
  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)                             134
  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"
D57V11, continuous
D57V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(13Q12.11) MUTATED   194   8   2  16
  DEL PEAK 28(13Q12.11) WILD-TYPE 150   5   2  10
D57V13, multiclass
    clus
vv   DEL PEAK 28(13Q12.11) MUTATED DEL PEAK 28(13Q12.11) WILD-TYPE
  R0                           194                             150
  R1                             8                               5
  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 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                          29   220
  DEL PEAK 28(13Q12.11) WILD-TYPE                        23   170
D57V14, multiclass
                                  clus
vv                                 DEL PEAK 28(13Q12.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      220
                                  clus
vv                                 DEL PEAK 28(13Q12.11) 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"
D57V15, binary
                                 cls
clus                                0   1
  DEL PEAK 28(13Q12.11) MUTATED     3 221
  DEL PEAK 28(13Q12.11) WILD-TYPE   4 163
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(13Q12.11) MUTATED      3  221
  DEL PEAK 28(13Q12.11) WILD-TYPE    4  163
                        clus
vv                       DEL PEAK 28(13Q12.11) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           221
                        clus
vv                       DEL PEAK 28(13Q12.11) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             163
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 29(13Q34) MUTATION ANALYSIS
D58V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 29(13Q34) MUTATED   154  83
  DEL PEAK 29(13Q34) WILD-TYPE 169  98
  DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE 
                         237                          267 
  DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE 
                          83                           98 
$`DEL PEAK 29(13Q34) MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-38-6178 TCGA-44-8119 TCGA-44-A47F TCGA-49-6761 
        8.02        20.05        14.73         9.37        11.08        11.64 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-7573 
       21.47        41.69        23.05        48.62         5.79        16.01 
TCGA-55-7724 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8207 
       23.18        19.66        19.73        17.98        16.93        32.12 
TCGA-55-A491 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-78-8660 
       20.58        20.65        13.87        52.60        82.68        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-93-8067 TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VN 
       85.32        13.71         6.12         2.86        15.65        18.18 
TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 
       20.19        20.52        17.75        24.30        23.80         6.35 
TCGA-L9-A444 TCGA-L9-A743 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 
       10.09        21.83         2.43        10.09         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 
       37.02         0.00        47.05        14.96        29.98        30.02 
TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-5423 TCGA-05-5425 TCGA-35-4122 
       21.99        25.02        25.02         4.96        29.00         7.40 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 
        5.98         8.68        97.74        49.05        44.61        46.98 
TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
       38.89        33.30        28.37        32.45        61.28        16.44 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
        7.17        36.07        18.87        12.66         8.55        15.98 
TCGA-44-A47B TCGA-49-4487 TCGA-49-4488 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
        9.44        28.11        28.57        14.07        32.84         8.81 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR9 
       29.46        29.75        55.33        22.26        62.24         8.55 
TCGA-49-AARO TCGA-4B-A93V TCGA-50-5051 TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 
      123.58         9.86        15.72        49.28         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5944 TCGA-50-5946 TCGA-50-6591 
       78.67         8.45        48.46        57.53        53.16         3.91 
TCGA-50-6593 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1596 
       11.05        10.13        27.25        13.94        35.21        67.89 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       30.58        80.52         5.62        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
       69.34        45.34        32.71        40.54       107.21        70.26 
TCGA-55-7570 TCGA-55-7576 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-7913 
       27.09        22.03        25.41        18.64        17.65        18.44 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 
       17.56        15.72         0.36        17.72        17.10        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
       14.66         1.58         0.92        19.99        39.98        42.38 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y 
       88.64        47.80        56.71        54.35        72.30        13.61 
TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 
       40.96        29.92        56.81        39.09        81.80        38.37 
TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 TCGA-67-3770 TCGA-69-7760 TCGA-69-7761 
        2.04        28.41        51.25        20.05         6.64         6.12 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K 
       13.61         5.42         4.41        13.41         4.24        19.43 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 TCGA-73-7499 
        8.42        23.38        26.30        15.35        30.31        50.33 
TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-78-7145 TCGA-78-7146 
       66.64        77.85        43.82        85.15        27.16         5.69 
TCGA-78-7154 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-8640 TCGA-78-8662 
       19.50        22.92         9.57       104.19       232.18       110.50 
TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
       27.09        31.13        34.39        38.04        32.78        19.89 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 
       35.24        37.74         4.08        31.20        23.05        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-A456 TCGA-86-A4D0 
       11.61        13.91        30.84         0.62        29.46         3.81 
TCGA-86-A4JF TCGA-91-6828 TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 
       24.23        10.62        41.36        10.19         2.60        12.23 
TCGA-91-8499 TCGA-93-A4JO TCGA-95-7039 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
        1.18         1.08        41.82        27.29         2.76        19.89 
TCGA-97-7554 TCGA-97-8171 TCGA-97-8174 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 
       25.48        18.67         5.39        21.60        20.58        21.44 
TCGA-97-A4M1 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 
       19.76        24.56        34.85        36.76         1.45        21.57 
TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4SV 
       18.08        32.48        19.00        18.58        15.65        86.14 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TI 
       37.35        86.04        58.85        41.59        11.05        14.10 
TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       19.13        71.05         0.13        47.08         0.49         0.43 
TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       19.82        20.28        59.11 

$`DEL PEAK 29(13Q34) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       19.96        14.01         9.96         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 
       15.02        28.41        35.28        11.64        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       38.10        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 
       29.00        29.23        46.72        16.04        17.16       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-55-6979 TCGA-55-7284 TCGA-55-7725 TCGA-55-7726 
       37.32        40.60         7.79         7.99        14.53        21.44 
TCGA-55-7914 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
        6.15        19.69        18.15        13.68        16.93        22.65 
TCGA-55-A492 TCGA-55-A4DF TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-91-7771 
       19.59        20.19        39.09         8.48        50.24        16.18 
TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VK TCGA-97-8172 
        1.45        17.29        16.54        15.68        21.40        17.92 
TCGA-97-A4M7 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-05-4249 TCGA-05-4397 
       20.68        27.19         5.29        31.23        50.07        24.03 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4422 TCGA-05-4426 TCGA-05-4433 TCGA-05-5428 
       19.00         2.99        12.00        26.01        24.00        22.03 
TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F 
        9.04         2.04         0.46       120.79        37.71         4.37 
TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
       44.42        44.94        42.77         3.19        25.02        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 
       38.24        34.06        33.73        26.56        28.01        23.77 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-7659 TCGA-44-7660 
       19.56        23.15        21.63        23.18        22.72        19.46 
TCGA-44-7672 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       23.64        15.32        11.54        13.64        13.45        76.21 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4514 TCGA-49-6743 TCGA-49-6767 TCGA-49-AAR2 
       12.66        35.54        55.89        53.29        22.26        73.12 
TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5045 
       28.90        40.41       221.33       164.12        20.52        71.47 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5939 TCGA-50-5942 
      101.72        60.16        47.41         8.22        15.12        60.72 
TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 
       42.35        25.55        12.16         6.21         0.72        36.99 
TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-6543 TCGA-55-6968 
       36.79        34.29        30.54        38.73        14.30        42.51 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6983 TCGA-55-6984 TCGA-55-7281 TCGA-55-7283 
       40.73        15.25        92.81        24.99        28.67        20.02 
TCGA-55-7574 TCGA-55-7727 TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 
       32.71         3.91        23.15        11.28        34.19        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       29.23        29.72        15.19        23.08         5.06        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8505 
       23.64        15.65        29.19        22.16        15.42        14.47 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8620 TCGA-55-A48Y 
       13.74        20.28        19.96        26.01        12.33        20.71 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8398 
       21.40         3.25        15.81        17.95         4.57        14.60 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46U TCGA-62-A470 TCGA-64-1680 TCGA-64-5774 
       49.25        19.53        67.96        39.25        37.02        87.98 
TCGA-64-5778 TCGA-64-5815 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
       42.90        28.47        20.05        18.84        14.04        12.66 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 
       14.73         5.72         4.64        22.68         7.56         6.05 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4670 TCGA-73-4676 
       13.51        14.01        13.45        26.73         4.31         9.24 
TCGA-73-4677 TCGA-73-A9RS TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
        1.25        11.18        49.84        36.66       108.66       100.57 
TCGA-78-7143 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
      163.10        19.27        20.58       129.53        21.90        39.95 
TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7163 
      119.51        38.50        32.09         5.88        64.90       238.29 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
       88.14        26.53        31.20         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 TCGA-86-6562 
       39.35        10.55        39.75        77.59        93.11        12.36 
TCGA-86-6851 TCGA-86-7714 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
        5.88        20.55         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8358 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 
       32.65        31.04        21.47        27.58        28.34        26.50 
TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
       13.64        26.47         1.97        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       16.60        14.27        19.82        22.45        17.46        23.61 
TCGA-93-A4JP TCGA-95-7567 TCGA-95-7944 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       19.00        18.67        12.39        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8175 TCGA-97-8176 
       61.48        18.54         0.59        15.91        18.12        15.39 
TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-AA5R TCGA-J2-A4AE 
       16.41        14.30        20.84        18.67        21.63        35.47 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW 
       14.30        14.53         1.91        38.63         2.76        58.45 
TCGA-MP-A4SY TCGA-MP-A4T7 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A5C7 
       49.35         5.49        29.46        24.36        11.15        73.91 
TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-S2-AA1A 
       74.33         1.64        16.87 

  DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE 
                        0.00                         0.46 
  DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE 
                      232.18                       238.29 
  DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE 
                       21.47                        21.90 
[1] "0.0 - 232.2 (21.5)" "0.5 - 238.3 (21.9)"
[1] "hr=" "1"  
D58V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 29(13Q34) MUTATED         2       59       65        1        23
  DEL PEAK 29(13Q34) WILD-TYPE       3       74       74        0        27
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 29(13Q34) MUTATED          37         36          4       11
  DEL PEAK 29(13Q34) WILD-TYPE        35         36          7       14
D58V3, multiclass
            clus
vv           DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE
  STAGE I                             2                            3
  STAGE IA                           59                           74
  STAGE IB                           65                           74
  STAGE II                            1                            0
  STAGE IIA                          23                           27
  STAGE IIB                          37                           35
  STAGE IIIA                         36                           36
  STAGE IIIB                          4                            7
  STAGE IV                           11                           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 29(13Q34) MUTATED    72 136  22  10
  DEL PEAK 29(13Q34) WILD-TYPE  99 142  24   9
D58V4, multiclass
    clus
vv   DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE
  T1                         72                           99
  T2                        136                          142
  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 29(13Q34) MUTATED   154  47    36
  DEL PEAK 29(13Q34) WILD-TYPE 179  49    40
D58V5, multiclass
       clus
vv      DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE
  N0                           154                          179
  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"
D58V6, binary
                              cls
clus                             0   1
  DEL PEAK 29(13Q34) MUTATED   160  11
  DEL PEAK 29(13Q34) WILD-TYPE 189  14
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(13Q34) MUTATED    160   11
  DEL PEAK 29(13Q34) WILD-TYPE  189   14
   clus
vv  DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE
  0                        160                          189
  1                         11                           14
[1] 2 2
[1] FALSE
D58V7, binary
                              cls
clus                             0   1
  DEL PEAK 29(13Q34) MUTATED   129 112
  DEL PEAK 29(13Q34) WILD-TYPE 147 128
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(13Q34) MUTATED    129  112
  DEL PEAK 29(13Q34) WILD-TYPE  147  128
        clus
vv       DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE
  FEMALE                        129                          147
  MALE                          112                          128
[1] 2 2
[1] FALSE
D58V8, binary
                              cls
clus                             0   1
  DEL PEAK 29(13Q34) MUTATED   196  28
  DEL PEAK 29(13Q34) WILD-TYPE 214  32
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(13Q34) MUTATED    196   28
  DEL PEAK 29(13Q34) WILD-TYPE  214   32
     clus
vv    DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE
  NO                         196                          214
  YES                         28                           32
[1] 2 2
[1] FALSE
D58V9, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 29(13Q34) MUTATED                            9
  DEL PEAK 29(13Q34) WILD-TYPE                          9
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 29(13Q34) MUTATED                                  47
  DEL PEAK 29(13Q34) WILD-TYPE                                60
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 29(13Q34) MUTATED                                                  157
  DEL PEAK 29(13Q34) WILD-TYPE                                                164
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 29(13Q34) MUTATED                                            1
  DEL PEAK 29(13Q34) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 29(13Q34) MUTATED                                               8
  DEL PEAK 29(13Q34) WILD-TYPE                                            11
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 29(13Q34) MUTATED                                1
  DEL PEAK 29(13Q34) WILD-TYPE                              1
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 29(13Q34) MUTATED                                    1
  DEL PEAK 29(13Q34) WILD-TYPE                                  2
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 29(13Q34) MUTATED                              0
  DEL PEAK 29(13Q34) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 29(13Q34) MUTATED                              11
  DEL PEAK 29(13Q34) WILD-TYPE                            12
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 29(13Q34) MUTATED                                 0
  DEL PEAK 29(13Q34) WILD-TYPE                               1
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 29(13Q34) MUTATED                                               4
  DEL PEAK 29(13Q34) WILD-TYPE                                             1
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 29(13Q34) MUTATED                              2
  DEL PEAK 29(13Q34) WILD-TYPE                            8
D58V10, multiclass
                                                    clus
vv                                                   DEL PEAK 29(13Q34) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  9
  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 29(13Q34) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          164
  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"
D58V11, continuous
D58V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 29(13Q34) MUTATED   155   8   2  14
  DEL PEAK 29(13Q34) WILD-TYPE 189   5   2  12
D58V13, multiclass
    clus
vv   DEL PEAK 29(13Q34) MUTATED DEL PEAK 29(13Q34) WILD-TYPE
  R0                        155                          189
  R1                          8                            5
  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 29(13Q34) MUTATED                                  1     6
  DEL PEAK 29(13Q34) WILD-TYPE                                0     1
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(13Q34) MUTATED                          26   178
  DEL PEAK 29(13Q34) WILD-TYPE                        26   212
D58V14, multiclass
                                  clus
vv                                 DEL PEAK 29(13Q34) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     6
  BLACK OR AFRICAN AMERICAN                                26
  WHITE                                                   178
                                  clus
vv                                 DEL PEAK 29(13Q34) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     212
[1] 4 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 29(13Q34) MUTATED     3 183
  DEL PEAK 29(13Q34) WILD-TYPE   4 201
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 29(13Q34) MUTATED      3  183
  DEL PEAK 29(13Q34) WILD-TYPE    4  201
                        clus
vv                       DEL PEAK 29(13Q34) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                        183
                        clus
vv                       DEL PEAK 29(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          201
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 30(14Q32.33) MUTATION ANALYSIS
D59V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 30(14Q32.33) MUTATED    94  55
  DEL PEAK 30(14Q32.33) WILD-TYPE 229 126
  DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE 
                            149                             355 
  DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE 
                             55                             126 
$`DEL PEAK 30(14Q32.33) MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-38-4631 
       19.96         9.96        20.05         9.01        26.01        11.64 
TCGA-44-2662 TCGA-44-6146 TCGA-44-7670 TCGA-44-7671 TCGA-44-A47F TCGA-49-6742 
       42.08        23.93        29.00        29.23        11.08        16.04 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-8619 TCGA-55-A491 
       21.47        41.69        23.05        48.62        13.68        20.58 
TCGA-55-A492 TCGA-67-6217 TCGA-73-4662 TCGA-78-8660 TCGA-91-7771 TCGA-95-7948 
       19.59        13.87        82.68        10.55        16.18        15.65 
TCGA-95-A4VN TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC 
       18.18         6.35        21.83        27.19         5.29         2.43 
TCGA-05-4395 TCGA-05-4420 TCGA-05-5425 TCGA-35-4122 TCGA-38-4628 TCGA-38-4632 
        0.00        29.98        29.00         7.40        49.05        44.61 
TCGA-44-2659 TCGA-44-3398 TCGA-44-5643 TCGA-44-5644 TCGA-44-6145 TCGA-44-6775 
       44.94        38.24        33.30        28.37        19.56        23.18 
TCGA-44-7659 TCGA-44-7667 TCGA-44-7669 TCGA-44-8120 TCGA-44-A4SS TCGA-49-4507 
       22.72        36.07        18.87         8.55        13.64         8.81 
TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR9 TCGA-49-AARE 
       29.46        55.89        53.29        55.33         8.55        40.41 
TCGA-50-5068 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-6592 TCGA-50-6593 
       49.28        14.27        78.67         8.45        25.55        11.05 
TCGA-50-6594 TCGA-50-8457 TCGA-53-7626 TCGA-55-1596 TCGA-55-6712 TCGA-55-6982 
       12.16        36.99        30.54        67.89         5.62        32.71 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7727 TCGA-55-7910 TCGA-55-8092 TCGA-55-8094 
       28.67        20.02         3.91        34.19         5.06        17.79 
TCGA-55-8097 TCGA-55-8505 TCGA-55-8508 TCGA-55-8514 TCGA-62-8398 TCGA-62-A46S 
       15.65        14.47        20.28        17.10        14.60        54.35 
TCGA-62-A46U TCGA-62-A471 TCGA-64-1680 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
       67.96        40.96        37.02        42.90        28.41        51.25 
TCGA-67-3771 TCGA-67-3774 TCGA-67-4679 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 
       20.05        12.66        14.73         6.64         6.12         5.42 
TCGA-69-7974 TCGA-69-7980 TCGA-69-A59K TCGA-73-4675 TCGA-73-A9RS TCGA-75-5125 
        6.05        13.51        19.43        30.31        11.18        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 
       77.85        43.82        85.15        36.66       100.57         5.69 
TCGA-78-7147 TCGA-78-7155 TCGA-78-7220 TCGA-78-7535 TCGA-78-8640 TCGA-86-7711 
       19.27        38.50        26.53        31.20       232.18        34.39 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 
       38.04        32.78        19.89        35.24        37.74         4.57 
TCGA-86-8279 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 TCGA-86-A4D0 
       31.20        14.60        13.91        30.84         0.62         3.81 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6848 TCGA-91-8497 TCGA-93-7347 TCGA-93-A4JO 
       41.36         1.97         7.36        14.27        22.45         1.08 
TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       41.82        18.67        12.39        19.89        42.25        64.60 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-A4M0 TCGA-99-8025 TCGA-99-8028 
        5.39        15.39        16.41        21.44        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A7SV 
        1.45        21.57        18.08        32.48        19.00        18.58 
TCGA-MP-A4SW TCGA-MP-A4T7 TCGA-MP-A4TK TCGA-NJ-A4YQ TCGA-NJ-A7XG 
       58.45         5.49        19.13        47.08        20.28 

$`DEL PEAK 30(14Q32.33) WILD-TYPE`
TCGA-05-4384 TCGA-05-4402 TCGA-05-4434 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 
       14.01         8.02        15.02        15.02        28.41        35.28 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6147 TCGA-44-6776 
       14.73        26.30        43.53        38.10        27.78        86.01 
TCGA-44-7661 TCGA-44-8119 TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
       18.31         9.37        46.72        17.16        11.64       156.66 
TCGA-49-AARN TCGA-50-5932 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 
       37.32        40.60         5.79         7.79         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8091 
       23.18        14.53        21.44         6.15        19.66        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8621 
       17.98        16.93        19.69        32.12        18.15        16.93 
TCGA-55-A48X TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 
       22.65        20.19        20.65        52.60        39.09         8.48 
TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ 
       50.24        85.32        13.71         1.45         6.12        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX 
       16.54         2.86        15.68        21.40        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A444 
       20.52        17.75        20.68        24.30        23.80        10.09 
TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
       31.23        10.09        50.07         3.98        45.01        37.02 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4422 
       24.03        47.05        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-05-5423 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 
        4.96        22.03         9.04         2.04         0.46         5.98 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F TCGA-44-2656 
        8.68        97.74       120.79        37.71         4.37        46.98 
TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 
       44.42        42.77         3.19        25.02        37.15        38.89 
TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6148 
       34.06        33.73        26.56        28.01        23.77        23.15 
TCGA-44-6774 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7662 
       21.63        32.45        61.28        16.44        19.46         7.17 
TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       23.64        12.66        15.98        15.32         9.44        11.54 
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-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 
       14.07        32.84        29.75        22.26        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       62.24        28.90       123.58       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5066 
       20.52        71.47       101.72        15.72        60.16        47.41 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        8.22         9.27        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 
       53.16        42.35         3.91         6.21         0.72        10.13 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       36.79        27.25        34.29        13.94        35.21        38.73 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 
       30.58        14.30        80.52        42.51        40.73        15.25 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 
       46.03        53.65         3.88        69.34        45.34        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7574 
       24.99        40.54       107.21        70.26        27.09        32.71 
TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 
       22.03        23.15        25.41        18.64        11.28        17.65 
TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       18.44        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 
       23.64        29.19        22.16        15.42        17.56        15.72 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
        0.36        13.74        17.72        19.96        26.01        17.62 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 
       14.66         1.58        12.33        20.71        21.40         3.25 
TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 
        0.92        15.81        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-64-1678 
       72.30        13.61        39.25        29.92        56.81        39.09 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5815 TCGA-67-3770 
       81.80        38.37        87.98         2.04        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-7764 
       18.84        14.04         5.72         4.64        22.68        13.61 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 
        7.56         4.41        13.41        14.01        13.45         4.24 
TCGA-69-8453 TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
       26.73         8.42        23.38        26.30        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-6212 TCGA-75-7025 TCGA-78-7143 
        9.24         1.25        50.33        49.84       108.66       163.10 
TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 
       27.16        20.58       129.53        21.90        39.95       119.51 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
       19.50        32.09         5.88        64.90        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 
      104.19       238.29        88.14         8.02        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       39.35        10.55        39.75        77.59       110.50        93.11 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7714 TCGA-86-8055 
       27.09        12.36         5.88        31.13        20.55         4.08 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
       24.33         0.79        22.82        32.65        31.04        23.05 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       21.47        11.61        27.58        28.34        26.50        29.46 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 
       24.23        13.64        26.47        10.62        10.19         2.60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BD 
       12.23        27.68         1.15        16.60         1.18        19.82 
TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-8039 TCGA-95-8494 TCGA-97-7552 
       17.46        23.61        19.00        27.29         2.76        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       61.48        25.48        18.54         0.59        15.91        18.67 
TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 
       18.12        14.30        21.60        20.58        19.76        20.84 
TCGA-97-A4M6 TCGA-99-7458 TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A50W 
       18.67        24.56        21.63        35.47        14.30        14.53 
TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY 
        1.91        15.65        38.63         2.76        86.14        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF 
       37.35        86.04        58.85        41.59        29.46        11.05 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG 
       24.36        14.10        11.15        73.91        71.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.13         1.64         0.49         0.43        19.82        59.11 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE 
                           0.00                            0.13 
  DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE 
                         232.18                          238.29 
  DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE 
                          20.58                           21.99 
[1] "0.0 - 232.2 (20.6)" "0.1 - 238.3 (22.0)"
[1] "hr=" "1.1"
D59V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 30(14Q32.33) MUTATED         2       31       32        0        20
  DEL PEAK 30(14Q32.33) WILD-TYPE       3      102      107        1        30
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 30(14Q32.33) MUTATED          29         26          3        5
  DEL PEAK 30(14Q32.33) WILD-TYPE        43         46          8       20
D59V3, multiclass
            clus
vv           DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE
  STAGE I                                2                               3
  STAGE IA                              31                             102
  STAGE IB                              32                             107
  STAGE II                               0                               1
  STAGE IIA                             20                              30
  STAGE IIB                             29                              43
  STAGE IIIA                            26                              46
  STAGE IIIB                             3                               8
  STAGE IV                               5                              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 30(14Q32.33) MUTATED    43  80  20   6
  DEL PEAK 30(14Q32.33) WILD-TYPE 128 198  26  13
D59V4, multiclass
    clus
vv   DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE
  T1                            43                             128
  T2                            80                             198
  T3                            20                              26
  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 30(14Q32.33) MUTATED    85  40    24
  DEL PEAK 30(14Q32.33) WILD-TYPE 248  56    52
D59V5, multiclass
       clus
vv      DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE
  N0                               85                             248
  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"
D59V6, binary
                                 cls
clus                                0   1
  DEL PEAK 30(14Q32.33) MUTATED   107   5
  DEL PEAK 30(14Q32.33) WILD-TYPE 242  20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(14Q32.33) MUTATED    107    5
  DEL PEAK 30(14Q32.33) WILD-TYPE  242   20
   clus
vv  DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE
  0                           107                             242
  1                             5                              20
[1] 2 2
[1] FALSE
D59V7, binary
                                 cls
clus                                0   1
  DEL PEAK 30(14Q32.33) MUTATED    77  73
  DEL PEAK 30(14Q32.33) WILD-TYPE 199 167
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(14Q32.33) MUTATED     77   73
  DEL PEAK 30(14Q32.33) WILD-TYPE  199  167
        clus
vv       DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE
  FEMALE                            77                             199
  MALE                              73                             167
[1] 2 2
[1] FALSE
D59V8, binary
                                 cls
clus                                0   1
  DEL PEAK 30(14Q32.33) MUTATED   119  21
  DEL PEAK 30(14Q32.33) WILD-TYPE 291  39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(14Q32.33) MUTATED    119   21
  DEL PEAK 30(14Q32.33) WILD-TYPE  291   39
     clus
vv    DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE
  NO                            119                             291
  YES                            21                              39
[1] 2 2
[1] FALSE
D59V9, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 30(14Q32.33) MUTATED                            6
  DEL PEAK 30(14Q32.33) WILD-TYPE                         12
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 30(14Q32.33) MUTATED                                  29
  DEL PEAK 30(14Q32.33) WILD-TYPE                                78
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 30(14Q32.33) MUTATED                                                   98
  DEL PEAK 30(14Q32.33) WILD-TYPE                                                223
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 30(14Q32.33) MUTATED                                            1
  DEL PEAK 30(14Q32.33) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 30(14Q32.33) MUTATED                                               4
  DEL PEAK 30(14Q32.33) WILD-TYPE                                            15
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 30(14Q32.33) MUTATED                                2
  DEL PEAK 30(14Q32.33) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 30(14Q32.33) MUTATED                                    0
  DEL PEAK 30(14Q32.33) WILD-TYPE                                  3
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 30(14Q32.33) MUTATED                              1
  DEL PEAK 30(14Q32.33) WILD-TYPE                            1
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 30(14Q32.33) MUTATED                               4
  DEL PEAK 30(14Q32.33) WILD-TYPE                            19
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 30(14Q32.33) MUTATED                                 0
  DEL PEAK 30(14Q32.33) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 30(14Q32.33) MUTATED                                               1
  DEL PEAK 30(14Q32.33) WILD-TYPE                                             4
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 30(14Q32.33) MUTATED                              4
  DEL PEAK 30(14Q32.33) WILD-TYPE                            6
D59V10, multiclass
                                                    clus
vv                                                   DEL PEAK 30(14Q32.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     6
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             29
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            98
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  4
  LUNG CLEAR CELL ADENOCARCINOMA                                                 2
  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 30(14Q32.33) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      12
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             223
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                   15
  LUNG CLEAR CELL ADENOCARCINOMA                                                   0
  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"
D59V11, continuous
D59V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 30(14Q32.33) MUTATED   100   1   0   8
  DEL PEAK 30(14Q32.33) WILD-TYPE 244  12   4  18
D59V13, multiclass
    clus
vv   DEL PEAK 30(14Q32.33) MUTATED DEL PEAK 30(14Q32.33) WILD-TYPE
  R0                           100                             244
  R1                             1                              12
  R2                             0                               4
  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 30(14Q32.33) MUTATED                                  0     2
  DEL PEAK 30(14Q32.33) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(14Q32.33) MUTATED                          23   105
  DEL PEAK 30(14Q32.33) WILD-TYPE                        29   285
D59V14, multiclass
                                  clus
vv                                 DEL PEAK 30(14Q32.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                      105
                                  clus
vv                                 DEL PEAK 30(14Q32.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     29
  WHITE                                                        285
[1] 4 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 30(14Q32.33) MUTATED     3 114
  DEL PEAK 30(14Q32.33) WILD-TYPE   4 270
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 30(14Q32.33) MUTATED      3  114
  DEL PEAK 30(14Q32.33) WILD-TYPE    4  270
                        clus
vv                       DEL PEAK 30(14Q32.33) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           114
                        clus
vv                       DEL PEAK 30(14Q32.33) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             270
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 31(15Q11.2) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(15Q11.2) MUTATED   167  89
  DEL PEAK 31(15Q11.2) WILD-TYPE 156  92
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                           256                            248 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                            89                             92 
$`DEL PEAK 31(15Q11.2) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4405 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 
       19.96         8.02        20.05        35.28        11.64        14.73 
TCGA-44-2662 TCGA-44-6147 TCGA-44-7661 TCGA-44-7670 TCGA-44-A47F TCGA-49-6745 
       42.08        27.78        18.31        29.00        11.08        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       11.64       156.66        37.32        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6979 TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 TCGA-55-8205 
       48.62         7.79         6.15        19.73        17.98        19.69 
TCGA-55-8207 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 
       32.12        22.65        20.58        20.19        20.65        13.87 
TCGA-73-4662 TCGA-80-5611 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7562 
       82.68        85.32        16.18         1.45         6.12         2.86 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       18.18        17.92        20.19        17.75        20.68        24.30 
TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD 
        6.35        10.09        27.19         5.29         2.43        10.09 
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
       50.07        45.01        37.02         0.00        24.03        47.05 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-5425 TCGA-05-5428 
       14.96        29.98        30.02        25.02        29.00        22.03 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4627 TCGA-38-4628 
        7.40         5.98         8.68        97.74        37.71        49.05 
TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-3917 TCGA-44-3918 
       44.61        46.98        44.42        44.94        38.89        34.06 
TCGA-44-3919 TCGA-44-6144 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-7660 
       33.73        23.77        21.63        23.18        32.45        19.46 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS 
        7.17        36.07        23.64        12.66         8.55        13.64 
TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4510 
       13.45        28.11        28.57        12.66        14.07        29.46 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AARE TCGA-49-AARO 
       29.75        55.89        55.33        22.26        40.41       123.58 
TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5933 
      221.33        71.47       101.72        15.72        47.41        78.67 
TCGA-50-5941 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 
       48.46        53.16         3.91        11.05        12.16         0.72 
TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6642 
       10.13        27.25        30.54        35.21        30.58        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 
        5.62        42.51        40.73        46.03        53.65        69.34 
TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 
       45.34        32.71        92.81        40.54        28.67        20.02 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 
       32.71        22.03         3.91        25.41        18.64        34.19 
TCGA-55-8089 TCGA-55-8094 TCGA-55-8301 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       23.08        17.79        17.56         0.36        13.74        20.28 
TCGA-55-8510 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z 
       17.72        17.62        14.66         1.58        12.33        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-A46R 
        3.25         0.92        19.99         4.57        42.38        56.71 
TCGA-62-A46S TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       54.35        13.61        29.92        56.81        39.09        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 
       38.37        87.98        42.90        28.41        20.05        20.05 
TCGA-67-3772 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       18.84         5.42         7.56         6.05         4.41        13.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       13.51        14.01        19.43        23.38        26.30        15.35 
TCGA-73-4675 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5146 TCGA-75-6212 
       30.31        50.33        11.18        66.64        77.85        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       36.66       108.66       163.10        27.16         5.69        19.27 
TCGA-78-7153 TCGA-78-7158 TCGA-78-7159 TCGA-78-7167 TCGA-78-7535 TCGA-78-7539 
      119.51         5.88        64.90        88.14        31.20        26.01 
TCGA-78-7542 TCGA-78-8640 TCGA-80-5608 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 
       10.55       232.18        93.11        12.36         5.88        31.13 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       32.78        19.89        35.24        24.33         0.79        22.82 
TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 
       31.20        21.47        14.60        11.61        30.84        27.58 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6835 TCGA-91-6840 
       29.46         3.81        24.23        10.62         2.60        12.23 
TCGA-91-6847 TCGA-91-8499 TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
       27.68         1.18        22.45        17.46        23.61         1.08 
TCGA-95-7039 TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 
       41.82        18.67         2.76        19.89        42.25        25.48 
TCGA-97-7937 TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M0 TCGA-97-A4M6 TCGA-99-7458 
       18.54         5.39        16.41        21.44        18.67        24.56 
TCGA-99-8028 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 
       36.76        32.48        19.00         1.91        18.58        15.65 
TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4TE 
       38.63        86.14        58.45        37.35        86.04        29.46 
TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YI 
       11.05        14.10        11.15        19.13        71.05         0.13 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.43        19.82        20.28        59.11 

$`DEL PEAK 31(15Q11.2) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 
       14.01         9.96         9.01        26.01        15.02        15.02 
TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 
       28.41        26.30        43.53        38.10        23.93        86.01 
TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 TCGA-50-5932 TCGA-55-6978 
       29.23         9.37        46.72        16.04        40.60         5.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 
        7.99        16.01        23.18        14.53        21.44        19.66 
TCGA-55-8204 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A492 TCGA-73-4658 
       16.93        18.15        13.68        16.93        19.59        52.60 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-91-6836 TCGA-93-A4JQ 
       39.09         8.48        50.24        10.55        13.71        17.29 
TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-A4M2 TCGA-J2-8194 
       16.54        15.68        15.65        21.40        20.52        23.80 
TCGA-L9-A743 TCGA-MP-A4TA TCGA-05-4250 TCGA-05-4403 TCGA-05-4415 TCGA-05-4422 
       21.83        31.23         3.98        19.00         2.99        12.00 
TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5429 
       21.99        26.01        25.02        24.00         4.96         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 TCGA-38-A44F TCGA-44-2665 TCGA-44-2666 
        2.04         0.46       120.79         4.37        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       25.02        37.15        38.24        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 
       28.01        19.56        23.15        61.28        16.44        22.72 
TCGA-44-7669 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 
       18.87        15.98        15.32         9.44        11.54        76.21 
TCGA-49-4494 TCGA-49-4506 TCGA-49-4507 TCGA-49-6743 TCGA-49-AAQV TCGA-49-AAR2 
       35.54        32.84         8.81        53.29        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       62.24        28.90         8.55       164.12         9.86        20.52 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5936 
       60.16        49.28         8.22         9.27        14.27         8.45 
TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 
       15.12        60.72        57.53        42.35        25.55         6.21 
TCGA-50-8457 TCGA-50-8459 TCGA-53-7624 TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 
       36.99        36.79        34.29        13.94        38.73        67.89 
TCGA-55-6543 TCGA-55-6970 TCGA-55-6975 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 
       14.30        15.25         3.88        24.99       107.21        70.26 
TCGA-55-7570 TCGA-55-7728 TCGA-55-7907 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 
       27.09        23.15        11.28        17.65        18.44        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
       29.23        29.72        15.19         5.06        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8512 
       29.19        22.16        15.42        15.72        14.47        19.96 
TCGA-55-8513 TCGA-55-8514 TCGA-55-A48Y TCGA-55-A494 TCGA-55-A57B TCGA-62-8395 
       26.01        17.10        20.71        15.81        17.95        39.98 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46U 
       14.60        88.64        49.25        47.80        19.53        67.96 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 
       72.30        39.25        40.96        37.02         2.04        51.25 
TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       28.47        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-8254 TCGA-69-8255 
        6.64         6.12        22.68        13.61        13.45         4.24 
TCGA-69-8453 TCGA-71-6725 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-75-5147 
       26.73         8.42         4.31         9.24         1.25        43.82 
TCGA-75-6206 TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
       85.15       100.57        20.58       129.53        21.90        39.95 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       19.50        38.50        32.09        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7220 TCGA-78-7536 TCGA-78-7537 TCGA-78-7540 TCGA-78-8648 
      238.29        26.53         8.02        53.33        39.35        39.75 
TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       77.59       110.50        27.09        34.39        38.04        20.55 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 
       37.74         4.08         4.57        32.65        31.04        23.05 
TCGA-86-8668 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 
       13.91         0.62        28.34        26.50        13.64        26.47 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       41.36         1.97        10.19         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-A4JP TCGA-95-7944 TCGA-95-8039 TCGA-97-7547 
       14.27        19.82        19.00        12.39        27.29        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 
       63.52        61.48         0.59        15.91        18.67        18.12 
TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 
       15.39        14.30        21.60        20.58        19.76        20.84 
TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE 
       34.85         1.45        21.57        21.63        18.08        35.47 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-MN-A4N5 TCGA-MP-A4SY TCGA-MP-A4T6 TCGA-MP-A4T7 
       14.30        14.53         2.76        49.35        58.85         5.49 
TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       41.59        24.36        73.91        74.33         1.64        47.08 
TCGA-NJ-A55A TCGA-S2-AA1A 
        0.49        16.87 

  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                          0.00                           0.46 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                        232.18                         238.29 
  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE 
                        22.550                         20.775 
[1] "0.0 - 232.2 (22.5)" "0.5 - 238.3 (20.8)"
[1] "hr=" "1.1"
D60V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 31(15Q11.2) MUTATED         4       64       71        0        34
  DEL PEAK 31(15Q11.2) WILD-TYPE       1       69       68        1        16
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 31(15Q11.2) MUTATED          32         35          6       13
  DEL PEAK 31(15Q11.2) WILD-TYPE        40         37          5       12
D60V3, multiclass
            clus
vv           DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                             64                             69
  STAGE IB                             71                             68
  STAGE II                              0                              1
  STAGE IIA                            34                             16
  STAGE IIB                            32                             40
  STAGE IIIA                           35                             37
  STAGE IIIB                            6                              5
  STAGE IV                             13                             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 31(15Q11.2) MUTATED    89 146  19   9
  DEL PEAK 31(15Q11.2) WILD-TYPE  82 132  27  10
D60V4, multiclass
    clus
vv   DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  T1                           89                             82
  T2                          146                            132
  T3                           19                             27
  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 31(15Q11.2) MUTATED   165  53    40
  DEL PEAK 31(15Q11.2) WILD-TYPE 168  43    36
D60V5, multiclass
       clus
vv      DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  N0                             165                            168
  N1                              53                             43
  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"
D60V6, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED   183  13
  DEL PEAK 31(15Q11.2) WILD-TYPE 166  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED    183   13
  DEL PEAK 31(15Q11.2) WILD-TYPE  166   12
   clus
vv  DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  0                          183                            166
  1                           13                             12
[1] 2 2
[1] FALSE
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED   147 116
  DEL PEAK 31(15Q11.2) WILD-TYPE 129 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED    147  116
  DEL PEAK 31(15Q11.2) WILD-TYPE  129  124
        clus
vv       DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  FEMALE                          147                            129
  MALE                            116                            124
[1] 2 2
[1] FALSE
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q11.2) MUTATED   208  35
  DEL PEAK 31(15Q11.2) WILD-TYPE 202  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED    208   35
  DEL PEAK 31(15Q11.2) WILD-TYPE  202   25
     clus
vv    DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  NO                           208                            202
  YES                           35                             25
[1] 2 2
[1] FALSE
D60V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                            8
  DEL PEAK 31(15Q11.2) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 31(15Q11.2) MUTATED                                  47
  DEL PEAK 31(15Q11.2) WILD-TYPE                                60
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 31(15Q11.2) MUTATED                                                  177
  DEL PEAK 31(15Q11.2) WILD-TYPE                                                144
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 31(15Q11.2) MUTATED                                            0
  DEL PEAK 31(15Q11.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 31(15Q11.2) MUTATED                                               7
  DEL PEAK 31(15Q11.2) WILD-TYPE                                            12
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                                1
  DEL PEAK 31(15Q11.2) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                                    3
  DEL PEAK 31(15Q11.2) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                              0
  DEL PEAK 31(15Q11.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                              13
  DEL PEAK 31(15Q11.2) WILD-TYPE                            10
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                                 1
  DEL PEAK 31(15Q11.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                                               3
  DEL PEAK 31(15Q11.2) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 31(15Q11.2) MUTATED                              3
  DEL PEAK 31(15Q11.2) WILD-TYPE                            7
D60V10, multiclass
                                                    clus
vv                                                   DEL PEAK 31(15Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            47
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          177
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 7
  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                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  3
                                                    clus
vv                                                   DEL PEAK 31(15Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  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                                                    2
  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"
D60V11, continuous
D60V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(15Q11.2) MUTATED   174   9   2  14
  DEL PEAK 31(15Q11.2) WILD-TYPE 170   4   2  12
D60V13, multiclass
    clus
vv   DEL PEAK 31(15Q11.2) MUTATED DEL PEAK 31(15Q11.2) WILD-TYPE
  R0                          174                            170
  R1                            9                              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 31(15Q11.2) MUTATED                                  1     3
  DEL PEAK 31(15Q11.2) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(15Q11.2) MUTATED                          27   197
  DEL PEAK 31(15Q11.2) WILD-TYPE                        25   193
D60V14, multiclass
                                  clus
vv                                 DEL PEAK 31(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     197
                                  clus
vv                                 DEL PEAK 31(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    25
  WHITE                                                       193
[1] 4 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 31(15Q11.2) MUTATED     3 192
  DEL PEAK 31(15Q11.2) WILD-TYPE   4 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q11.2) MUTATED      3  192
  DEL PEAK 31(15Q11.2) WILD-TYPE    4  192
                        clus
vv                       DEL PEAK 31(15Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          192
                        clus
vv                       DEL PEAK 31(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            192
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 32(15Q15.1) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(15Q15.1) MUTATED   170  98
  DEL PEAK 32(15Q15.1) WILD-TYPE 153  83
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                           268                            236 
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                            98                             83 
$`DEL PEAK 32(15Q15.1) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-44-2662 
       19.96         8.02        35.28        11.64        14.73        42.08 
TCGA-44-6147 TCGA-44-7661 TCGA-44-7670 TCGA-44-A47F TCGA-49-4501 TCGA-49-6745 
       27.78        18.31        29.00        11.08        46.72        17.16 
TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
       11.64       156.66        37.32        21.47        41.69        23.05 
TCGA-55-1595 TCGA-55-6979 TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 TCGA-55-8205 
       48.62         7.79         6.15        19.73        17.98        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-A48X TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 
       32.12        18.15        22.65        20.58        20.19        20.65 
TCGA-67-6217 TCGA-73-4662 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC 
       13.87        82.68        85.32        13.71        16.18         1.45 
TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
        6.12        17.29         2.86        18.18        17.92        20.19 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A444 TCGA-MN-A4N1 
       17.75        20.68        24.30         6.35        10.09        27.19 
TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4389 TCGA-05-4395 
        5.29         2.43        10.09        50.07        45.01         0.00 
TCGA-05-4397 TCGA-05-4398 TCGA-05-4417 TCGA-05-4420 TCGA-05-4424 TCGA-05-4430 
       24.03        47.05        14.96        29.98        30.02        25.02 
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-38-4632 TCGA-44-2656 TCGA-44-2657 
       97.74        37.71        49.05        44.61        46.98        44.42 
TCGA-44-2659 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-6144 
       44.94        25.02        38.89        34.06        33.73        23.77 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 
       21.63        23.18        32.45        61.28        19.46         7.17 
TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS TCGA-44-A4SU 
       36.07        23.64        12.66         8.55        13.64        13.45 
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-49-4514 TCGA-49-6744 TCGA-49-6767 TCGA-49-AARE TCGA-49-AARO 
       29.46        55.89        55.33        22.26        40.41       123.58 
TCGA-49-AARQ TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5930 
      221.33        71.47       101.72        15.72        47.41         9.27 
TCGA-50-5933 TCGA-50-5941 TCGA-50-5946 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 
       78.67        48.46        53.16         3.91        25.55        11.05 
TCGA-50-6594 TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 TCGA-53-7626 TCGA-53-7813 
       12.16         0.72        10.13        27.25        30.54        13.94 
TCGA-53-A4EZ TCGA-55-1596 TCGA-55-5899 TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 
       35.21        67.89        30.58        80.52         5.62        42.51 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       40.73        46.03        53.65        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 
       92.81        40.54        28.67        20.02        32.71        22.03 
TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7994 TCGA-55-8089 
        3.91        25.41        18.64        34.19        19.82        23.08 
TCGA-55-8094 TCGA-55-8301 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       17.79        17.56         0.36        13.74        20.28        17.72 
TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 
       17.62        14.66         1.58        12.33        21.40         3.25 
TCGA-55-A493 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8397 TCGA-62-A46P TCGA-62-A46R 
        0.92        19.99         4.57        42.38        19.53        56.71 
TCGA-62-A46S TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 
       54.35        13.61        29.92        56.81        39.09        81.80 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 
       38.37        87.98        42.90        28.41        20.05        20.05 
TCGA-67-3772 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
       18.84         5.42         7.56         6.05         4.41        13.41 
TCGA-69-7980 TCGA-69-A59K TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4675 
       13.51        19.43        23.38        26.30        15.35        30.31 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       50.33        66.64        77.85        49.84        36.66       108.66 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7153 TCGA-78-7158 
      163.10        27.16         5.69        19.27       119.51         5.88 
TCGA-78-7159 TCGA-78-7167 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 
       64.90        88.14        31.20         8.02        26.01        10.55 
TCGA-78-8640 TCGA-80-5608 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7954 
      232.18        93.11        12.36         5.88        31.13        19.89 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8359 
        4.08        24.33         0.79        22.82        31.20        14.60 
TCGA-86-8669 TCGA-86-8671 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6828 
       30.84        27.58        29.46         3.81        24.23        10.62 
TCGA-91-6829 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       41.36        10.19         2.60        12.23        27.68         7.36 
TCGA-91-8499 TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-95-7039 
        1.18        22.45        17.46        23.61         1.08        41.82 
TCGA-95-7567 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 
       18.67         2.76        19.89        42.25        25.48        18.54 
TCGA-97-8174 TCGA-97-8177 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-99-7458 TCGA-99-8025 
        5.39        16.41        21.44        19.76        24.56        34.85 
TCGA-99-8028 TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 
       36.76        18.08        32.48        19.00        18.58        15.65 
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-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YI 
       29.46        11.05        14.10        11.15        19.13         0.13 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.43        19.82        20.28        59.11 

$`DEL PEAK 32(15Q15.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
       14.01         9.96        20.05         9.01        26.01        15.02 
TCGA-05-5420 TCGA-38-4629 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 
       15.02        28.41        26.30        43.53        38.10        23.93 
TCGA-44-6776 TCGA-44-7671 TCGA-44-8119 TCGA-49-6742 TCGA-50-5932 TCGA-55-6978 
       86.01        29.23         9.37        16.04        40.60         5.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 
        7.99        16.01        23.18        14.53        21.44        19.66 
TCGA-55-8204 TCGA-55-8619 TCGA-55-8621 TCGA-55-A492 TCGA-73-4658 TCGA-73-7498 
       16.93        13.68        16.93        19.59        52.60        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 
        8.48        50.24        10.55        16.54        15.68        15.65 
TCGA-95-A4VK TCGA-97-A4M2 TCGA-J2-8194 TCGA-L9-A743 TCGA-MP-A4TA TCGA-05-4250 
       21.40        20.52        23.80        21.83        31.23         3.98 
TCGA-05-4390 TCGA-05-4403 TCGA-05-4415 TCGA-05-4422 TCGA-05-4425 TCGA-05-4426 
       37.02        19.00         2.99        12.00        21.99        26.01 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4626 
       24.00         4.96         9.04         2.04         0.46       120.79 
TCGA-38-A44F TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 
        4.37        42.77         3.19        37.15        38.24        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6779 
       33.30        28.37        28.01        19.56        23.15        16.44 
TCGA-44-7659 TCGA-44-7669 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       22.72        18.87        15.98        15.32         9.44        11.54 
TCGA-49-4486 TCGA-49-4506 TCGA-49-4512 TCGA-49-6743 TCGA-49-AAQV TCGA-49-AAR2 
       76.21        32.84        29.75        53.29        22.26        73.12 
TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       62.24        28.90         8.55       164.12         9.86        20.52 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 TCGA-50-5931 TCGA-50-5936 TCGA-50-5939 
       60.16        49.28         8.22        14.27         8.45        15.12 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6595 TCGA-50-8457 TCGA-50-8459 
       60.72        57.53        42.35         6.21        36.99        36.79 
TCGA-53-7624 TCGA-55-1594 TCGA-55-6543 TCGA-55-6970 TCGA-55-6975 TCGA-55-6984 
       34.29        38.73        14.30        15.25         3.88        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7728 TCGA-55-7907 TCGA-55-7911 
      107.21        70.26        27.09        23.15        11.28        17.65 
TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 
       18.44        29.23        29.72        15.19         5.06        23.64 
TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 
       15.65        29.19        22.16        15.42        15.72        14.47 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-A48Y TCGA-55-A494 TCGA-55-A57B 
       19.96        26.01        17.10        20.71        15.81        17.95 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46U 
       39.98        14.60        88.64        49.25        47.80        67.96 
TCGA-62-A46V TCGA-62-A470 TCGA-62-A471 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 
       72.30        39.25        40.96        37.02         2.04        51.25 
TCGA-64-5815 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       28.47        14.04        12.66        14.73         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-73-4670 TCGA-73-4676 TCGA-73-4677 
        4.24        26.73         8.42         4.31         9.24         1.25 
TCGA-73-A9RS TCGA-75-5147 TCGA-75-6206 TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 
       11.18        43.82        85.15       100.57        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7160 
       21.90        39.95        19.50        38.50        32.09        22.92 
TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 TCGA-78-7537 TCGA-78-7540 
        9.57       104.19       238.29        26.53        53.33        39.35 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-7711 TCGA-86-7713 
       39.75        77.59       110.50        27.09        34.39        38.04 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 
       20.55        32.78        35.24        37.74         4.57        32.65 
TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8585 TCGA-86-8668 TCGA-86-8672 
       31.04        23.05        21.47        11.61        13.91         0.62 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6849 
       28.34        26.50        13.64        26.47         1.97         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-A4JP TCGA-95-7944 TCGA-95-8039 
       16.60        14.27        19.82        19.00        12.39        27.29 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 
       64.60        63.52        61.48         0.59        15.91        18.67 
TCGA-97-8175 TCGA-97-8176 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M5 
       18.12        15.39        14.30        21.60        20.58        20.84 
TCGA-97-A4M6 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AE TCGA-L4-A4E6 
       18.67         1.45        21.57        21.63        35.47        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       14.53         1.91         2.76        58.85         5.49        41.59 
TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       24.36        73.91        71.05        74.33         1.64        47.08 
TCGA-NJ-A55A TCGA-S2-AA1A 
        0.49        16.87 

  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                          0.00                           0.46 
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                        232.18                         238.29 
  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE 
                        22.355                         21.420 
[1] "0.0 - 232.2 (22.4)" "0.5 - 238.3 (21.4)"
[1] "hr=" "1"  
D61V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 32(15Q15.1) MUTATED         4       65       75        0        34
  DEL PEAK 32(15Q15.1) WILD-TYPE       1       68       64        1        16
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 32(15Q15.1) MUTATED          34         40          7       12
  DEL PEAK 32(15Q15.1) WILD-TYPE        38         32          4       13
D61V3, multiclass
            clus
vv           DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE
  STAGE I                               4                              1
  STAGE IA                             65                             68
  STAGE IB                             75                             64
  STAGE II                              0                              1
  STAGE IIA                            34                             16
  STAGE IIB                            34                             38
  STAGE IIIA                           40                             32
  STAGE IIIB                            7                              4
  STAGE IV                             12                             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 32(15Q15.1) MUTATED    89 155  21  10
  DEL PEAK 32(15Q15.1) WILD-TYPE  82 123  25   9
D61V4, multiclass
    clus
vv   DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE
  T1                           89                             82
  T2                          155                            123
  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 32(15Q15.1) MUTATED   171  56    43
  DEL PEAK 32(15Q15.1) WILD-TYPE 162  40    33
D61V5, multiclass
       clus
vv      DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE
  N0                             171                            162
  N1                              56                             40
  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 32(15Q15.1) MUTATED   189  12
  DEL PEAK 32(15Q15.1) WILD-TYPE 160  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.1) MUTATED    189   12
  DEL PEAK 32(15Q15.1) WILD-TYPE  160   13
   clus
vv  DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE
  0                          189                            160
  1                           12                             13
[1] 2 2
[1] FALSE
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.1) MUTATED   149 126
  DEL PEAK 32(15Q15.1) WILD-TYPE 127 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.1) MUTATED    149  126
  DEL PEAK 32(15Q15.1) WILD-TYPE  127  114
        clus
vv       DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE
  FEMALE                          149                            127
  MALE                            126                            114
[1] 2 2
[1] FALSE
D61V8, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q15.1) MUTATED   216  37
  DEL PEAK 32(15Q15.1) WILD-TYPE 194  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.1) MUTATED    216   37
  DEL PEAK 32(15Q15.1) WILD-TYPE  194   23
     clus
vv    DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE
  NO                           216                            194
  YES                           37                             23
[1] 2 2
[1] FALSE
D61V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 32(15Q15.1) MUTATED                            9
  DEL PEAK 32(15Q15.1) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 32(15Q15.1) MUTATED                                  46
  DEL PEAK 32(15Q15.1) WILD-TYPE                                61
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 32(15Q15.1) MUTATED                                                  188
  DEL PEAK 32(15Q15.1) WILD-TYPE                                                133
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 32(15Q15.1) MUTATED                                            0
  DEL PEAK 32(15Q15.1) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 32(15Q15.1) MUTATED                                               9
  DEL PEAK 32(15Q15.1) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 32(15Q15.1) MUTATED                                1
  DEL PEAK 32(15Q15.1) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 32(15Q15.1) MUTATED                                    3
  DEL PEAK 32(15Q15.1) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(15Q15.1) MUTATED                              0
  DEL PEAK 32(15Q15.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 32(15Q15.1) MUTATED                              13
  DEL PEAK 32(15Q15.1) WILD-TYPE                            10
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 32(15Q15.1) MUTATED                                 1
  DEL PEAK 32(15Q15.1) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 32(15Q15.1) MUTATED                                               2
  DEL PEAK 32(15Q15.1) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 32(15Q15.1) MUTATED                              3
  DEL PEAK 32(15Q15.1) WILD-TYPE                            7
D61V10, multiclass
                                                    clus
vv                                                   DEL PEAK 32(15Q15.1) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            46
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          188
  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 32(15Q15.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              61
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            133
  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"
D61V11, continuous
D61V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(15Q15.1) MUTATED   183   7   2  14
  DEL PEAK 32(15Q15.1) WILD-TYPE 161   6   2  12
D61V13, multiclass
    clus
vv   DEL PEAK 32(15Q15.1) MUTATED DEL PEAK 32(15Q15.1) WILD-TYPE
  R0                          183                            161
  R1                            7                              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 32(15Q15.1) MUTATED                                  1     4
  DEL PEAK 32(15Q15.1) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(15Q15.1) MUTATED                          25   211
  DEL PEAK 32(15Q15.1) WILD-TYPE                        27   179
D61V14, multiclass
                                  clus
vv                                 DEL PEAK 32(15Q15.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     211
                                  clus
vv                                 DEL PEAK 32(15Q15.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    27
  WHITE                                                       179
[1] 4 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 32(15Q15.1) MUTATED     3 203
  DEL PEAK 32(15Q15.1) WILD-TYPE   4 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q15.1) MUTATED      3  203
  DEL PEAK 32(15Q15.1) WILD-TYPE    4  181
                        clus
vv                       DEL PEAK 32(15Q15.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          203
                        clus
vv                       DEL PEAK 32(15Q15.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            181
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 33(16P13.3) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(16P13.3) MUTATED    74  35
  DEL PEAK 33(16P13.3) WILD-TYPE 249 146
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                           109                            395 
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                            35                            146 
$`DEL PEAK 33(16P13.3) MUTATED`
TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-38-4630 TCGA-44-7661 TCGA-44-8119 
        9.96         9.01        26.01        35.28        18.31         9.37 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-55-6978 TCGA-55-6979 TCGA-55-7914 
       16.04        17.16        11.64         5.79         7.79         6.15 
TCGA-55-8204 TCGA-55-8205 TCGA-55-A491 TCGA-64-1677 TCGA-95-A4VN TCGA-L9-A444 
       16.93        19.69        20.58        20.65        18.18        10.09 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-05-4389 TCGA-05-4395 TCGA-05-4398 
       27.19         5.29        31.23        45.01         0.00        47.05 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4432 TCGA-05-5428 TCGA-35-4122 TCGA-44-3917 
        2.99        29.98        25.02        22.03         7.40        38.89 
TCGA-44-5643 TCGA-44-5644 TCGA-44-7660 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 
       33.30        28.37        19.46        36.07        23.64        12.66 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4510 TCGA-49-4514 TCGA-49-6767 TCGA-49-AARE 
       28.57        35.54        29.46        55.89        22.26        40.41 
TCGA-49-AARQ TCGA-50-5066 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-53-7624 
      221.33        47.41        53.16         3.91        11.05        34.29 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6968 TCGA-55-6971 TCGA-55-6975 
       13.94        35.21        30.58        42.51        46.03         3.88 
TCGA-55-6986 TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 TCGA-55-7913 TCGA-55-7994 
      107.21        22.03         3.91        18.64        18.44        19.82 
TCGA-55-8089 TCGA-55-8094 TCGA-55-8505 TCGA-55-8507 TCGA-55-8615 TCGA-55-8616 
       23.08        17.79        14.47        13.74        14.66         1.58 
TCGA-55-A494 TCGA-62-8397 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46U TCGA-62-A46V 
       15.81        42.38        49.25        47.80        67.96        72.30 
TCGA-62-A471 TCGA-62-A472 TCGA-64-5774 TCGA-64-5779 TCGA-67-3771 TCGA-69-7763 
       40.96        29.92        87.98        28.41        20.05        22.68 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-73-A9RS 
        6.05         4.41        13.41         4.24        19.43        11.18 
TCGA-75-5146 TCGA-78-7146 TCGA-78-7149 TCGA-78-7167 TCGA-78-7536 TCGA-83-5908 
       77.85         5.69       129.53        88.14         8.02        27.09 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7955 TCGA-86-8054 TCGA-86-8073 TCGA-91-6831 
       31.13        38.04        35.24        37.74        24.33        10.19 
TCGA-91-6847 TCGA-91-8499 TCGA-93-A4JO TCGA-95-7567 TCGA-95-A4VP TCGA-L4-A4E5 
       27.68         1.18         1.08        18.67        19.89        19.00 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TJ 
       18.58        15.65         5.49        11.05        14.10        11.15 
TCGA-NJ-A4YF 
       71.05 

$`DEL PEAK 33(16P13.3) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4434 TCGA-05-5420 
       19.96        14.01         8.02        20.05        15.02        15.02 
TCGA-38-4629 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 
       28.41        11.64        14.73        26.30        43.53        38.10 
TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 
       42.08        23.93        27.78        86.01        29.00        29.23 
TCGA-44-A47F TCGA-49-4501 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 
       11.08        46.72       156.66        37.32        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1595 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       41.69        23.05        48.62         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8203 TCGA-55-8207 
       14.53        21.44        19.66        19.73        17.98        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF 
       18.15        13.68        16.93        22.65        19.59        20.19 
TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       13.87        52.60        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 
       10.55        85.32        13.71        16.18         1.45         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
       17.29        16.54         2.86        15.68        15.65        21.40 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8192 
       17.92        20.19        20.52        17.75        20.68        24.30 
TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A743 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 
       23.80         6.35        21.83         2.43        10.09        50.07 
TCGA-05-4250 TCGA-05-4390 TCGA-05-4397 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 
        3.98        37.02        24.03        19.00        14.96        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 
       30.02        21.99        26.01        25.02        24.00         4.96 
TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4123 TCGA-35-5375 
       29.00         9.04         2.04         0.46         5.98         8.68 
TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F 
       97.74       120.79        37.71        49.05        44.61         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       46.98        44.42        44.94        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       37.15        38.24        34.06        33.73        26.56        28.01 
TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 
       23.77        19.56        23.15        21.63        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7669 TCGA-44-8120 
       61.28        16.44        22.72         7.17        18.87         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU 
       15.98        15.32         9.44        11.54        13.64        13.45 
TCGA-49-4486 TCGA-49-4487 TCGA-49-4490 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 
       76.21        28.11        12.66        14.07        32.84         8.81 
TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
       29.75        53.29        55.33        22.26        73.12        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       28.90         8.55       123.58       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5072 
       71.47       101.72        15.72        60.16        49.28         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        48.46 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 
       60.72        57.53        42.35        25.55        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
        0.72        10.13        36.99        36.79        27.25        30.54 
TCGA-55-1594 TCGA-55-1596 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 
       38.73        67.89        14.30        80.52         5.62        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 
       15.25        53.65        69.34        45.34        32.71        92.81 
TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 
       24.99        40.54        70.26        28.67        20.02        27.09 
TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       32.71        23.15        25.41        11.28        34.19        17.65 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 
       29.23        29.72        15.19         5.06        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
       29.19        22.16        15.42        17.56        15.72         0.36 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       20.28        17.72        19.96        26.01        17.10        17.62 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG 
       12.33        20.71        21.40         3.25         0.92        19.99 
TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46P 
       17.95         4.57        39.98        14.60        88.64        19.53 
TCGA-62-A46R TCGA-62-A46S TCGA-62-A46Y TCGA-62-A470 TCGA-64-1676 TCGA-64-1678 
       56.71        54.35        13.61        39.25        56.81        39.09 
TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 
       81.80        37.02        38.37         2.04        42.90        51.25 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       28.47        20.05        18.84        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
        5.72         4.64         6.64         6.12        13.61         5.42 
TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-71-6725 
        7.56        13.51        14.01        13.45        26.73         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 
       23.38        26.30        15.35         4.31        30.31         9.24 
TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
        1.25        50.33        66.64        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 
       36.66       108.66       100.57       163.10        27.16        19.27 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       20.58        21.90        39.95       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       32.09         5.88        64.90        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
      238.29        26.53        31.20        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       10.55       232.18        39.75        77.59       110.50        93.11 
TCGA-86-6562 TCGA-86-6851 TCGA-86-7711 TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 
       12.36         5.88        34.39        20.55        32.78        19.89 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
        4.08         4.57         0.79        22.82        32.65        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 
       31.20        23.05        21.47        14.60        11.61        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        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 
        3.81        24.23        13.64        26.47        10.62        41.36 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        1.97         2.60        12.23         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP 
       14.27        19.82        22.45        17.46        23.61        19.00 
TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7547 
       41.82        12.39        27.29         2.76        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       18.67         5.39        18.12        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       21.60        20.58        21.44        19.76        20.84        18.67 
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        21.57        21.63 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP 
       18.08        35.47        32.48        14.30        14.53         1.91 
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-A4T6 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TK 
       86.04        58.85        41.59        29.46        24.36        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A 
       73.91        74.33         0.13         1.64        47.08         0.49 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.43        19.82        20.28        59.11        16.87 

  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                          0.00                           0.13 
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                        221.33                         238.29 
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                         20.05                          21.83 
[1] "0.0 - 221.3 (20.1)" "0.1 - 238.3 (21.8)"
[1] "hr=" "1"  
D62V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 33(16P13.3) MUTATED         2       22       26        0        12
  DEL PEAK 33(16P13.3) WILD-TYPE       3      111      113        1        38
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 33(16P13.3) MUTATED          18         17          6        7
  DEL PEAK 33(16P13.3) WILD-TYPE        54         55          5       18
D62V3, multiclass
            clus
vv           DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             22                            111
  STAGE IB                             26                            113
  STAGE II                              0                              1
  STAGE IIA                            12                             38
  STAGE IIB                            18                             54
  STAGE IIIA                           17                             55
  STAGE IIIB                            6                              5
  STAGE IV                              7                             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 33(16P13.3) MUTATED    31  63  11   6
  DEL PEAK 33(16P13.3) WILD-TYPE 140 215  35  13
D62V4, multiclass
    clus
vv   DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  T1                           31                            140
  T2                           63                            215
  T3                           11                             35
  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 33(16P13.3) MUTATED    71  20    20
  DEL PEAK 33(16P13.3) WILD-TYPE 262  76    56
D62V5, multiclass
       clus
vv      DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  N0                              71                            262
  N1                              20                             76
  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"
D62V6, binary
                                cls
clus                               0   1
  DEL PEAK 33(16P13.3) MUTATED    72   7
  DEL PEAK 33(16P13.3) WILD-TYPE 277  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(16P13.3) MUTATED     72    7
  DEL PEAK 33(16P13.3) WILD-TYPE  277   18
   clus
vv  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  0                           72                            277
  1                            7                             18
[1] 2 2
[1] FALSE
D62V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(16P13.3) MUTATED    56  55
  DEL PEAK 33(16P13.3) WILD-TYPE 220 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(16P13.3) MUTATED     56   55
  DEL PEAK 33(16P13.3) WILD-TYPE  220  185
        clus
vv       DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  FEMALE                           56                            220
  MALE                             55                            185
[1] 2 2
[1] FALSE
D62V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(16P13.3) MUTATED    88  14
  DEL PEAK 33(16P13.3) WILD-TYPE 322  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(16P13.3) MUTATED     88   14
  DEL PEAK 33(16P13.3) WILD-TYPE  322   46
     clus
vv    DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  NO                            88                            322
  YES                           14                             46
[1] 2 2
[1] FALSE
D62V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 33(16P13.3) MUTATED                            5
  DEL PEAK 33(16P13.3) WILD-TYPE                         13
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 33(16P13.3) MUTATED                                  27
  DEL PEAK 33(16P13.3) WILD-TYPE                                80
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 33(16P13.3) MUTATED                                                   69
  DEL PEAK 33(16P13.3) WILD-TYPE                                                252
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 33(16P13.3) MUTATED                                            0
  DEL PEAK 33(16P13.3) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 33(16P13.3) MUTATED                                               3
  DEL PEAK 33(16P13.3) WILD-TYPE                                            16
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 33(16P13.3) MUTATED                                0
  DEL PEAK 33(16P13.3) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 33(16P13.3) MUTATED                                    0
  DEL PEAK 33(16P13.3) WILD-TYPE                                  3
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(16P13.3) MUTATED                              0
  DEL PEAK 33(16P13.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 33(16P13.3) MUTATED                               3
  DEL PEAK 33(16P13.3) WILD-TYPE                            20
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 33(16P13.3) MUTATED                                 1
  DEL PEAK 33(16P13.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 33(16P13.3) MUTATED                                               2
  DEL PEAK 33(16P13.3) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 33(16P13.3) MUTATED                              1
  DEL PEAK 33(16P13.3) WILD-TYPE                            9
D62V10, multiclass
                                                    clus
vv                                                   DEL PEAK 33(16P13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           69
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 3
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            0
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 3
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  1
                                                    clus
vv                                                   DEL PEAK 33(16P13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     13
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              80
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            252
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  16
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              3
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  20
  LUNG SIGNET RING ADENOCARCINOMA                                                 0
  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"
D62V11, continuous
D62V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 33(16P13.3) MUTATED    78   1   0   3
  DEL PEAK 33(16P13.3) WILD-TYPE 266  12   4  23
D62V13, multiclass
    clus
vv   DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  R0                           78                            266
  R1                            1                             12
  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 33(16P13.3) MUTATED                                  0     0
  DEL PEAK 33(16P13.3) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(16P13.3) MUTATED                          14    81
  DEL PEAK 33(16P13.3) WILD-TYPE                        38   309
D62V14, multiclass
                                  clus
vv                                 DEL PEAK 33(16P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                      81
                                  clus
vv                                 DEL PEAK 33(16P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    38
  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"
D62V15, binary
                                cls
clus                               0   1
  DEL PEAK 33(16P13.3) MUTATED     3  80
  DEL PEAK 33(16P13.3) WILD-TYPE   4 304
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(16P13.3) MUTATED      3   80
  DEL PEAK 33(16P13.3) WILD-TYPE    4  304
                        clus
vv                       DEL PEAK 33(16P13.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           80
                        clus
vv                       DEL PEAK 33(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            304
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 34(16Q23.1) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(16Q23.1) MUTATED   106  59
  DEL PEAK 34(16Q23.1) WILD-TYPE 217 122
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                           165                            339 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                            59                            122 
$`DEL PEAK 34(16Q23.1) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 
       19.96         8.02        20.05         9.01        26.01        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-44-2661 TCGA-44-7661 TCGA-44-8119 TCGA-49-6742 
       35.28        11.64        38.10        18.31         9.37        16.04 
TCGA-49-6745 TCGA-49-6761 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7724 
       17.16        11.64        48.62         5.79         7.79        23.18 
TCGA-55-7726 TCGA-55-8091 TCGA-55-8205 TCGA-55-8207 TCGA-55-A48X TCGA-55-A491 
       21.44        19.73        19.69        32.12        22.65        20.58 
TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 
       20.65        52.60        82.68        13.71        16.18         6.12 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-A4VN TCGA-97-A4M3 TCGA-L9-A443 TCGA-L9-A444 
       17.29         2.86        18.18        17.75         6.35        10.09 
TCGA-MN-A4N1 TCGA-MP-A4TC TCGA-05-4389 TCGA-05-4390 TCGA-05-4398 TCGA-05-4415 
       27.19         2.43        45.01        37.02        47.05         2.99 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 
       29.98        30.02        25.02        22.03         7.40         5.98 
TCGA-38-4625 TCGA-38-4628 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
       97.74        49.05        34.06        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-6775 TCGA-44-6777 TCGA-44-7660 TCGA-44-7669 TCGA-44-8117 
       28.37        23.18        32.45        19.46        18.87        12.66 
TCGA-44-A47B TCGA-49-4487 TCGA-49-4494 TCGA-49-4507 TCGA-49-4510 TCGA-49-6743 
        9.44        28.11        35.54         8.81        29.46        53.29 
TCGA-49-6744 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5933 TCGA-50-5936 
       55.33       101.72        47.41        49.28        78.67         8.45 
TCGA-50-5939 TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-8457 TCGA-53-7624 
       15.12        53.16         3.91        11.05        36.99        34.29 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-6712 TCGA-55-6968 TCGA-55-6971 TCGA-55-6986 
       13.94        35.21         5.62        42.51        46.03       107.21 
TCGA-55-7281 TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 TCGA-55-7913 TCGA-55-8505 
       28.67        22.03         3.91        18.64        18.44        14.47 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8514 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z 
        0.36        13.74        17.10         1.58        12.33        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-62-8394 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46U 
        3.25         0.92         4.57        42.38        47.80        67.96 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 TCGA-64-5774 TCGA-64-5778 
       39.25        40.96        29.92        81.80        87.98        42.90 
TCGA-64-5779 TCGA-69-7763 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 
       28.41        22.68         6.05         4.41        13.41         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4675 TCGA-75-5125 TCGA-75-5146 TCGA-75-6214 
       19.43         8.42        30.31        66.64        77.85        36.66 
TCGA-78-7143 TCGA-78-7146 TCGA-78-7150 TCGA-78-7152 TCGA-78-7155 TCGA-78-7159 
      163.10         5.69        21.90        39.95        38.50        64.90 
TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-83-5908 TCGA-86-6851 
       88.14        26.53        31.20         8.02        27.09         5.88 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8073 
       34.39        38.04        32.78        19.89        37.74        24.33 
TCGA-86-8075 TCGA-86-8278 TCGA-86-8359 TCGA-86-8668 TCGA-86-8672 TCGA-86-A4JF 
       22.82        31.04        14.60        13.91         0.62        24.23 
TCGA-91-6847 TCGA-91-8499 TCGA-93-7348 TCGA-93-A4JO TCGA-95-7567 TCGA-95-8494 
       27.68         1.18        17.46         1.08        18.67         2.76 
TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8175 TCGA-97-A4M0 
       42.25        25.48        18.54        18.67        18.12        21.44 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4TF TCGA-NJ-A4YG 
       32.48        19.00        18.58         2.76        11.05        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A7XG 
        0.13         1.64        20.28 

$`DEL PEAK 34(16Q23.1) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4434 TCGA-05-5420 TCGA-38-6178 TCGA-38-7271 
       14.01         9.96        15.02        15.02        14.73        26.30 
TCGA-44-2655 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7670 
       43.53        42.08        23.93        27.78        86.01        29.00 
TCGA-44-7671 TCGA-44-A47F TCGA-49-4501 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 
       29.23        11.08        46.72       156.66        37.32        40.60 
TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 
       21.47        41.69        23.05         7.99        16.01        14.53 
TCGA-55-7914 TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 TCGA-55-8511 TCGA-55-8619 
        6.15        19.66        17.98        16.93        18.15        13.68 
TCGA-55-8621 TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-7498 TCGA-78-7166 
       16.93        19.59        20.19        13.87        39.09         8.48 
TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-A4BC TCGA-95-7043 TCGA-95-7947 
       50.24        10.55        85.32         1.45        16.54        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 
       15.65        21.40        17.92        20.19        20.52        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A743 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD 
       24.30        23.80        21.83         5.29        31.23        10.09 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 TCGA-05-4417 
       50.07         3.98         0.00        24.03        19.00        14.96 
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-05-5425 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 
       29.00         9.04         2.04         0.46         8.68       120.79 
TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 
       37.71        44.61         4.37        46.98        44.42        44.94 
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-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6778 
       28.01        23.77        19.56        23.15        21.63        61.28 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7672 TCGA-44-8120 
       16.44        22.72         7.17        36.07        23.64         8.55 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.98        15.32        11.54        13.64        13.45        76.21 
TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4506 TCGA-49-4512 TCGA-49-4514 
       28.57        12.66        14.07        32.84        29.75        55.89 
TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 
       22.26        22.26        73.12        62.24        28.90         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       40.41       123.58       221.33       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
       71.47        15.72        60.16         8.22         9.27        14.27 
TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 TCGA-50-6594 
       48.46        60.72        57.53        42.35        25.55        12.16 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 
        6.21         0.72        10.13        36.79        27.25        30.54 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6969 
       38.73        67.89        30.58        14.30        80.52        40.73 
TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
       15.25        53.65         3.88        69.34        45.34        32.71 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 
       92.81        24.99        40.54        70.26        20.02        27.09 
TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       32.71        23.15        25.41        11.28        34.19        17.65 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 
       19.82        29.23        29.72        15.19        23.08         5.06 
TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       17.79        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8513 
       17.56        15.72        20.28        17.72        19.96        26.01 
TCGA-55-8614 TCGA-55-8615 TCGA-55-A48Y TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B 
       17.62        14.66        20.71        15.81        19.99        17.95 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R 
       39.98        14.60        88.64        49.25        19.53        56.71 
TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 
       54.35        72.30        13.61        56.81        39.09        37.02 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
       38.37         2.04        51.25        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       18.84        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7980 
        6.64         6.12        13.61         5.42         7.56        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
       14.01        13.45        26.73        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5147 
        4.31         9.24         1.25        50.33        11.18        43.82 
TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7147 
       85.15        49.84       108.66       100.57        27.16        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
       20.58       129.53       119.51        19.50        32.09         5.88 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7537 TCGA-78-7539 
       22.92         9.57       104.19       238.29        53.33        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-80-5608 TCGA-86-6562 TCGA-86-7701 TCGA-86-7714 TCGA-86-7955 TCGA-86-8055 
       93.11        12.36        31.13        20.55        35.24         4.08 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 
        4.57         0.79        32.65        31.20        23.05        21.47 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       11.61        30.84        27.58        28.34        26.50        29.46 
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-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
       10.19         2.60        12.23         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7039 
       14.27        19.82        22.45        23.61        19.00        41.82 
TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       12.39        27.29        19.89        64.60        63.52        61.48 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
        0.59        15.91         5.39        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 
       21.60        20.58        19.76        20.84        18.67        24.56 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD 
       34.85        36.76         1.45        21.57        21.63        18.08 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 
       35.47        14.30        14.53         1.91        15.65        38.63 
TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 
       86.14        58.45        49.35        37.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
        5.49        41.59        29.46        24.36        14.10        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O 
       19.13        73.91        71.05        47.08         0.49         0.43 
TCGA-NJ-A55R TCGA-O1-A52J TCGA-S2-AA1A 
       19.82        59.11        16.87 

  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                        163.10                         238.29 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                         21.44                          21.63 
[1] "0.1 - 163.1 (21.4)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1.1"
D63V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 34(16Q23.1) MUTATED         1       34       51        0        19
  DEL PEAK 34(16Q23.1) WILD-TYPE       4       99       88        1        31
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 34(16Q23.1) MUTATED          24         26          6        8
  DEL PEAK 34(16Q23.1) WILD-TYPE        48         46          5       17
D63V3, multiclass
            clus
vv           DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             34                             99
  STAGE IB                             51                             88
  STAGE II                              0                              1
  STAGE IIA                            19                             31
  STAGE IIB                            24                             48
  STAGE IIIA                           26                             46
  STAGE IIIB                            6                              5
  STAGE IV                              8                             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 34(16Q23.1) MUTATED    48 100  15   6
  DEL PEAK 34(16Q23.1) WILD-TYPE 123 178  31  13
D63V4, multiclass
    clus
vv   DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  T1                           48                            123
  T2                          100                            178
  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 34(16Q23.1) MUTATED   104  32    30
  DEL PEAK 34(16Q23.1) WILD-TYPE 229  64    46
D63V5, multiclass
       clus
vv      DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  N0                             104                            229
  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"
D63V6, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED   117   8
  DEL PEAK 34(16Q23.1) WILD-TYPE 232  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED    117    8
  DEL PEAK 34(16Q23.1) WILD-TYPE  232   17
   clus
vv  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  0                          117                            232
  1                            8                             17
[1] 2 2
[1] FALSE
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED    88  81
  DEL PEAK 34(16Q23.1) WILD-TYPE 188 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED     88   81
  DEL PEAK 34(16Q23.1) WILD-TYPE  188  159
        clus
vv       DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  FEMALE                           88                            188
  MALE                             81                            159
[1] 2 2
[1] FALSE
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED   138  21
  DEL PEAK 34(16Q23.1) WILD-TYPE 272  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED    138   21
  DEL PEAK 34(16Q23.1) WILD-TYPE  272   39
     clus
vv    DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  NO                           138                            272
  YES                           21                             39
[1] 2 2
[1] FALSE
D63V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                            8
  DEL PEAK 34(16Q23.1) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 34(16Q23.1) MUTATED                                  36
  DEL PEAK 34(16Q23.1) WILD-TYPE                                71
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 34(16Q23.1) MUTATED                                                  103
  DEL PEAK 34(16Q23.1) WILD-TYPE                                                218
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 34(16Q23.1) MUTATED                                            1
  DEL PEAK 34(16Q23.1) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 34(16Q23.1) MUTATED                                               6
  DEL PEAK 34(16Q23.1) WILD-TYPE                                            13
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                                2
  DEL PEAK 34(16Q23.1) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                                    1
  DEL PEAK 34(16Q23.1) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                              0
  DEL PEAK 34(16Q23.1) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                               7
  DEL PEAK 34(16Q23.1) WILD-TYPE                            16
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                                 0
  DEL PEAK 34(16Q23.1) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                                               3
  DEL PEAK 34(16Q23.1) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 34(16Q23.1) MUTATED                              2
  DEL PEAK 34(16Q23.1) WILD-TYPE                            8
D63V10, multiclass
                                                    clus
vv                                                   DEL PEAK 34(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 34(16Q23.1) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              71
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            218
  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"
D63V11, continuous
D63V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(16Q23.1) MUTATED   109   3   1  10
  DEL PEAK 34(16Q23.1) WILD-TYPE 235  10   3  16
D63V13, multiclass
    clus
vv   DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  R0                          109                            235
  R1                            3                             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 34(16Q23.1) MUTATED                                  0     4
  DEL PEAK 34(16Q23.1) WILD-TYPE                                1     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(16Q23.1) MUTATED                          13   132
  DEL PEAK 34(16Q23.1) WILD-TYPE                        39   258
D63V14, multiclass
                                  clus
vv                                 DEL PEAK 34(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                     132
                                  clus
vv                                 DEL PEAK 34(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       258
[1] 4 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 34(16Q23.1) MUTATED     5 122
  DEL PEAK 34(16Q23.1) WILD-TYPE   2 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED      5  122
  DEL PEAK 34(16Q23.1) WILD-TYPE    2  262
                        clus
vv                       DEL PEAK 34(16Q23.1) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          122
                        clus
vv                       DEL PEAK 34(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            262
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 35(16Q24.3) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(16Q24.3) MUTATED   122  62
  DEL PEAK 35(16Q24.3) WILD-TYPE 201 119
  DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE 
                           184                            320 
  DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE 
                            62                            119 
$`DEL PEAK 35(16Q24.3) MUTATED`
TCGA-05-4382 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 
       19.96         8.02        20.05         9.01        26.01        28.41 
TCGA-38-4630 TCGA-38-4631 TCGA-44-2661 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 
       35.28        11.64        38.10        18.31        29.00         9.37 
TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 
       16.04        17.16        11.64        48.62         5.79         7.79 
TCGA-55-7724 TCGA-55-7726 TCGA-55-8091 TCGA-55-8205 TCGA-55-8207 TCGA-55-A48X 
       23.18        21.44        19.73        19.69        32.12        22.65 
TCGA-55-A491 TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-91-7771 TCGA-93-8067 
       20.58        20.65        52.60        82.68        16.18         6.12 
TCGA-93-A4JQ TCGA-95-7562 TCGA-95-A4VN TCGA-97-A4M3 TCGA-L9-A443 TCGA-L9-A444 
       17.29         2.86        18.18        17.75         6.35        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-05-4389 TCGA-05-4390 
       21.83        27.19         5.29         2.43        45.01        37.02 
TCGA-05-4398 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4432 TCGA-05-5428 
       47.05         2.99        29.98        30.02        25.02        22.03 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4626 TCGA-38-4628 TCGA-44-3918 
        7.40         5.98        97.74       120.79        49.05        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 TCGA-44-6774 TCGA-44-6775 
       33.73        26.56        33.30        28.37        21.63        23.18 
TCGA-44-6777 TCGA-44-7660 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-49-4487 
       32.45        19.46        18.87        23.64        12.66        28.11 
TCGA-49-4494 TCGA-49-4510 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AARQ 
       35.54        29.46        53.29        55.33        22.26       221.33 
TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
      101.72        47.41        49.28        78.67         8.45        15.12 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 TCGA-53-7813 
       53.16         3.91        11.05        12.16        36.99        13.94 
TCGA-53-A4EZ TCGA-55-6712 TCGA-55-6968 TCGA-55-6971 TCGA-55-6986 TCGA-55-7281 
       35.21         5.62        42.51        46.03       107.21        28.67 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 TCGA-55-7913 TCGA-55-8094 TCGA-55-8302 
       22.03         3.91        18.64        18.44        17.79        15.72 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 
       14.47         0.36        13.74        17.72        17.10        14.66 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-62-8394 
        1.58        12.33        21.40         3.25         0.92         4.57 
TCGA-62-8397 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 
       42.38        49.25        47.80        67.96        39.25        40.96 
TCGA-64-1679 TCGA-64-5774 TCGA-64-5779 TCGA-67-3770 TCGA-67-3771 TCGA-69-7763 
       81.80        87.98        28.41        20.05        20.05        22.68 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
        6.05         4.41        13.41         4.24        19.43         8.42 
TCGA-73-4675 TCGA-75-5125 TCGA-75-5146 TCGA-75-6214 TCGA-78-7143 TCGA-78-7150 
       30.31        66.64        77.85        36.66       163.10        21.90 
TCGA-78-7152 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7167 TCGA-78-7220 
       39.95        38.50        64.90         9.57        88.14        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-8640 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 
       31.20         8.02       232.18        27.09         5.88        34.39 
TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8073 TCGA-86-8075 
       38.04        32.78        19.89        37.74        24.33        22.82 
TCGA-86-8278 TCGA-86-8359 TCGA-86-8668 TCGA-86-8672 TCGA-86-8673 TCGA-86-A4JF 
       31.04        14.60        13.91         0.62        28.34        24.23 
TCGA-91-6831 TCGA-91-6847 TCGA-91-8496 TCGA-91-8499 TCGA-93-7348 TCGA-93-A4JO 
       10.19        27.68        16.60         1.18        17.46         1.08 
TCGA-95-7567 TCGA-95-8494 TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 
       18.67         2.76        42.25        25.48        18.54        18.67 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8552 TCGA-97-A4M0 TCGA-99-7458 TCGA-99-8028 
        5.39        18.12        20.58        21.44        24.56        36.76 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4TF 
       32.48        19.00        18.58         2.76        86.14        11.05 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A7XG 
       74.33         0.13         1.64        20.28 

$`DEL PEAK 35(16Q24.3) WILD-TYPE`
TCGA-05-4384 TCGA-05-4396 TCGA-05-4434 TCGA-05-5420 TCGA-38-6178 TCGA-38-7271 
       14.01         9.96        15.02        15.02        14.73        26.30 
TCGA-44-2655 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7671 
       43.53        42.08        23.93        27.78        86.01        29.23 
TCGA-44-A47F TCGA-49-4501 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 
       11.08        46.72       156.66        37.32        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 TCGA-55-7914 
       41.69        23.05         7.99        16.01        14.53         6.15 
TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       19.66        17.98        16.93        18.15        13.68        16.93 
TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       19.59        20.19        13.87        39.09         8.48        50.24 
TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-A4BC TCGA-95-7043 TCGA-95-7947 
       10.55        85.32        13.71         1.45        16.54        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M7 
       15.65        21.40        17.92        20.19        20.52        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
       24.30        23.80        31.23        10.09        50.07         3.98 
TCGA-05-4395 TCGA-05-4397 TCGA-05-4403 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 
        0.00        24.03        19.00        14.96        12.00        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 
       26.01        25.02        24.00         4.96        29.00         9.04 
TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4627 TCGA-38-4632 TCGA-38-A44F 
        2.04         0.46         8.68        37.71        44.61         4.37 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       46.98        44.42        44.94        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 
       37.15        38.24        38.89        28.01        23.77        19.56 
TCGA-44-6148 TCGA-44-6778 TCGA-44-6779 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 
       23.15        61.28        16.44        22.72         7.17        36.07 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
        8.55        15.98        15.32         9.44        11.54        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4506 
       13.45        76.21        28.57        12.66        14.07        32.84 
TCGA-49-4507 TCGA-49-4512 TCGA-49-4514 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 
        8.81        29.75        55.89        22.26        73.12        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-50-5072 TCGA-50-5930 
       20.52        71.47        15.72        60.16         8.22         9.27 
TCGA-50-5931 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6592 
       14.27        48.46        60.72        57.53        42.35        25.55 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 
        6.21         0.72        10.13        36.79        27.25        34.29 
TCGA-53-7626 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
       30.54        38.73        67.89        30.58        14.30        80.52 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       40.73        15.25        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6987 TCGA-55-7283 
       32.71        92.81        24.99        40.54        70.26        20.02 
TCGA-55-7570 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 
       27.09        32.71        23.15        25.41        11.28        34.19 
TCGA-55-7911 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
       17.65        19.82        29.23        29.72        15.19        23.08 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
        5.06        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-A48Y 
       17.56        20.28        19.96        26.01        17.62        20.71 
TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 
       15.81        19.99        17.95        39.98        14.60        88.64 
TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 
       19.53        56.71        54.35        72.30        13.61        29.92 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 
       56.81        39.09        37.02        38.37         2.04        42.90 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
       51.25        28.47        18.84        14.04        12.66        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
        5.72         4.64         6.64         6.12        13.61         5.42 
TCGA-69-7973 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4659 
        7.56        13.51        14.01        13.45        26.73        23.38 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 
       26.30        15.35         4.31         9.24         1.25        50.33 
TCGA-73-A9RS TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 TCGA-75-7027 
       11.18        43.82        85.15        49.84       108.66       100.57 
TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 
       27.16         5.69        19.27        20.58       129.53       119.51 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 
       19.50        32.09         5.88        22.92       104.19       238.29 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 
       53.33        26.01        39.35        10.55        39.75        77.59 
TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 TCGA-86-7701 TCGA-86-7714 TCGA-86-7955 
      110.50        93.11        12.36        31.13        20.55        35.24 
TCGA-86-8055 TCGA-86-8056 TCGA-86-8074 TCGA-86-8076 TCGA-86-8279 TCGA-86-8280 
        4.08         4.57         0.79        32.65        31.20        23.05 
TCGA-86-8358 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8674 TCGA-86-A456 
       21.47        11.61        30.84        27.58        26.50        29.46 
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-91-6835 TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8497 TCGA-91-A4BD 
        2.60        12.23         7.36         1.15        14.27        19.82 
TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-8039 
       22.45        23.61        19.00        41.82        12.39        27.29 
TCGA-95-A4VP TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 TCGA-97-7941 
       19.89        64.60        63.52        61.48         0.59        15.91 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-A4M1 TCGA-97-A4M5 
       15.39        16.41        14.30        21.60        19.76        20.84 
TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD 
       18.67        34.85         1.45        21.57        21.63        18.08 
TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 
       35.47        14.30        14.53         1.91        15.65        38.63 
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-A4TE TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
       41.59        29.46        24.36        14.10        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R 
       73.91        71.05        47.08         0.49         0.43        19.82 
TCGA-O1-A52J TCGA-S2-AA1A 
       59.11        16.87 

  DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE 
                          0.13                           0.00 
  DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE 
                        232.18                         238.29 
  DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE 
                        21.535                         21.615 
[1] "0.1 - 232.2 (21.5)" "0.0 - 238.3 (21.6)"
[1] "hr=" "1.1"
D64V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 35(16Q24.3) MUTATED         3       38       54        0        23
  DEL PEAK 35(16Q24.3) WILD-TYPE       2       95       85        1        27
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 35(16Q24.3) MUTATED          25         30          6        8
  DEL PEAK 35(16Q24.3) WILD-TYPE        47         42          5       17
D64V3, multiclass
            clus
vv           DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             38                             95
  STAGE IB                             54                             85
  STAGE II                              0                              1
  STAGE IIA                            23                             27
  STAGE IIB                            25                             47
  STAGE IIIA                           30                             42
  STAGE IIIB                            6                              5
  STAGE IV                              8                             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 35(16Q24.3) MUTATED    56 108  17   7
  DEL PEAK 35(16Q24.3) WILD-TYPE 115 170  29  12
D64V4, multiclass
    clus
vv   DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE
  T1                           56                            115
  T2                          108                            170
  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 35(16Q24.3) MUTATED   116  34    34
  DEL PEAK 35(16Q24.3) WILD-TYPE 217  62    42
D64V5, multiclass
       clus
vv      DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE
  N0                             116                            217
  N1                              34                             62
  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"
D64V6, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q24.3) MUTATED   129   8
  DEL PEAK 35(16Q24.3) WILD-TYPE 220  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q24.3) MUTATED    129    8
  DEL PEAK 35(16Q24.3) WILD-TYPE  220   17
   clus
vv  DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE
  0                          129                            220
  1                            8                             17
[1] 2 2
[1] FALSE
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q24.3) MUTATED   100  88
  DEL PEAK 35(16Q24.3) WILD-TYPE 176 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q24.3) MUTATED    100   88
  DEL PEAK 35(16Q24.3) WILD-TYPE  176  152
        clus
vv       DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE
  FEMALE                          100                            176
  MALE                             88                            152
[1] 2 2
[1] FALSE
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK 35(16Q24.3) MUTATED   153  22
  DEL PEAK 35(16Q24.3) WILD-TYPE 257  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q24.3) MUTATED    153   22
  DEL PEAK 35(16Q24.3) WILD-TYPE  257   38
     clus
vv    DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE
  NO                           153                            257
  YES                           22                             38
[1] 2 2
[1] FALSE
D64V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 35(16Q24.3) MUTATED                            8
  DEL PEAK 35(16Q24.3) WILD-TYPE                         10
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 35(16Q24.3) MUTATED                                  37
  DEL PEAK 35(16Q24.3) WILD-TYPE                                70
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 35(16Q24.3) MUTATED                                                  117
  DEL PEAK 35(16Q24.3) WILD-TYPE                                                204
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 35(16Q24.3) MUTATED                                            1
  DEL PEAK 35(16Q24.3) WILD-TYPE                                          4
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 35(16Q24.3) MUTATED                                               9
  DEL PEAK 35(16Q24.3) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 35(16Q24.3) MUTATED                                2
  DEL PEAK 35(16Q24.3) WILD-TYPE                              0
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 35(16Q24.3) MUTATED                                    1
  DEL PEAK 35(16Q24.3) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(16Q24.3) MUTATED                              0
  DEL PEAK 35(16Q24.3) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 35(16Q24.3) MUTATED                               8
  DEL PEAK 35(16Q24.3) WILD-TYPE                            15
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 35(16Q24.3) MUTATED                                 0
  DEL PEAK 35(16Q24.3) WILD-TYPE                               1
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 35(16Q24.3) MUTATED                                               3
  DEL PEAK 35(16Q24.3) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 35(16Q24.3) MUTATED                              2
  DEL PEAK 35(16Q24.3) WILD-TYPE                            8
D64V10, multiclass
                                                    clus
vv                                                   DEL PEAK 35(16Q24.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            37
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          117
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 9
  LUNG CLEAR CELL ADENOCARCINOMA                                                2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 8
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  MUCINOUS (COLLOID) CARCINOMA                                                  2
                                                    clus
vv                                                   DEL PEAK 35(16Q24.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                     10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              70
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            204
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  10
  LUNG CLEAR CELL ADENOCARCINOMA                                                  0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  15
  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"
D64V11, continuous
D64V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 35(16Q24.3) MUTATED   120   4   1  10
  DEL PEAK 35(16Q24.3) WILD-TYPE 224   9   3  16
D64V13, multiclass
    clus
vv   DEL PEAK 35(16Q24.3) MUTATED DEL PEAK 35(16Q24.3) WILD-TYPE
  R0                          120                            224
  R1                            4                              9
  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(16Q24.3) MUTATED                                  0     4
  DEL PEAK 35(16Q24.3) WILD-TYPE                                1     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(16Q24.3) MUTATED                          18   143
  DEL PEAK 35(16Q24.3) WILD-TYPE                        34   247
D64V14, multiclass
                                  clus
vv                                 DEL PEAK 35(16Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                     143
                                  clus
vv                                 DEL PEAK 35(16Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       247
[1] 4 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 35(16Q24.3) MUTATED     5 136
  DEL PEAK 35(16Q24.3) WILD-TYPE   2 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(16Q24.3) MUTATED      5  136
  DEL PEAK 35(16Q24.3) WILD-TYPE    2  248
                        clus
vv                       DEL PEAK 35(16Q24.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          136
                        clus
vv                       DEL PEAK 35(16Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            248
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 36(17P13.3) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(17P13.3) MUTATED   181  94
  DEL PEAK 36(17P13.3) WILD-TYPE 142  87
  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                           275                            229 
  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                            94                             87 
$`DEL PEAK 36(17P13.3) MUTATED`
TCGA-05-4396 TCGA-05-4402 TCGA-05-4427 TCGA-05-5420 TCGA-38-4631 TCGA-38-6178 
        9.96         8.02        26.01        15.02        11.64        14.73 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6147 TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 
       38.10        42.08        27.78        18.31        29.00         9.37 
TCGA-49-4501 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-6597 
       46.72        17.16        11.64       156.66        37.32        41.69 
TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7573 TCGA-55-7726 
       23.05        48.62         5.79         7.79        16.01        21.44 
TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
        6.15        19.73        17.98        19.69        32.12        18.15 
TCGA-55-A48X TCGA-55-A491 TCGA-67-6217 TCGA-73-4658 TCGA-80-5611 TCGA-91-6836 
       22.65        20.58        13.87        52.60        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7562 TCGA-95-7947 
       16.18         1.45         6.12        17.29         2.86        15.68 
TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-J2-8192 TCGA-L9-A443 TCGA-L9-A743 
       15.65        21.40        18.18        24.30         6.35        21.83 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 
       27.19         5.29        10.09        50.07        45.01        37.02 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 
        0.00        47.05         2.99        14.96        29.98        21.99 
TCGA-05-4426 TCGA-05-4430 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 
       26.01        25.02        24.00        29.00        22.03         9.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 
        7.40         5.98        97.74        44.61        46.98        44.42 
TCGA-44-2659 TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3917 TCGA-44-3918 
       44.94        42.77        25.02        37.15        38.89        34.06 
TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-6144 TCGA-44-6775 TCGA-44-6777 
       33.73        26.56        33.30        23.77        23.18        32.45 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 TCGA-44-8117 TCGA-44-8120 
       61.28        16.44        19.46        36.07        12.66         8.55 
TCGA-44-A47B TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-6743 
        9.44        12.66        14.07         8.81        29.46        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
       55.33        22.26        22.26         8.55        40.41       123.58 
TCGA-49-AARQ TCGA-50-5049 TCGA-50-5051 TCGA-50-5068 TCGA-50-5931 TCGA-50-5936 
      221.33       101.72        15.72        49.28        14.27         8.45 
TCGA-50-5941 TCGA-50-5944 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 
       48.46        57.53         3.91        11.05        12.16         0.72 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 
       10.13        34.29        30.54        13.94        38.73        67.89 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
        5.62        42.51        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6984 TCGA-55-6985 TCGA-55-7281 TCGA-55-7574 TCGA-55-7576 
       32.71        24.99        40.54        28.67        32.71        22.03 
TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7994 
        3.91        25.41        18.64        34.19        17.65        19.82 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8094 TCGA-55-8097 TCGA-55-8302 
       29.23        29.72        23.08        17.79        15.65        15.72 
TCGA-55-8506 TCGA-55-8510 TCGA-55-8514 TCGA-55-8614 TCGA-55-8620 TCGA-55-A48Y 
        0.36        17.72        17.10        17.62        12.33        20.71 
TCGA-55-A48Z TCGA-55-A57B TCGA-62-8394 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46R 
       21.40        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        81.80 
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        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-69-7760 TCGA-69-7761 
       20.05        18.84        14.04         5.72         6.64         6.12 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 
       13.61         5.42         6.05         4.41        13.41         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 
       26.73        19.43         8.42        23.38        15.35         4.31 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        11.18        66.64        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       36.66       108.66       163.10        27.16         5.69        19.27 
TCGA-78-7150 TCGA-78-7154 TCGA-78-7159 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
       21.90        19.50        64.90        31.20         8.02        26.01 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-80-5608 TCGA-86-6851 
       39.35        10.55       232.18        77.59        93.11         5.88 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
       31.13        34.39        38.04        32.78        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 
       37.74         4.08         4.57        24.33        22.82        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-8669 TCGA-86-A4JF 
       31.20        23.05        21.47        13.91        30.84        24.23 
TCGA-91-6828 TCGA-91-6831 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-93-7347 
       10.62        10.19         2.60        12.23        27.68        22.45 
TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 
        1.08        41.82        18.67        12.39        27.29         2.76 
TCGA-95-A4VP TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-8175 TCGA-97-8547 
       19.89        25.48        18.54         0.59        18.12        21.60 
TCGA-97-A4M0 TCGA-97-A4M5 TCGA-97-A4M6 TCGA-99-7458 TCGA-99-8025 TCGA-99-8033 
       21.44        20.84        18.67        24.56        34.85        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV TCGA-L9-A8F4 
       18.08        35.47        19.00        14.53        18.58        15.65 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T4 
       38.63         2.76        86.14        58.45        49.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ 
       58.85        29.46        11.05        24.36        14.10        11.15 
TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-O1-A52J 
       71.05        74.33         0.13        47.08        59.11 

$`DEL PEAK 36(17P13.3) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 TCGA-38-4629 
       19.96        14.01        20.05         9.01        15.02        28.41 
TCGA-38-4630 TCGA-38-7271 TCGA-44-2655 TCGA-44-6146 TCGA-44-6776 TCGA-44-7671 
       35.28        26.30        43.53        23.93        86.01        29.23 
TCGA-44-A47F TCGA-49-6742 TCGA-50-5932 TCGA-50-5935 TCGA-55-7284 TCGA-55-7724 
       11.08        16.04        40.60        21.47         7.99        23.18 
TCGA-55-7725 TCGA-55-8090 TCGA-55-8204 TCGA-55-8619 TCGA-55-8621 TCGA-55-A492 
       14.53        19.66        16.93        13.68        16.93        19.59 
TCGA-55-A4DF TCGA-64-1677 TCGA-73-4662 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       20.19        20.65        82.68        39.09         8.48        50.24 
TCGA-78-8660 TCGA-95-7043 TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       10.55        16.54        17.92        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A444 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4250 
       20.68        23.80        10.09        31.23         2.43         3.98 
TCGA-05-4397 TCGA-05-4403 TCGA-05-4422 TCGA-05-4424 TCGA-05-4432 TCGA-05-5423 
       24.03        19.00        12.00        30.02        25.02         4.96 
TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
        2.04         0.46         8.68       120.79        37.71        49.05 
TCGA-38-A44F TCGA-44-2666 TCGA-44-3398 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 
        4.37         3.19        38.24        28.37        28.01        19.56 
TCGA-44-6148 TCGA-44-6774 TCGA-44-7659 TCGA-44-7662 TCGA-44-7669 TCGA-44-7672 
       23.15        21.63        22.72         7.17        18.87        23.64 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       15.98        15.32        11.54        13.64        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4512 TCGA-49-4514 
       28.11        28.57        35.54        32.84        29.75        55.89 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       73.12        62.24        28.90       164.12         9.86        20.52 
TCGA-50-5045 TCGA-50-5055 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5933 
       71.47        60.16        47.41         8.22         9.27        78.67 
TCGA-50-5939 TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6592 TCGA-50-6595 
       15.12        60.72        53.16        42.35        25.55         6.21 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6543 
       36.99        36.79        27.25        35.21        30.58        14.30 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6983 TCGA-55-6986 
       80.52        40.73        15.25        46.03        92.81       107.21 
TCGA-55-6987 TCGA-55-7283 TCGA-55-7570 TCGA-55-7728 TCGA-55-7907 TCGA-55-7913 
       70.26        20.02        27.09        23.15        11.28        18.44 
TCGA-55-8087 TCGA-55-8092 TCGA-55-8096 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       15.19         5.06        23.64        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
       17.56        14.47        13.74        20.28        19.96        26.01 
TCGA-55-8615 TCGA-55-8616 TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG 
       14.66         1.58         3.25         0.92        15.81        19.99 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46V 
       39.98        14.60        88.64        49.25        19.53        72.30 
TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1680 TCGA-64-5775 TCGA-64-5781 
       13.61        39.25        40.96        37.02         2.04        51.25 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6216 TCGA-69-7763 TCGA-69-7973 TCGA-69-7980 
       12.66        14.73         4.64        22.68         7.56        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
       14.01        13.45        26.30        30.31         9.24         1.25 
TCGA-75-5146 TCGA-75-7027 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
       77.85       100.57        20.58       129.53        39.95       119.51 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       38.50        32.09         5.88        22.92         9.57       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-8648 TCGA-78-8662 
      238.29        88.14        26.53        53.33        39.75       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-7714 TCGA-86-8074 TCGA-86-8076 TCGA-86-8359 
       27.09        12.36        20.55         0.79        32.65        14.60 
TCGA-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       11.61        27.58         0.62        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 TCGA-91-6830 TCGA-91-6848 
        3.81        13.64        26.47        41.36         1.97         7.36 
TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7348 
        1.15        16.60        14.27         1.18        19.82        17.46 
TCGA-93-A4JN TCGA-93-A4JP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
       23.61        19.00        42.25        64.60        63.52        61.48 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       15.91        18.67         5.39        15.39        16.41        14.30 
TCGA-97-8552 TCGA-97-A4M1 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AG 
       20.58        19.76        36.76         1.45        21.63        32.48 
TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TK 
       14.30         1.91        37.35         5.49        41.59        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       73.91         1.64         0.49         0.43        19.82        20.28 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                          0.00                           0.43 
  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                        232.18                         238.29 
  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE 
                         22.26                          20.52 
[1] "0.0 - 232.2 (22.3)" "0.4 - 238.3 (20.5)"
[1] "hr=" "1.1"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 36(17P13.3) MUTATED         3       65       78        1        32
  DEL PEAK 36(17P13.3) WILD-TYPE       2       68       61        0        18
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 36(17P13.3) MUTATED          42         38          7       13
  DEL PEAK 36(17P13.3) WILD-TYPE        30         34          4       12
D65V3, multiclass
            clus
vv           DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             65                             68
  STAGE IB                             78                             61
  STAGE II                              1                              0
  STAGE IIA                            32                             18
  STAGE IIB                            42                             30
  STAGE IIIA                           38                             34
  STAGE IIIB                            7                              4
  STAGE IV                             13                             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  86 114  25   9
D65V4, multiclass
    clus
vv   DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  T1                           85                             86
  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  55    41
  DEL PEAK 36(17P13.3) WILD-TYPE 154  41    35
D65V5, multiclass
       clus
vv      DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  N0                             179                            154
  N1                              55                             41
  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"
D65V6, binary
                                cls
clus                               0   1
  DEL PEAK 36(17P13.3) MUTATED   198  13
  DEL PEAK 36(17P13.3) WILD-TYPE 151  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17P13.3) MUTATED    198   13
  DEL PEAK 36(17P13.3) WILD-TYPE  151   12
   clus
vv  DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  0                          198                            151
  1                           13                             12
[1] 2 2
[1] FALSE
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(17P13.3) MUTATED   158 123
  DEL PEAK 36(17P13.3) WILD-TYPE 118 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17P13.3) MUTATED    158  123
  DEL PEAK 36(17P13.3) WILD-TYPE  118  117
        clus
vv       DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  FEMALE                          158                            118
  MALE                            123                            117
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(17P13.3) MUTATED   229  28
  DEL PEAK 36(17P13.3) WILD-TYPE 181  32
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17P13.3) MUTATED    229   28
  DEL PEAK 36(17P13.3) WILD-TYPE  181   32
     clus
vv    DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  NO                           229                            181
  YES                           28                             32
[1] 2 2
[1] FALSE
D65V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 36(17P13.3) MUTATED                            9
  DEL PEAK 36(17P13.3) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 36(17P13.3) MUTATED                                  53
  DEL PEAK 36(17P13.3) WILD-TYPE                                54
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 36(17P13.3) MUTATED                                                  189
  DEL PEAK 36(17P13.3) WILD-TYPE                                                132
                                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                               7
  DEL PEAK 36(17P13.3) WILD-TYPE                            16
                                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
D65V10, multiclass
                                                    clus
vv                                                   DEL PEAK 36(17P13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          189
  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                                                 7
  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                                              54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            132
  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                                                  16
  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"
D65V11, continuous
D65V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(17P13.3) MUTATED   194   5   1  17
  DEL PEAK 36(17P13.3) WILD-TYPE 150   8   3   9
D65V13, multiclass
    clus
vv   DEL PEAK 36(17P13.3) MUTATED DEL PEAK 36(17P13.3) WILD-TYPE
  R0                          194                            150
  R1                            5                              8
  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                          29   207
  DEL PEAK 36(17P13.3) WILD-TYPE                        23   183
D65V14, multiclass
                                  clus
vv                                 DEL PEAK 36(17P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  29
  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                                                       183
[1] 4 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 36(17P13.3) MUTATED     5 201
  DEL PEAK 36(17P13.3) WILD-TYPE   2 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17P13.3) MUTATED      5  201
  DEL PEAK 36(17P13.3) WILD-TYPE    2  183
                        clus
vv                       DEL PEAK 36(17P13.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          201
                        clus
vv                       DEL PEAK 36(17P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            183
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 37(18Q21.32) MUTATION ANALYSIS
D66V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 37(18Q21.32) MUTATED   155  96
  DEL PEAK 37(18Q21.32) WILD-TYPE 168  85
  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                            251                             253 
  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                             96                              85 
$`DEL PEAK 37(18Q21.32) MUTATED`
TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 
        9.96         8.02        20.05         9.01        26.01        15.02 
TCGA-38-4631 TCGA-38-6178 TCGA-44-2662 TCGA-44-6146 TCGA-44-7670 TCGA-44-A47F 
       11.64        14.73        42.08        23.93        29.00        11.08 
TCGA-49-4501 TCGA-49-6742 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN TCGA-50-6597 
       46.72        16.04        11.64       156.66        37.32        41.69 
TCGA-55-1595 TCGA-55-6979 TCGA-55-7573 TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 
       48.62         7.79        16.01        14.53        21.44        19.66 
TCGA-55-8091 TCGA-55-8207 TCGA-55-8511 TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 
       19.73        32.12        18.15        20.58        19.59        13.87 
TCGA-73-4662 TCGA-73-7498 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 
       82.68        39.09        10.55        85.32        13.71        16.18 
TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VN TCGA-97-A4LX 
        1.45        17.29        16.54        15.68        18.18        20.19 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-05-4249 TCGA-05-4250 
       24.30        23.80        21.83        27.19        50.07         3.98 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4417 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 
        0.00        47.05        14.96        12.00        30.02        21.99 
TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5429 TCGA-05-5715 
       26.01        24.00         4.96        29.00         9.04         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4627 TCGA-38-4628 TCGA-38-4632 
        7.40         5.98         8.68        37.71        49.05        44.61 
TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2668 TCGA-44-3917 TCGA-44-3918 
       46.98        44.42        42.77        25.02        38.89        34.06 
TCGA-44-6145 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7662 TCGA-44-7667 
       19.56        23.18        32.45        16.44         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-A4SU TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
       18.87        23.64        13.45        28.11        28.57        12.66 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-6743 TCGA-49-6767 
       14.07        32.84         8.81        29.75        53.29        22.26 
TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
       22.26        62.24        28.90         8.55        40.41       123.58 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5933 TCGA-50-5936 
       15.72        47.41        49.28         8.22        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5946 TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 
       15.12        48.46        53.16        11.05        12.16        36.99 
TCGA-50-8459 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 
       36.79        34.29        30.54        35.21        38.73        67.89 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 
        5.62        42.51        46.03        53.65         3.88        69.34 
TCGA-55-6982 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 
       32.71        40.54        28.67        20.02        32.71        22.03 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 
        3.91        23.15        34.19        19.82        29.23        15.19 
TCGA-55-8089 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8301 TCGA-55-8505 
       23.08        17.79        23.64        15.65        17.56        14.47 
TCGA-55-8507 TCGA-55-8510 TCGA-55-8616 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
       13.74        17.72         1.58        21.40         3.25         0.92 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46R 
       19.99        17.95         4.57        42.38        47.80        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1679 
       54.35        67.96        39.25        40.96        29.92        81.80 
TCGA-64-1681 TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 
       38.37         2.04        42.90        51.25        28.47        20.05 
TCGA-67-3771 TCGA-67-3772 TCGA-67-6216 TCGA-69-7760 TCGA-69-7765 TCGA-69-7978 
       20.05        18.84         4.64         6.64         5.42         4.41 
TCGA-69-7979 TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 
       13.41        13.45        26.73        19.43        26.30         4.31 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5147 TCGA-75-6212 TCGA-75-6214 
       50.33        11.18        66.64        43.82        49.84        36.66 
TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
      108.66       100.57       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         9.57        31.20         8.02        26.01 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 
       27.09         5.88        31.13        34.39        38.04        20.55 
TCGA-86-7954 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 
       19.89         4.08        24.33         0.79        22.82        31.04 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 
       31.20        23.05        21.47        14.60        11.61         0.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
       41.36         1.97        10.19        12.23        27.68         7.36 
TCGA-91-A4BD TCGA-93-7348 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 
       19.82        17.46        18.67        27.29         2.76        42.25 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8176 
       64.60        63.52        18.54        15.91         5.39        15.39 
TCGA-97-8177 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M6 TCGA-99-8033 
       16.41        21.60        20.58        21.44        18.67        21.57 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L9-A50W TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 
       18.08        35.47        14.53        15.65        38.63         2.76 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TF 
       58.45        37.35        86.04        58.85         5.49        11.05 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A55O 
       14.10        11.15        19.13        71.05         0.43 

$`DEL PEAK 37(18Q21.32) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 
       19.96        14.01        15.02        28.41        35.28        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-7671 
       43.53        38.10        27.78        86.01        18.31        29.23 
TCGA-44-8119 TCGA-49-6745 TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 TCGA-55-6978 
        9.37        17.16        40.60        21.47        23.05         5.79 
TCGA-55-7284 TCGA-55-7724 TCGA-55-7914 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
        7.99        23.18         6.15        17.98        16.93        19.69 
TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A4DF TCGA-64-1677 TCGA-73-4658 
       13.68        16.93        22.65        20.19        20.65        52.60 
TCGA-78-7166 TCGA-78-7633 TCGA-93-8067 TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK 
        8.48        50.24         6.12         2.86        15.65        21.40 
TCGA-97-8172 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-L9-A443 TCGA-L9-A444 
       17.92        20.52        17.75        20.68         6.35        10.09 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4389 TCGA-05-4390 
        5.29        31.23         2.43        10.09        45.01        37.02 
TCGA-05-4397 TCGA-05-4403 TCGA-05-4415 TCGA-05-4420 TCGA-05-4430 TCGA-05-4432 
       24.03        19.00         2.99        29.98        25.02        25.02 
TCGA-05-5428 TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-A44F TCGA-44-2659 
       22.03         0.46        97.74       120.79         4.37        44.94 
TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        3.19        37.15        38.24        33.73        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6148 TCGA-44-6774 TCGA-44-6778 
       28.37        28.01        23.77        23.15        21.63        61.28 
TCGA-44-7659 TCGA-44-7660 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
       22.72        19.46        12.66         8.55        15.98        15.32 
TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4510 
        9.44        11.54        13.64        76.21        35.54        29.46 
TCGA-49-4514 TCGA-49-6744 TCGA-49-AAR2 TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       55.89        55.33        73.12       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5930 TCGA-50-5931 
       20.52        71.47       101.72        60.16         9.27        14.27 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 
       60.72        57.53        42.35         3.91        25.55         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-55-5899 TCGA-55-6543 
        0.72        10.13        27.25        13.94        30.58        14.30 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6970 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 
       80.52        40.73        15.25        45.34        92.81        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
      107.21        70.26        27.09        25.41        18.64        11.28 
TCGA-55-7911 TCGA-55-7913 TCGA-55-8085 TCGA-55-8092 TCGA-55-8206 TCGA-55-8208 
       17.65        18.44        29.72         5.06        29.19        22.16 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 
       15.42        15.72         0.36        20.28        19.96        26.01 
TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A494 
       17.10        17.62        14.66        12.33        20.71        15.81 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46V 
       39.98        14.60        88.64        49.25        19.53        72.30 
TCGA-62-A46Y TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 TCGA-64-5779 
       13.61        56.81        39.09        37.02        87.98        28.41 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-69-7761 TCGA-69-7763 
       14.04        12.66        14.73         5.72         6.12        22.68 
TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 
       13.61         7.56         6.05        13.51        14.01         4.24 
TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
        8.42        23.38        15.35        30.31         9.24         1.25 
TCGA-75-5146 TCGA-75-6206 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
       77.85        85.15        20.58       129.53        39.95       119.51 
TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 
       19.50        32.09         5.88        64.90        22.92       104.19 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 
      238.29        88.14        26.53        53.33        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 
      232.18        39.75        77.59       110.50        93.11        12.36 
TCGA-86-7953 TCGA-86-7955 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8668 
       32.78        35.24        37.74         4.57        32.65        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       30.84        27.58        28.34        26.50        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6835 TCGA-91-6849 
       24.23        13.64        26.47        10.62         2.60         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-93-7347 TCGA-93-A4JN TCGA-93-A4JO 
       16.60        14.27         1.18        22.45        23.61         1.08 
TCGA-93-A4JP TCGA-95-7039 TCGA-95-7944 TCGA-95-A4VP TCGA-97-7553 TCGA-97-7554 
       19.00        41.82        12.39        19.89        61.48        25.48 
TCGA-97-7938 TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 TCGA-97-A4M1 TCGA-97-A4M5 
        0.59        18.67        18.12        14.30        19.76        20.84 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AG 
       24.56        34.85        36.76         1.45        21.63        32.48 
TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A7SV TCGA-MP-A4SV TCGA-MP-A4SY 
       19.00        14.30         1.91        18.58        86.14        49.35 
TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI 
       41.59        29.46        24.36        73.91        74.33         0.13 
TCGA-NJ-A4YP TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        1.64        47.08         0.49        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                           0.00                            0.13 
  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                         163.10                          238.29 
  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE 
                          21.57                           21.63 
[1] "0.0 - 163.1 (21.6)" "0.1 - 238.3 (21.6)"
[1] "hr=" "1.3"
D66V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 37(18Q21.32) MUTATED         1       52       70        1        31
  DEL PEAK 37(18Q21.32) WILD-TYPE       4       81       69        0        19
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 37(18Q21.32) MUTATED          46         33          6       13
  DEL PEAK 37(18Q21.32) WILD-TYPE        26         39          5       12
D66V3, multiclass
            clus
vv           DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                              52                              81
  STAGE IB                              70                              69
  STAGE II                               1                               0
  STAGE IIA                             31                              19
  STAGE IIB                             46                              26
  STAGE IIIA                            33                              39
  STAGE IIIB                             6                               5
  STAGE IV                              13                              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    75 144  26   9
  DEL PEAK 37(18Q21.32) WILD-TYPE  96 134  20  10
D66V4, multiclass
    clus
vv   DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  T1                            75                              96
  T2                           144                             134
  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   156  60    34
  DEL PEAK 37(18Q21.32) WILD-TYPE 177  36    42
D66V5, multiclass
       clus
vv      DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  N0                              156                             177
  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"
D66V6, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18Q21.32) MUTATED   160  13
  DEL PEAK 37(18Q21.32) WILD-TYPE 189  12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18Q21.32) MUTATED    160   13
  DEL PEAK 37(18Q21.32) WILD-TYPE  189   12
   clus
vv  DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  0                           160                             189
  1                            13                              12
[1] 2 2
[1] FALSE
D66V7, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18Q21.32) MUTATED   142 113
  DEL PEAK 37(18Q21.32) WILD-TYPE 134 127
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18Q21.32) MUTATED    142  113
  DEL PEAK 37(18Q21.32) WILD-TYPE  134  127
        clus
vv       DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  FEMALE                           142                             134
  MALE                             113                             127
[1] 2 2
[1] FALSE
D66V8, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18Q21.32) MUTATED   198  29
  DEL PEAK 37(18Q21.32) WILD-TYPE 212  31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18Q21.32) MUTATED    198   29
  DEL PEAK 37(18Q21.32) WILD-TYPE  212   31
     clus
vv    DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  NO                            198                             212
  YES                            29                              31
[1] 2 2
[1] FALSE
D66V9, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 37(18Q21.32) MUTATED                            9
  DEL PEAK 37(18Q21.32) WILD-TYPE                          9
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 37(18Q21.32) MUTATED                                  55
  DEL PEAK 37(18Q21.32) WILD-TYPE                                52
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 37(18Q21.32) MUTATED                                                  160
  DEL PEAK 37(18Q21.32) WILD-TYPE                                                161
                                 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
D66V10, multiclass
                                                    clus
vv                                                   DEL PEAK 37(18Q21.32) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             55
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           160
  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                                               52
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             161
  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"
D66V11, continuous
D66V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 37(18Q21.32) MUTATED   172   9   3   7
  DEL PEAK 37(18Q21.32) WILD-TYPE 172   4   1  19
D66V13, multiclass
    clus
vv   DEL PEAK 37(18Q21.32) MUTATED DEL PEAK 37(18Q21.32) WILD-TYPE
  R0                           172                             172
  R1                             9                               4
  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
  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   191
  DEL PEAK 37(18Q21.32) WILD-TYPE                        26   199
D66V14, multiclass
                                  clus
vv                                 DEL PEAK 37(18Q21.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      191
                                  clus
vv                                 DEL PEAK 37(18Q21.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     26
  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"
D66V15, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18Q21.32) MUTATED     5 189
  DEL PEAK 37(18Q21.32) WILD-TYPE   2 195
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18Q21.32) MUTATED      5  189
  DEL PEAK 37(18Q21.32) WILD-TYPE    2  195
                        clus
vv                       DEL PEAK 37(18Q21.32) MUTATED
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           189
                        clus
vv                       DEL PEAK 37(18Q21.32) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             195
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 38(18Q23) MUTATION ANALYSIS
D67V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 38(18Q23) MUTATED   155  90
  DEL PEAK 38(18Q23) WILD-TYPE 168  91
  DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE 
                         245                          259 
  DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE 
                          90                           91 
$`DEL PEAK 38(18Q23) MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-05-4434 TCGA-38-4631 
        8.02        20.05         9.01        26.01        15.02        11.64 
TCGA-38-6178 TCGA-44-2662 TCGA-44-6146 TCGA-44-7670 TCGA-44-A47F TCGA-49-4501 
       14.73        42.08        23.93        29.00        11.08        46.72 
TCGA-49-6742 TCGA-49-6761 TCGA-49-AARN TCGA-50-6597 TCGA-55-1595 TCGA-55-6979 
       16.04        11.64        37.32        41.69        48.62         7.79 
TCGA-55-7573 TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 TCGA-55-8091 TCGA-55-8207 
       16.01        14.53        21.44        19.66        19.73        32.12 
TCGA-55-8511 TCGA-55-A491 TCGA-55-A492 TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 
       18.15        20.58        19.59        13.87        82.68        39.09 
TCGA-78-8660 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7947 
       10.55        13.71        16.18         1.45        17.29        15.68 
TCGA-95-A4VN TCGA-97-A4LX TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A743 TCGA-MN-A4N1 
       18.18        20.19        24.30        23.80        21.83        27.19 
TCGA-05-4249 TCGA-05-4250 TCGA-05-4395 TCGA-05-4398 TCGA-05-4417 TCGA-05-4422 
       50.07         3.98         0.00        47.05        14.96        12.00 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       30.02        21.99        26.01        24.00         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-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 TCGA-44-2668 
       49.05        44.61        46.98        44.42        42.77        25.02 
TCGA-44-3918 TCGA-44-5644 TCGA-44-6145 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 
       34.06        28.37        19.56        23.18        32.45        16.44 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-A4SU TCGA-49-4490 
        7.17        36.07        18.87        23.64        13.45        12.66 
TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4512 TCGA-49-6743 TCGA-49-6767 
       14.07        32.84         8.81        29.75        53.29        22.26 
TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARE TCGA-49-AARO TCGA-50-5051 
       22.26        62.24        28.90        40.41       123.58        15.72 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 
       47.41        49.28         8.22        78.67         8.45        15.12 
TCGA-50-5941 TCGA-50-5946 TCGA-50-6593 TCGA-50-6594 TCGA-50-8457 TCGA-50-8459 
       48.46        53.16        11.05        12.16        36.99        36.79 
TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 TCGA-55-6712 
       34.29        30.54        35.21        38.73        67.89         5.62 
TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6982 TCGA-55-6985 
       46.03        53.65         3.88        69.34        32.71        40.54 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 
       28.67        20.02        32.71        22.03         3.91        23.15 
TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8087 TCGA-55-8089 TCGA-55-8094 
       34.19        19.82        29.23        15.19        23.08        17.79 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8301 TCGA-55-8505 TCGA-55-8507 TCGA-55-8510 
       23.64        15.65        17.56        14.47        13.74        17.72 
TCGA-55-8616 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-55-A57B 
        1.58        21.40         3.25         0.92        19.99        17.95 
TCGA-62-8394 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46S TCGA-62-A46U 
        4.57        42.38        47.80        56.71        54.35        67.96 
TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 
       39.25        40.96        29.92        56.81        81.80        38.37 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        2.04        42.90        51.25        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-6216 TCGA-69-7760 TCGA-69-7765 TCGA-69-7978 TCGA-69-7979 
       18.84         4.64         6.64         5.42         4.41        13.41 
TCGA-69-8254 TCGA-69-8453 TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 TCGA-73-7499 
       13.45        26.73        19.43        26.30         4.31        50.33 
TCGA-73-A9RS TCGA-75-5125 TCGA-75-5147 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       11.18        66.64        43.82        49.84        36.66       108.66 
TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7155 
      100.57        27.16         5.69        19.27        21.90        38.50 
TCGA-78-7161 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-8662 TCGA-83-5908 
        9.57        31.20         8.02        26.01       110.50        27.09 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 
        5.88        31.13        34.39        20.55        19.89        37.74 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 
        4.08        24.33         0.79        22.82        31.04        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8672 TCGA-91-6829 
       23.05        21.47        14.60        11.61         0.62        41.36 
TCGA-91-6830 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7348 
        1.97        12.23         7.36         1.18        19.82        17.46 
TCGA-95-7039 TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-97-7546 TCGA-97-7552 
       41.82        18.67        27.29         2.76        42.25        63.52 
TCGA-97-7937 TCGA-97-7941 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8547 
       18.54        15.91         5.39        15.39        16.41        21.60 
TCGA-97-A4M0 TCGA-97-A4M6 TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-J2-A4AE 
       21.44        18.67        34.85        21.57        18.08        35.47 
TCGA-L9-A50W TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 
       14.53        15.65        38.63         2.76        58.45        37.35 
TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       86.04        58.85         5.49        11.05        24.36        14.10 
TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55O 
       11.15        19.13        71.05        47.08         0.43 

$`DEL PEAK 38(18Q23) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 
       19.96        14.01         9.96        15.02        28.41        35.28 
TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       26.30        43.53        38.10        27.78        86.01        18.31 
TCGA-44-7671 TCGA-44-8119 TCGA-49-6745 TCGA-49-AAR0 TCGA-50-5932 TCGA-50-5935 
       29.23         9.37        17.16       156.66        40.60        21.47 
TCGA-55-1592 TCGA-55-6978 TCGA-55-7284 TCGA-55-7724 TCGA-55-7914 TCGA-55-8203 
       23.05         5.79         7.99        23.18         6.15        17.98 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A4DF 
       16.93        19.69        13.68        16.93        22.65        20.19 
TCGA-64-1677 TCGA-73-4658 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-93-8067 
       20.65        52.60         8.48        50.24        85.32         6.12 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4M2 
       16.54         2.86        15.65        21.40        17.92        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4T8 TCGA-MP-A4TA 
       17.75        20.68         6.35        10.09         5.29        31.23 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4389 TCGA-05-4390 TCGA-05-4397 TCGA-05-4403 
        2.43        10.09        45.01        37.02        24.03        19.00 
TCGA-05-4415 TCGA-05-4420 TCGA-05-4430 TCGA-05-4432 TCGA-05-5428 TCGA-35-3615 
        2.99        29.98        25.02        25.02        22.03         0.46 
TCGA-38-4625 TCGA-38-4626 TCGA-38-A44F TCGA-44-2659 TCGA-44-2666 TCGA-44-3396 
       97.74       120.79         4.37        44.94         3.19        37.15 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
       38.24        38.89        33.73        26.56        33.30        28.01 
TCGA-44-6144 TCGA-44-6148 TCGA-44-6774 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 
       23.77        23.15        21.63        61.28        22.72        19.46 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G 
       12.66         8.55        15.98        15.32         9.44        11.54 
TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4510 
       13.64        76.21        28.11        28.57        35.54        29.46 
TCGA-49-4514 TCGA-49-6744 TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARQ TCGA-49-AARR 
       55.89        55.33        73.12         8.55       221.33       164.12 
TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5930 
        9.86        20.52        71.47       101.72        60.16         9.27 
TCGA-50-5931 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
       14.27        60.72        57.53        42.35         3.91        25.55 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8460 TCGA-53-7813 TCGA-55-5899 
        6.21         0.72        10.13        27.25        13.94        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6981 
       14.30        80.52        42.51        40.73        15.25        45.34 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 TCGA-55-7570 TCGA-55-7815 
       92.81        24.99       107.21        70.26        27.09        25.41 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7913 TCGA-55-8085 TCGA-55-8092 
       18.64        11.28        17.65        18.44        29.72         5.06 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8302 TCGA-55-8506 TCGA-55-8508 
       29.19        22.16        15.42        15.72         0.36        20.28 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 
       19.96        26.01        17.10        17.62        14.66        12.33 
TCGA-55-A48Y TCGA-55-A494 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
       20.71        15.81        39.98        14.60        88.64        49.25 
TCGA-62-A46P TCGA-62-A46V TCGA-62-A46Y TCGA-64-1678 TCGA-64-1680 TCGA-64-5774 
       19.53        72.30        13.61        39.09        37.02        87.98 
TCGA-64-5779 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-69-7761 
       28.41        14.04        12.66        14.73         5.72         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 TCGA-69-8253 
       22.68        13.61         7.56         6.05        13.51        14.01 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
        4.24         8.42        23.38        15.35        30.31         9.24 
TCGA-73-4677 TCGA-75-5146 TCGA-75-6206 TCGA-78-7143 TCGA-78-7148 TCGA-78-7149 
        1.25        77.85        85.15       163.10        20.58       129.53 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
       39.95       119.51        19.50        32.09         5.88        64.90 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 TCGA-78-7537 
       22.92       104.19       238.29        88.14        26.53        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-80-5608 
       39.35        10.55       232.18        39.75        77.59        93.11 
TCGA-86-6562 TCGA-86-7713 TCGA-86-7953 TCGA-86-7955 TCGA-86-8056 TCGA-86-8076 
       12.36        38.04        32.78        35.24         4.57        32.65 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 
       13.91        30.84        27.58        28.34        26.50        29.46 
TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6831 
        3.81        24.23        13.64        26.47        10.62        10.19 
TCGA-91-6835 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-93-7347 
        2.60        27.68         1.15        16.60        14.27        22.45 
TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 TCGA-95-A4VP TCGA-97-7547 
       23.61         1.08        19.00        12.39        19.89        64.60 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 
       61.48        25.48         0.59        18.67        18.12        14.30 
TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8028 TCGA-99-8032 
       20.58        19.76        20.84        24.56        36.76         1.45 
TCGA-99-AA5R TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A7SV 
       21.63        32.48        19.00        14.30         1.91        18.58 
TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A5C7 TCGA-NJ-A4YG 
       86.14        49.35        41.59        29.46        73.91        74.33 
TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.13         1.64         0.49        19.82        20.28        59.11 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE 
                        0.00                         0.13 
  DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE 
                      123.58                       238.29 
  DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE 
                       21.60                        21.63 
[1] "0.0 - 123.6 (21.6)" "0.1 - 238.3 (21.6)"
[1] "hr=" "1.2"
D67V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 38(18Q23) MUTATED         0       52       66        1        30
  DEL PEAK 38(18Q23) WILD-TYPE       5       81       73        0        20
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 38(18Q23) MUTATED          47         34          5       12
  DEL PEAK 38(18Q23) WILD-TYPE        25         38          6       13
D67V3, multiclass
            clus
vv           DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE
  STAGE I                             0                            5
  STAGE IA                           52                           81
  STAGE IB                           66                           73
  STAGE II                            1                            0
  STAGE IIA                          30                           20
  STAGE IIB                          47                           25
  STAGE IIIA                         34                           38
  STAGE IIIB                          5                            6
  STAGE IV                           12                           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 38(18Q23) MUTATED    73 140  27   8
  DEL PEAK 38(18Q23) WILD-TYPE  98 138  19  11
D67V4, multiclass
    clus
vv   DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE
  T1                         73                           98
  T2                        140                          138
  T3                         27                           19
  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 38(18Q23) MUTATED   149  60    35
  DEL PEAK 38(18Q23) WILD-TYPE 184  36    41
D67V5, multiclass
       clus
vv      DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE
  N0                           149                          184
  N1                            60                           36
  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"
D67V6, binary
                              cls
clus                             0   1
  DEL PEAK 38(18Q23) MUTATED   160  12
  DEL PEAK 38(18Q23) WILD-TYPE 189  13
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(18Q23) MUTATED    160   12
  DEL PEAK 38(18Q23) WILD-TYPE  189   13
   clus
vv  DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE
  0                        160                          189
  1                         12                           13
[1] 2 2
[1] FALSE
D67V7, binary
                              cls
clus                             0   1
  DEL PEAK 38(18Q23) MUTATED   141 108
  DEL PEAK 38(18Q23) WILD-TYPE 135 132
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(18Q23) MUTATED    141  108
  DEL PEAK 38(18Q23) WILD-TYPE  135  132
        clus
vv       DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE
  FEMALE                        141                          135
  MALE                          108                          132
[1] 2 2
[1] FALSE
D67V8, binary
                              cls
clus                             0   1
  DEL PEAK 38(18Q23) MUTATED   196  26
  DEL PEAK 38(18Q23) WILD-TYPE 214  34
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(18Q23) MUTATED    196   26
  DEL PEAK 38(18Q23) WILD-TYPE  214   34
     clus
vv    DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE
  NO                         196                          214
  YES                         26                           34
[1] 2 2
[1] FALSE
D67V9, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 38(18Q23) MUTATED                           10
  DEL PEAK 38(18Q23) WILD-TYPE                          8
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 38(18Q23) MUTATED                                  53
  DEL PEAK 38(18Q23) WILD-TYPE                                54
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 38(18Q23) MUTATED                                                  159
  DEL PEAK 38(18Q23) WILD-TYPE                                                162
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 38(18Q23) MUTATED                                            1
  DEL PEAK 38(18Q23) WILD-TYPE                                          4
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 38(18Q23) MUTATED                                               8
  DEL PEAK 38(18Q23) WILD-TYPE                                            11
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 38(18Q23) MUTATED                                2
  DEL PEAK 38(18Q23) WILD-TYPE                              0
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 38(18Q23) MUTATED                                    2
  DEL PEAK 38(18Q23) WILD-TYPE                                  1
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 38(18Q23) MUTATED                              1
  DEL PEAK 38(18Q23) WILD-TYPE                            1
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 38(18Q23) MUTATED                               4
  DEL PEAK 38(18Q23) WILD-TYPE                            19
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 38(18Q23) MUTATED                                 1
  DEL PEAK 38(18Q23) WILD-TYPE                               0
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 38(18Q23) MUTATED                                               2
  DEL PEAK 38(18Q23) WILD-TYPE                                             3
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 38(18Q23) MUTATED                              6
  DEL PEAK 38(18Q23) WILD-TYPE                            4
D67V10, multiclass
                                                    clus
vv                                                   DEL PEAK 38(18Q23) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                 10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          53
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                        159
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                  1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                               8
  LUNG CLEAR CELL ADENOCARCINOMA                                              2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                          2
  LUNG MUCINOUS ADENOCARCINOMA                                                1
  LUNG PAPILLARY ADENOCARCINOMA                                               4
  LUNG SIGNET RING ADENOCARCINOMA                                             1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                               2
  MUCINOUS (COLLOID) CARCINOMA                                                6
                                                    clus
vv                                                   DEL PEAK 38(18Q23) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            54
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          162
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                11
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  1
  LUNG PAPILLARY ADENOCARCINOMA                                                19
  LUNG SIGNET RING ADENOCARCINOMA                                               0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 3
  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"
D67V11, continuous
D67V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 38(18Q23) MUTATED   168   9   3   8
  DEL PEAK 38(18Q23) WILD-TYPE 176   4   1  18
D67V13, multiclass
    clus
vv   DEL PEAK 38(18Q23) MUTATED DEL PEAK 38(18Q23) WILD-TYPE
  R0                        168                          176
  R1                          9                            4
  R2                          3                            1
  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 38(18Q23) MUTATED                                  0     2
  DEL PEAK 38(18Q23) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(18Q23) MUTATED                          25   187
  DEL PEAK 38(18Q23) WILD-TYPE                        27   203
D67V14, multiclass
                                  clus
vv                                 DEL PEAK 38(18Q23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                25
  WHITE                                                   187
                                  clus
vv                                 DEL PEAK 38(18Q23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  27
  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 38(18Q23) MUTATED     5 185
  DEL PEAK 38(18Q23) WILD-TYPE   2 199
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(18Q23) MUTATED      5  185
  DEL PEAK 38(18Q23) WILD-TYPE    2  199
                        clus
vv                       DEL PEAK 38(18Q23) MUTATED
  HISPANIC OR LATINO                              5
  NOT HISPANIC OR LATINO                        185
                        clus
vv                       DEL PEAK 38(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          199
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 39(19P13.3) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(19P13.3) MUTATED   162 109
  DEL PEAK 39(19P13.3) WILD-TYPE 161  72
  DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE 
                           271                            233 
  DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE 
                           109                             72 
$`DEL PEAK 39(19P13.3) MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96         8.02         9.01        26.01 
TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-44-2655 TCGA-44-6146 
       15.02        35.28        11.64        14.73        43.53        23.93 
TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       86.01        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 
       16.04        17.16       156.66        40.60        21.47        41.69 
TCGA-55-1592 TCGA-55-6978 TCGA-55-7914 TCGA-55-8203 TCGA-55-A48X TCGA-55-A491 
       23.05         5.79         6.15        17.98        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-67-6217 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 
       19.59        20.19        13.87        39.09         8.48        50.24 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 
       85.32        13.71        16.18         6.12        17.29        16.54 
TCGA-95-7562 TCGA-95-7948 TCGA-95-A4VK TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX 
        2.86        15.65        21.40        18.18        17.92        20.19 
TCGA-J2-8192 TCGA-L9-A443 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-05-4250 TCGA-05-4389 
       24.30         6.35         5.29        31.23         3.98        45.01 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4415 TCGA-05-4422 
       37.02         0.00        24.03        47.05         2.99        12.00 
TCGA-05-4424 TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 
       30.02        24.00        29.00        22.03         7.40         5.98 
TCGA-35-5375 TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-44-3917 
        8.68        49.05        44.61        46.98        44.42        38.89 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 
       33.30        28.37        23.77        21.63        61.28        16.44 
TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-8120 TCGA-44-A479 TCGA-44-A4SS 
       19.46        36.07        18.87         8.55        15.98        13.64 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 
       13.45        76.21        12.66        14.07         8.81        29.46 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR9 
       55.89        53.29        55.33        22.26        73.12         8.55 
TCGA-49-AARE TCGA-49-AARO TCGA-49-AARQ TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 
       40.41       123.58       221.33       101.72        15.72        47.41 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 
       49.28         8.22         9.27        14.27        78.67         8.45 
TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 
       15.12        48.46        57.53         3.91        25.55        12.16 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-1596 
       10.13        34.29        13.94        35.21        38.73        67.89 
TCGA-55-5899 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6981 TCGA-55-6982 
       30.58        46.03        53.65         3.88        45.34        32.71 
TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7907 TCGA-55-7910 TCGA-55-7913 
       27.09        22.03         3.91        11.28        34.19        18.44 
TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
       19.82        29.23        29.72        23.08         5.06        17.79 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8614 TCGA-55-8616 
       15.72        14.47        20.28        19.96        17.62         1.58 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
        3.25         0.92        15.81        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R 
       42.38        14.60        88.64        49.25        47.80        56.71 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 
       54.35        67.96        39.25        40.96        56.81        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        20.05        20.05        18.84 
TCGA-67-3774 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 
       12.66         6.12        22.68        13.61         7.56         4.41 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 
       13.51        14.01         4.24        26.73        19.43         8.42 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4677 
       23.38        26.30        15.35         4.31        30.31         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 
       50.33        66.64        77.85        43.82        85.15        49.84 
TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
       36.66       108.66       100.57        27.16         5.69        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7156 TCGA-78-7160 
       20.58       129.53        21.90       119.51        32.09        22.92 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
      104.19        88.14        26.53        31.20         8.02        26.01 
TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
       93.11        27.09        31.13        34.39        38.04        32.78 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       19.89        35.24         4.08        24.33         0.79        22.82 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8358 TCGA-86-8669 TCGA-86-8672 TCGA-86-8674 
       31.20        23.05        21.47        30.84         0.62        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       29.46         3.81        10.62        41.36         1.97        10.19 
TCGA-91-6840 TCGA-91-6848 TCGA-91-6849 TCGA-91-8497 TCGA-95-7039 TCGA-95-7944 
       12.23         7.36         1.15        14.27        41.82        12.39 
TCGA-97-7937 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-A4M1 TCGA-97-A4M6 
       18.54        18.67         5.39        15.39        19.76        18.67 
TCGA-99-7458 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV 
       24.56        21.57        18.08        19.00        14.53        18.58 
TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T4 TCGA-MP-A4T6 
       15.65        38.63        86.14        49.35        86.04        58.85 
TCGA-MP-A4T7 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
        5.49        11.05        24.36        14.10        11.15        19.13 
TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
       73.91        71.05        47.08         0.43        19.82        20.28 
TCGA-O1-A52J 
       59.11 

$`DEL PEAK 39(19P13.3) WILD-TYPE`
TCGA-05-4405 TCGA-05-4434 TCGA-38-4629 TCGA-38-7271 TCGA-44-2661 TCGA-44-2662 
       20.05        15.02        28.41        26.30        38.10        42.08 
TCGA-44-6147 TCGA-44-7661 TCGA-49-6761 TCGA-49-AARN TCGA-55-1595 TCGA-55-6979 
       27.78        18.31        11.64        37.32        48.62         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-8090 
        7.99        16.01        23.18        14.53        21.44        19.66 
TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       19.73        16.93        19.69        32.12        18.15        13.68 
TCGA-55-8621 TCGA-64-1677 TCGA-73-4658 TCGA-73-4662 TCGA-78-8660 TCGA-91-A4BC 
       16.93        20.65        52.60        82.68        10.55         1.45 
TCGA-95-7947 TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A444 
       15.68        20.52        17.75        20.68        23.80        10.09 
TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4403 
       21.83        27.19         2.43        10.09        50.07        19.00 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       14.96        29.98        21.99        26.01        25.02        25.02 
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-A44F TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 
       37.71         4.37        44.94        42.77         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
       37.15        38.24        34.06        33.73        26.56        28.01 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7662 
       19.56        23.15        23.18        32.45        22.72         7.17 
TCGA-44-7672 TCGA-44-8117 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4487 
       23.64        12.66        15.32         9.44        11.54        28.11 
TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4512 TCGA-49-AAQV TCGA-49-AAR3 
       28.57        35.54        32.84        29.75        22.26        62.24 
TCGA-49-AAR4 TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 
       28.90       164.12         9.86        20.52        71.47        60.16 
TCGA-50-5942 TCGA-50-5946 TCGA-50-6590 TCGA-50-6593 TCGA-50-6595 TCGA-50-6673 
       60.72        53.16        42.35        11.05         6.21         0.72 
TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-6543 TCGA-55-6642 
       36.99        36.79        27.25        30.54        14.30        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6980 TCGA-55-6983 
        5.62        42.51        40.73        15.25        69.34        92.81 
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        28.67        20.02 
TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-8087 
       32.71        23.15        25.41        18.64        17.65        15.19 
TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
       23.64        15.65        29.19        22.16        15.42        17.56 
TCGA-55-8506 TCGA-55-8507 TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 TCGA-55-8615 
        0.36        13.74        17.72        26.01        17.10        14.66 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A57B TCGA-62-A46P TCGA-62-A46V 
       12.33        20.71        21.40        17.95        19.53        72.30 
TCGA-62-A46Y TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-5775 
       13.61        29.92        39.09        81.80        37.02         2.04 
TCGA-64-5781 TCGA-64-5815 TCGA-67-3773 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       51.25        28.47        14.04        14.73         5.72         4.64 
TCGA-69-7760 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 TCGA-69-8254 TCGA-73-4676 
        6.64         5.42         6.05        13.41        13.45         9.24 
TCGA-73-A9RS TCGA-78-7143 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 
       11.18       163.10        39.95        19.50        38.50         5.88 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7163 TCGA-78-7537 TCGA-78-7540 TCGA-78-7542 
       64.90         9.57       238.29        53.33        39.35        10.55 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-86-6562 TCGA-86-6851 
      232.18        39.75        77.59       110.50        12.36         5.88 
TCGA-86-7714 TCGA-86-8054 TCGA-86-8056 TCGA-86-8076 TCGA-86-8278 TCGA-86-8359 
       20.55        37.74         4.57        32.65        31.04        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-A4JF TCGA-86-A4P7 
       11.61        13.91        27.58        28.34        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6847 TCGA-91-8496 TCGA-91-8499 TCGA-91-A4BD 
       26.47         2.60        27.68        16.60         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7567 
       22.45        17.46        23.61         1.08        19.00        18.67 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7938 TCGA-97-7941 TCGA-97-8175 TCGA-97-8177 
       61.48        25.48         0.59        15.91        18.12        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 TCGA-99-8025 
       14.30        21.60        20.58        21.44        20.84        34.85 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       36.76         1.45        21.63        35.47        32.48        14.30 
TCGA-L9-A5IP TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TE 
        1.91         2.76        58.45        37.35        41.59        29.46 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-S2-AA1A 
       74.33         0.13         1.64         0.49        16.87 

  DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE 
                          0.00                           0.13 
  DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE 
                        221.33                         238.29 
  DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE 
                         21.63                          21.60 
[1] "0.0 - 221.3 (21.6)" "0.1 - 238.3 (21.6)"
[1] "hr=" "1.2"
D68V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 39(19P13.3) MUTATED         3       62       69        0        34
  DEL PEAK 39(19P13.3) WILD-TYPE       2       71       70        1        16
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 39(19P13.3) MUTATED          41         41          8       16
  DEL PEAK 39(19P13.3) WILD-TYPE        31         31          3        9
D68V3, multiclass
            clus
vv           DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE
  STAGE I                               3                              2
  STAGE IA                             62                             71
  STAGE IB                             69                             70
  STAGE II                              0                              1
  STAGE IIA                            34                             16
  STAGE IIB                            41                             31
  STAGE IIIA                           41                             31
  STAGE IIIB                            8                              3
  STAGE IV                             16                              9
[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(19P13.3) MUTATED    81 159  22  13
  DEL PEAK 39(19P13.3) WILD-TYPE  90 119  24   6
D68V4, multiclass
    clus
vv   DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE
  T1                           81                             90
  T2                          159                            119
  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 39(19P13.3) MUTATED   168  62    42
  DEL PEAK 39(19P13.3) WILD-TYPE 165  34    34
D68V5, multiclass
       clus
vv      DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE
  N0                             168                            165
  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"
D68V6, binary
                                cls
clus                               0   1
  DEL PEAK 39(19P13.3) MUTATED   194  16
  DEL PEAK 39(19P13.3) WILD-TYPE 155   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(19P13.3) MUTATED    194   16
  DEL PEAK 39(19P13.3) WILD-TYPE  155    9
   clus
vv  DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE
  0                          194                            155
  1                           16                              9
[1] 2 2
[1] FALSE
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(19P13.3) MUTATED   134 142
  DEL PEAK 39(19P13.3) WILD-TYPE 142  98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(19P13.3) MUTATED    134  142
  DEL PEAK 39(19P13.3) WILD-TYPE  142   98
        clus
vv       DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE
  FEMALE                          134                            142
  MALE                            142                             98
[1] 2 2
[1] FALSE
D68V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(19P13.3) MUTATED   219  32
  DEL PEAK 39(19P13.3) WILD-TYPE 191  28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(19P13.3) MUTATED    219   32
  DEL PEAK 39(19P13.3) WILD-TYPE  191   28
     clus
vv    DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE
  NO                           219                            191
  YES                           32                             28
[1] 2 2
[1] FALSE
D68V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 39(19P13.3) MUTATED                            9
  DEL PEAK 39(19P13.3) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 39(19P13.3) MUTATED                                  56
  DEL PEAK 39(19P13.3) WILD-TYPE                                51
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 39(19P13.3) MUTATED                                                  175
  DEL PEAK 39(19P13.3) WILD-TYPE                                                146
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 39(19P13.3) MUTATED                                            0
  DEL PEAK 39(19P13.3) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 39(19P13.3) MUTATED                                               9
  DEL PEAK 39(19P13.3) WILD-TYPE                                            10
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 39(19P13.3) MUTATED                                1
  DEL PEAK 39(19P13.3) WILD-TYPE                              1
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 39(19P13.3) MUTATED                                    3
  DEL PEAK 39(19P13.3) WILD-TYPE                                  0
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 39(19P13.3) MUTATED                              1
  DEL PEAK 39(19P13.3) WILD-TYPE                            1
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 39(19P13.3) MUTATED                              13
  DEL PEAK 39(19P13.3) WILD-TYPE                            10
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 39(19P13.3) MUTATED                                 1
  DEL PEAK 39(19P13.3) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 39(19P13.3) MUTATED                                               3
  DEL PEAK 39(19P13.3) WILD-TYPE                                             2
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 39(19P13.3) MUTATED                              5
  DEL PEAK 39(19P13.3) WILD-TYPE                            5
D68V10, multiclass
                                                    clus
vv                                                   DEL PEAK 39(19P13.3) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            56
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          175
  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(19P13.3) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              51
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            146
  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"
D68V11, continuous
D68V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(19P13.3) MUTATED   183   4   2  15
  DEL PEAK 39(19P13.3) WILD-TYPE 161   9   2  11
D68V13, multiclass
    clus
vv   DEL PEAK 39(19P13.3) MUTATED DEL PEAK 39(19P13.3) WILD-TYPE
  R0                          183                            161
  R1                            4                              9
  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 39(19P13.3) MUTATED                                  1     5
  DEL PEAK 39(19P13.3) WILD-TYPE                                0     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(19P13.3) MUTATED                          31   201
  DEL PEAK 39(19P13.3) WILD-TYPE                        21   189
D68V14, multiclass
                                  clus
vv                                 DEL PEAK 39(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  31
  WHITE                                                     201
                                  clus
vv                                 DEL PEAK 39(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    21
  WHITE                                                       189
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V15, binary
                                cls
clus                               0   1
  DEL PEAK 39(19P13.3) MUTATED     5 202
  DEL PEAK 39(19P13.3) WILD-TYPE   2 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(19P13.3) MUTATED      5  202
  DEL PEAK 39(19P13.3) WILD-TYPE    2  182
                        clus
vv                       DEL PEAK 39(19P13.3) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          202
                        clus
vv                       DEL PEAK 39(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            182
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 40(19P13.2) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(19P13.2) MUTATED   162 102
  DEL PEAK 40(19P13.2) WILD-TYPE 161  79
  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                           264                            240 
  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                           102                             79 
$`DEL PEAK 40(19P13.2) MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4418 TCGA-05-4427 
       19.96        14.01         9.96         8.02         9.01        26.01 
TCGA-05-5420 TCGA-38-4631 TCGA-38-6178 TCGA-44-2655 TCGA-44-2662 TCGA-44-6146 
       15.02        11.64        14.73        43.53        42.08        23.93 
TCGA-44-6776 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-4501 
       86.01        29.00        29.23         9.37        11.08        46.72 
TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 TCGA-50-5932 TCGA-50-6597 TCGA-55-1592 
       16.04        17.16       156.66        40.60        41.69        23.05 
TCGA-55-6978 TCGA-55-7914 TCGA-55-8203 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 
        5.79         6.15        17.98        22.65        20.58        19.59 
TCGA-55-A4DF TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 
       20.19        39.09         8.48        50.24        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VK 
       16.18         1.45        17.29        16.54        15.65        21.40 
TCGA-95-A4VN TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M3 TCGA-J2-8192 TCGA-L9-A443 
       18.18        17.92        20.19        17.75        24.30         6.35 
TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4250 TCGA-05-4389 TCGA-05-4390 
        5.29        31.23         2.43         3.98        45.01        37.02 
TCGA-05-4395 TCGA-05-4398 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4432 
        0.00        47.05        29.98        12.00        30.02        25.02 
TCGA-05-4433 TCGA-05-5425 TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
       24.00        29.00        22.03         7.40         5.98         8.68 
TCGA-38-4628 TCGA-38-4632 TCGA-44-2656 TCGA-44-2657 TCGA-44-3917 TCGA-44-5644 
       49.05        44.61        46.98        44.42        38.89        28.37 
TCGA-44-6144 TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-7667 
       23.77        21.63        61.28        16.44        19.46        36.07 
TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 
       18.87        12.66         8.55        13.64        13.45        76.21 
TCGA-49-4490 TCGA-49-4505 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 
       12.66        14.07         8.81        29.46        55.89        53.29 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARO 
       55.33        22.26        73.12         8.55        40.41       123.58 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
      101.72        15.72        47.41         8.22         9.27        14.27 
TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 TCGA-50-6593 
       78.67         8.45        15.12        48.46        57.53        11.05 
TCGA-50-6594 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 
       12.16        10.13        34.29        13.94        35.21        38.73 
TCGA-55-1596 TCGA-55-5899 TCGA-55-6968 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       67.89        30.58        42.51        46.03        53.65         3.88 
TCGA-55-6981 TCGA-55-6982 TCGA-55-7570 TCGA-55-7576 TCGA-55-7727 TCGA-55-7907 
       45.34        32.71        27.09        22.03         3.91        11.28 
TCGA-55-7910 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 
       34.19        18.44        19.82        29.23        29.72        23.08 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
        5.06        17.79        15.72        14.47        13.74        20.28 
TCGA-55-8512 TCGA-55-8614 TCGA-55-8615 TCGA-55-8616 TCGA-55-A490 TCGA-55-A493 
       19.96        17.62        14.66         1.58         3.25         0.92 
TCGA-55-A494 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       15.81        19.99         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
       88.64        49.25        47.80        19.53        56.71        54.35 
TCGA-62-A46U TCGA-62-A470 TCGA-62-A471 TCGA-64-1676 TCGA-64-1681 TCGA-64-5774 
       67.96        39.25        40.96        56.81        38.37        87.98 
TCGA-64-5778 TCGA-64-5779 TCGA-67-3770 TCGA-67-3772 TCGA-67-3774 TCGA-69-7761 
       42.90        28.41        20.05        18.84        12.66         6.12 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7973 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
       22.68        13.61         7.56         4.41        13.51        14.01 
TCGA-69-8255 TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 
        4.24        26.73        19.43         8.42        23.38        26.30 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 
       15.35         4.31         1.25        50.33        66.64        77.85 
TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 
       43.82        85.15        49.84        36.66       108.66       100.57 
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       129.53        21.90 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7162 TCGA-78-7167 
      119.51        32.09        64.90        22.92       104.19        88.14 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-80-5608 TCGA-86-7701 
       26.53        31.20         8.02        26.01        93.11        31.13 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
       34.39        38.04        32.78        19.89        35.24        37.74 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 
        4.08        24.33         0.79        22.82        31.20        23.05 
TCGA-86-8669 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 
       30.84         0.62        26.50        29.46         3.81        10.62 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6849 TCGA-95-7039 TCGA-95-7567 
       41.36         1.97        10.19         1.15        41.82        18.67 
TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 
       18.67         5.39        15.39        19.76        18.67        24.56 
TCGA-99-8025 TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-L9-A8F4 
       34.85        21.57        18.08        19.00        18.58        15.65 
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-A4T7 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK 
        5.49        11.05        24.36        14.10        11.15        19.13 
TCGA-NJ-A4YF TCGA-NJ-A4YQ TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
       71.05        47.08         0.43        19.82        20.28        59.11 

$`DEL PEAK 40(19P13.2) WILD-TYPE`
TCGA-05-4405 TCGA-05-4434 TCGA-38-4629 TCGA-38-4630 TCGA-38-7271 TCGA-44-2661 
       20.05        15.02        28.41        35.28        26.30        38.10 
TCGA-44-6147 TCGA-44-7661 TCGA-49-6761 TCGA-49-AARN TCGA-50-5935 TCGA-55-1595 
       27.78        18.31        11.64        37.32        21.47        48.62 
TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 
        7.79         7.99        16.01        23.18        14.53        21.44 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 TCGA-55-8511 
       19.66        19.73        16.93        19.69        32.12        18.15 
TCGA-55-8619 TCGA-55-8621 TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       13.68        16.93        20.65        13.87        52.60        82.68 
TCGA-78-8660 TCGA-93-8067 TCGA-95-7562 TCGA-95-7947 TCGA-97-A4M2 TCGA-97-A4M7 
       10.55         6.12         2.86        15.68        20.52        20.68 
TCGA-J2-8194 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4TD TCGA-05-4249 
       23.80        10.09        21.83        27.19        10.09        50.07 
TCGA-05-4397 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4425 TCGA-05-4426 
       24.03        19.00         2.99        14.96        21.99        26.01 
TCGA-05-4430 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-38-4625 
       25.02         4.96         9.04         2.04         0.46        97.74 
TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 
      120.79        37.71         4.37        44.94        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        33.73        26.56 
TCGA-44-5643 TCGA-44-5645 TCGA-44-6145 TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 
       33.30        28.01        19.56        23.15        23.18        32.45 
TCGA-44-7659 TCGA-44-7662 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B 
       22.72         7.17        23.64        15.98        15.32         9.44 
TCGA-44-A47G TCGA-49-4487 TCGA-49-4488 TCGA-49-4494 TCGA-49-4506 TCGA-49-4512 
       11.54        28.11        28.57        35.54        32.84        29.75 
TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V 
       22.26        62.24        28.90       221.33       164.12         9.86 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5055 TCGA-50-5068 TCGA-50-5942 TCGA-50-5946 
       20.52        71.47        60.16        49.28        60.72        53.16 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6595 TCGA-50-6673 TCGA-50-8457 
       42.35         3.91        25.55         6.21         0.72        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       36.79        27.25        30.54        14.30        80.52         5.62 
TCGA-55-6969 TCGA-55-6970 TCGA-55-6980 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       40.73        15.25        69.34        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7574 TCGA-55-7728 
      107.21        70.26        28.67        20.02        32.71        23.15 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7911 TCGA-55-8087 TCGA-55-8096 TCGA-55-8097 
       25.41        18.64        17.65        15.19        23.64        15.65 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 
       29.19        22.16        15.42        17.56         0.36        17.72 
TCGA-55-8513 TCGA-55-8514 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A57B 
       26.01        17.10        12.33        20.71        21.40        17.95 
TCGA-62-A46V TCGA-62-A46Y TCGA-62-A472 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
       72.30        13.61        29.92        39.09        81.80        37.02 
TCGA-64-5775 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 TCGA-67-3773 TCGA-67-4679 
        2.04        51.25        28.47        20.05        14.04        14.73 
TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7765 TCGA-69-7974 TCGA-69-7979 
        5.72         4.64         6.64         5.42         6.05        13.41 
TCGA-69-8254 TCGA-73-4675 TCGA-73-4676 TCGA-73-A9RS TCGA-78-7143 TCGA-78-7152 
       13.45        30.31         9.24        11.18       163.10        39.95 
TCGA-78-7154 TCGA-78-7155 TCGA-78-7158 TCGA-78-7161 TCGA-78-7163 TCGA-78-7537 
       19.50        38.50         5.88         9.57       238.29        53.33 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 
       39.35        10.55       232.18        39.75        77.59       110.50 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7714 TCGA-86-8056 TCGA-86-8076 
       27.09        12.36         5.88        20.55         4.57        32.65 
TCGA-86-8278 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8671 
       31.04        21.47        14.60        11.61        13.91        27.58 
TCGA-86-8673 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6840 
       28.34        24.23        13.64        26.47         2.60        12.23 
TCGA-91-6847 TCGA-91-6848 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD 
       27.68         7.36        16.60        14.27         1.18        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 
       22.45        17.46        23.61         1.08        19.00        12.39 
TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
       27.29         2.76        19.89        42.25        64.60        63.52 
TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8175 
       61.48        25.48        18.54         0.59        15.91        18.12 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 
       16.41        14.30        21.60        20.58        21.44        20.84 
TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 
       36.76         1.45        21.63        35.47        32.48        14.30 
TCGA-L9-A50W TCGA-L9-A5IP TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TE 
       14.53         1.91        58.45        37.35        41.59        29.46 
TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-S2-AA1A 
       73.91        74.33         0.13         1.64         0.49        16.87 

  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                          0.00                           0.13 
  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                        156.66                         238.29 
  DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE 
                        21.965                         21.470 
[1] "0.0 - 156.7 (22.0)" "0.1 - 238.3 (21.5)"
[1] "hr=" "1.1"
D69V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 40(19P13.2) MUTATED         2       60       66        0        32
  DEL PEAK 40(19P13.2) WILD-TYPE       3       73       73        1        18
                                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        30         30          4        9
D69V3, multiclass
            clus
vv           DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  STAGE I                               2                              3
  STAGE IA                             60                             73
  STAGE IB                             66                             73
  STAGE II                              0                              1
  STAGE IIA                            32                             18
  STAGE IIB                            42                             30
  STAGE IIIA                           42                             30
  STAGE IIIB                            7                              4
  STAGE IV                             16                              9
[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    81 152  23  12
  DEL PEAK 40(19P13.2) WILD-TYPE  90 126  23   7
D69V4, multiclass
    clus
vv   DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  T1                           81                             90
  T2                          152                            126
  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 171  37    33
D69V5, multiclass
       clus
vv      DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  N0                             162                            171
  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"
D69V6, binary
                                cls
clus                               0   1
  DEL PEAK 40(19P13.2) MUTATED   192  16
  DEL PEAK 40(19P13.2) WILD-TYPE 157   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.2) MUTATED    192   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                          192                            157
  1                           16                              9
[1] 2 2
[1] FALSE
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(19P13.2) MUTATED   126 143
  DEL PEAK 40(19P13.2) WILD-TYPE 150  97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.2) MUTATED    126  143
  DEL PEAK 40(19P13.2) WILD-TYPE  150   97
        clus
vv       DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  FEMALE                          126                            150
  MALE                            143                             97
[1] 2 2
[1] FALSE
D69V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(19P13.2) MUTATED   214  31
  DEL PEAK 40(19P13.2) WILD-TYPE 196  29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.2) MUTATED    214   31
  DEL PEAK 40(19P13.2) WILD-TYPE  196   29
     clus
vv    DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  NO                           214                            196
  YES                           31                             29
[1] 2 2
[1] FALSE
D69V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 40(19P13.2) MUTATED                           10
  DEL PEAK 40(19P13.2) WILD-TYPE                          8
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 40(19P13.2) MUTATED                                  60
  DEL PEAK 40(19P13.2) WILD-TYPE                                47
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 40(19P13.2) MUTATED                                                  165
  DEL PEAK 40(19P13.2) WILD-TYPE                                                156
                                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
D69V10, multiclass
                                                    clus
vv                                                   DEL PEAK 40(19P13.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   10
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            60
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          165
  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                                                      8
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              47
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            156
  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"
D69V11, continuous
D69V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(19P13.2) MUTATED   183   3   2  12
  DEL PEAK 40(19P13.2) WILD-TYPE 161  10   2  14
D69V13, multiclass
    clus
vv   DEL PEAK 40(19P13.2) MUTATED DEL PEAK 40(19P13.2) WILD-TYPE
  R0                          183                            161
  R1                            3                             10
  R2                            2                              2
  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 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                          26   200
  DEL PEAK 40(19P13.2) WILD-TYPE                        26   190
D69V14, multiclass
                                  clus
vv                                 DEL PEAK 40(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  26
  WHITE                                                     200
                                  clus
vv                                 DEL PEAK 40(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    26
  WHITE                                                       190
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V15, binary
                                cls
clus                               0   1
  DEL PEAK 40(19P13.2) MUTATED     5 194
  DEL PEAK 40(19P13.2) WILD-TYPE   2 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.2) MUTATED      5  194
  DEL PEAK 40(19P13.2) WILD-TYPE    2  190
                        clus
vv                       DEL PEAK 40(19P13.2) MUTATED
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          194
                        clus
vv                       DEL PEAK 40(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            190
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 41(19Q13.33) MUTATION ANALYSIS
D70V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 41(19Q13.33) MUTATED   119  73
  DEL PEAK 41(19Q13.33) WILD-TYPE 204 108
  DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE 
                            192                             312 
  DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE 
                             73                             108 
$`DEL PEAK 41(19Q13.33) MUTATED`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4434 TCGA-05-5420 
       19.96        14.01         9.96         8.02        15.02        15.02 
TCGA-38-4630 TCGA-38-6178 TCGA-44-2655 TCGA-44-2662 TCGA-44-7670 TCGA-44-7671 
       35.28        14.73        43.53        42.08        29.00        29.23 
TCGA-44-8119 TCGA-49-6742 TCGA-49-6745 TCGA-49-AAR0 TCGA-50-5932 TCGA-50-5935 
        9.37        16.04        17.16       156.66        40.60        21.47 
TCGA-50-6597 TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-8091 TCGA-55-8203 
       41.69        23.05         5.79         7.79        19.73        17.98 
TCGA-55-8511 TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-73-4662 TCGA-73-7498 
       18.15        22.65        20.58        19.59        82.68        39.09 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-95-7948 TCGA-95-A4VK 
       85.32        13.71        16.18         1.45        15.65        21.40 
TCGA-95-A4VN TCGA-97-A4LX TCGA-J2-8192 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       18.18        20.19        24.30        27.19         5.29        31.23 
TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4389 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 
       10.09         3.98        45.01         0.00        24.03        47.05 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4426 TCGA-05-5425 TCGA-05-5715 TCGA-35-4122 
       29.98        12.00        26.01        29.00         2.04         7.40 
TCGA-35-4123 TCGA-38-4625 TCGA-38-4632 TCGA-44-2656 TCGA-44-2665 TCGA-44-2668 
        5.98        97.74        44.61        46.98        42.77        25.02 
TCGA-44-3917 TCGA-44-5644 TCGA-44-6144 TCGA-44-6778 TCGA-44-6779 TCGA-44-8117 
       38.89        28.37        23.77        61.28        16.44        12.66 
TCGA-44-8120 TCGA-44-A4SU TCGA-49-4488 TCGA-49-4490 TCGA-49-4505 TCGA-49-4506 
        8.55        13.45        28.57        12.66        14.07        32.84 
TCGA-49-4507 TCGA-49-4514 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AARE 
        8.81        55.89        22.26        22.26        73.12        40.41 
TCGA-49-AARO TCGA-50-5051 TCGA-50-5072 TCGA-50-5939 TCGA-50-5941 TCGA-50-5944 
      123.58        15.72         8.22        15.12        48.46        57.53 
TCGA-50-5946 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-55-1596 TCGA-55-5899 
       53.16         3.91        11.05        12.16        67.89        30.58 
TCGA-55-6972 TCGA-55-6975 TCGA-55-6982 TCGA-55-6985 TCGA-55-7283 TCGA-55-7570 
       53.65         3.88        32.71        40.54        20.02        27.09 
TCGA-55-7727 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8094 TCGA-55-8507 
        3.91        19.82        29.23        29.72        17.79        13.74 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 
       17.10        14.66         1.58        19.99         4.57        39.98 
TCGA-62-8397 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46R TCGA-62-A46V TCGA-62-A470 
       42.38        49.25        47.80        56.71        72.30        39.25 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1681 TCGA-67-3770 
       40.96        56.81        39.09        81.80        38.37        20.05 
TCGA-67-3772 TCGA-69-7760 TCGA-69-7764 TCGA-69-7978 TCGA-69-7979 TCGA-69-8255 
       18.84         6.64        13.61         4.41        13.41         4.24 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4670 TCGA-73-4677 
       19.43         8.42        23.38        26.30         4.31         1.25 
TCGA-73-7499 TCGA-75-5146 TCGA-75-5147 TCGA-75-6212 TCGA-75-6214 TCGA-78-7146 
       50.33        77.85        43.82        49.84        36.66         5.69 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 TCGA-78-7156 TCGA-78-7161 TCGA-78-7162 
       20.58       129.53       119.51        32.09         9.57       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        35.24         0.79        31.20        30.84         0.62 
TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       29.46         3.81        10.62        41.36         1.97        10.19 
TCGA-91-6848 TCGA-91-8499 TCGA-95-7039 TCGA-95-7567 TCGA-95-8494 TCGA-97-8171 
        7.36         1.18        41.82        18.67         2.76        18.67 
TCGA-97-8174 TCGA-97-8176 TCGA-97-8547 TCGA-97-A4M1 TCGA-97-A4M6 TCGA-99-7458 
        5.39        15.39        21.60        19.76        18.67        24.56 
TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-MN-A4N5 TCGA-MP-A4SV 
       21.57        18.08        19.00        18.58         2.76        86.14 
TCGA-MP-A4SW TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T6 TCGA-MP-A4TI TCGA-MP-A4TK 
       58.45        49.35        37.35        58.85        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        47.08        19.82        20.28        59.11 

$`DEL PEAK 41(19Q13.33) WILD-TYPE`
TCGA-05-4405 TCGA-05-4418 TCGA-05-4427 TCGA-38-4629 TCGA-38-4631 TCGA-38-7271 
       20.05         9.01        26.01        28.41        11.64        26.30 
TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 TCGA-44-A47F 
       38.10        23.93        27.78        86.01        18.31        11.08 
TCGA-49-4501 TCGA-49-6761 TCGA-49-AARN TCGA-55-1595 TCGA-55-7284 TCGA-55-7573 
       46.72        11.64        37.32        48.62         7.99        16.01 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 TCGA-55-8204 
       23.18        14.53        21.44         6.15        19.66        16.93 
TCGA-55-8205 TCGA-55-8207 TCGA-55-8619 TCGA-55-8621 TCGA-55-A4DF TCGA-64-1677 
       19.69        32.12        13.68        16.93        20.19        20.65 
TCGA-67-6217 TCGA-73-4658 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-93-8067 
       13.87        52.60         8.48        50.24        10.55         6.12 
TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-97-8172 TCGA-97-A4M2 
       17.29        16.54         2.86        15.68        17.92        20.52 
TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
       17.75        20.68        23.80         6.35        10.09        21.83 
TCGA-MP-A4TC TCGA-05-4249 TCGA-05-4390 TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 
        2.43        50.07        37.02        19.00         2.99        14.96 
TCGA-05-4424 TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 
       30.02        21.99        25.02        25.02        24.00         4.96 
TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 TCGA-35-5375 TCGA-38-4626 TCGA-38-4627 
       22.03         9.04         0.46         8.68       120.79        37.71 
TCGA-38-4628 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2666 TCGA-44-3396 
       49.05         4.37        44.42        44.94         3.19        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5645 
       38.24        34.06        33.73        26.56        33.30        28.01 
TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 
       19.56        23.15        21.63        23.18        32.45        22.72 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-A479 
       19.46         7.17        36.07        18.87        23.64        15.98 
TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4487 
       15.32         9.44        11.54        13.64        76.21        28.11 
TCGA-49-4494 TCGA-49-4510 TCGA-49-4512 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAR3 
       35.54        29.46        29.75        53.29        55.33        62.24 
TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
       28.90         8.55       221.33       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       101.72        60.16        47.41        49.28         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5936 TCGA-50-5942 TCGA-50-6590 TCGA-50-6592 
       14.27        78.67         8.45        60.72        42.35        25.55 
TCGA-50-6595 TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-50-8460 
        6.21         0.72        10.13        36.99        36.79        27.25 
TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6543 
       34.29        30.54        13.94        35.21        38.73        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       80.52         5.62        42.51        40.73        15.25        46.03 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6983 TCGA-55-6984 TCGA-55-6986 TCGA-55-6987 
       69.34        45.34        92.81        24.99       107.21        70.26 
TCGA-55-7281 TCGA-55-7574 TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 
       28.67        32.71        22.03        23.15        25.41        18.64 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-8087 TCGA-55-8089 
       11.28        34.19        17.65        18.44        15.19        23.08 
TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
        5.06        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8508 TCGA-55-8510 
       17.56        15.72        14.47         0.36        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
       19.96        26.01        17.62        12.33        20.71        21.40 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8398 TCGA-62-8399 
        3.25         0.92        15.81        17.95        14.60        88.64 
TCGA-62-A46P TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A472 TCGA-64-1680 
       19.53        54.35        67.96        13.61        29.92        37.02 
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-67-3771 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 
       20.05        14.04        12.66        14.73         5.72         4.64 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7980 
        6.12        22.68         5.42         7.56         6.05        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8453 TCGA-73-4668 TCGA-73-4675 TCGA-73-4676 
       14.01        13.45        26.73        15.35        30.31         9.24 
TCGA-73-A9RS TCGA-75-5125 TCGA-75-6206 TCGA-75-7025 TCGA-75-7027 TCGA-78-7143 
       11.18        66.64        85.15       108.66       100.57       163.10 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7150 TCGA-78-7152 TCGA-78-7154 TCGA-78-7155 
       27.16        19.27        21.90        39.95        19.50        38.50 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 TCGA-78-7537 TCGA-78-7539 
        5.88        64.90        22.92       238.29        53.33        26.01 
TCGA-78-7540 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 
       39.35       232.18        39.75        77.59       110.50        93.11 
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        38.04        20.55 
TCGA-86-7953 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 
       32.78        37.74         4.08         4.57        24.33        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
       32.65        31.04        23.05        21.47        14.60        11.61 
TCGA-86-8668 TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4JF TCGA-86-A4P7 
       13.91        27.58        28.34        26.50        24.23        13.64 
TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8496 
       26.47         2.60        12.23        27.68         1.15        16.60 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JO 
       14.27        19.82        22.45        17.46        23.61         1.08 
TCGA-93-A4JP TCGA-95-7944 TCGA-95-8039 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 
       19.00        12.39        27.29        19.89        42.25        64.60 
TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 
       63.52        61.48        25.48        18.54         0.59        15.91 
TCGA-97-8175 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M5 
       18.12        16.41        14.30        20.58        21.44        20.84 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG 
       34.85        36.76         1.45        21.63        35.47        32.48 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4T4 
       14.30        14.53         1.91        15.65        38.63        86.04 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ 
        5.49        41.59        29.46        11.05        24.36        11.15 
TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O TCGA-S2-AA1A 
       74.33         0.13         1.64         0.49         0.43        16.87 

  DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE 
                           0.00                            0.13 
  DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE 
                         156.66                          238.29 
  DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE 
                         21.435                          21.865 
[1] "0.0 - 156.7 (21.4)" "0.1 - 238.3 (21.9)"
[1] "hr=" "1.1"
D70V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 41(19Q13.33) MUTATED         1       46       49        1        16
  DEL PEAK 41(19Q13.33) WILD-TYPE       4       87       90        0        34
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 41(19Q13.33) MUTATED          30         32          5       12
  DEL PEAK 41(19Q13.33) WILD-TYPE        42         40          6       13
D70V3, multiclass
            clus
vv           DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                              46                              87
  STAGE IB                              49                              90
  STAGE II                               1                               0
  STAGE IIA                             16                              34
  STAGE IIB                             30                              42
  STAGE IIIA                            32                              40
  STAGE IIIB                             5                               6
  STAGE IV                              12                              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 41(19Q13.33) MUTATED    57 110  18   9
  DEL PEAK 41(19Q13.33) WILD-TYPE 114 168  28  10
D70V4, multiclass
    clus
vv   DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE
  T1                            57                             114
  T2                           110                             168
  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 41(19Q13.33) MUTATED   121  41    31
  DEL PEAK 41(19Q13.33) WILD-TYPE 212  55    45
D70V5, multiclass
       clus
vv      DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE
  N0                              121                             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"
D70V6, binary
                                 cls
clus                                0   1
  DEL PEAK 41(19Q13.33) MUTATED   138  12
  DEL PEAK 41(19Q13.33) WILD-TYPE 211  13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(19Q13.33) MUTATED    138   12
  DEL PEAK 41(19Q13.33) WILD-TYPE  211   13
   clus
vv  DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE
  0                           138                             211
  1                            12                              13
[1] 2 2
[1] FALSE
D70V7, binary
                                 cls
clus                                0   1
  DEL PEAK 41(19Q13.33) MUTATED    99  96
  DEL PEAK 41(19Q13.33) WILD-TYPE 177 144
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(19Q13.33) MUTATED     99   96
  DEL PEAK 41(19Q13.33) WILD-TYPE  177  144
        clus
vv       DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE
  FEMALE                            99                             177
  MALE                              96                             144
[1] 2 2
[1] FALSE
D70V8, binary
                                 cls
clus                                0   1
  DEL PEAK 41(19Q13.33) MUTATED   155  20
  DEL PEAK 41(19Q13.33) WILD-TYPE 255  40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(19Q13.33) MUTATED    155   20
  DEL PEAK 41(19Q13.33) WILD-TYPE  255   40
     clus
vv    DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE
  NO                            155                             255
  YES                            20                              40
[1] 2 2
[1] FALSE
D70V9, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 41(19Q13.33) MUTATED                            5
  DEL PEAK 41(19Q13.33) WILD-TYPE                         13
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 41(19Q13.33) MUTATED                                  48
  DEL PEAK 41(19Q13.33) WILD-TYPE                                59
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 41(19Q13.33) MUTATED                                                  122
  DEL PEAK 41(19Q13.33) WILD-TYPE                                                199
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 41(19Q13.33) MUTATED                                            0
  DEL PEAK 41(19Q13.33) WILD-TYPE                                          5
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 41(19Q13.33) MUTATED                                               5
  DEL PEAK 41(19Q13.33) WILD-TYPE                                            14
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 41(19Q13.33) MUTATED                                0
  DEL PEAK 41(19Q13.33) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 41(19Q13.33) MUTATED                                    1
  DEL PEAK 41(19Q13.33) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 41(19Q13.33) MUTATED                              0
  DEL PEAK 41(19Q13.33) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 41(19Q13.33) MUTATED                              10
  DEL PEAK 41(19Q13.33) WILD-TYPE                            13
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 41(19Q13.33) MUTATED                                 0
  DEL PEAK 41(19Q13.33) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 41(19Q13.33) MUTATED                                               3
  DEL PEAK 41(19Q13.33) WILD-TYPE                                             2
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 41(19Q13.33) MUTATED                              1
  DEL PEAK 41(19Q13.33) WILD-TYPE                            9
D70V10, multiclass
                                                    clus
vv                                                   DEL PEAK 41(19Q13.33) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             48
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           122
  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 41(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"
D70V11, continuous
D70V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 41(19Q13.33) MUTATED   127   4   3   9
  DEL PEAK 41(19Q13.33) WILD-TYPE 217   9   1  17
D70V13, multiclass
    clus
vv   DEL PEAK 41(19Q13.33) MUTATED DEL PEAK 41(19Q13.33) WILD-TYPE
  R0                           127                             217
  R1                             4                               9
  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 41(19Q13.33) MUTATED                                  0     4
  DEL PEAK 41(19Q13.33) WILD-TYPE                                1     3
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(19Q13.33) MUTATED                          17   146
  DEL PEAK 41(19Q13.33) WILD-TYPE                        35   244
D70V14, multiclass
                                  clus
vv                                 DEL PEAK 41(19Q13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      146
                                  clus
vv                                 DEL PEAK 41(19Q13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          3
  BLACK OR AFRICAN AMERICAN                                     35
  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"
D70V15, binary
                                 cls
clus                                0   1
  DEL PEAK 41(19Q13.33) MUTATED     2 140
  DEL PEAK 41(19Q13.33) WILD-TYPE   5 244
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 41(19Q13.33) MUTATED      2  140
  DEL PEAK 41(19Q13.33) WILD-TYPE    5  244
                        clus
vv                       DEL PEAK 41(19Q13.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           140
                        clus
vv                       DEL PEAK 41(19Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             244
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 42(20P13) MUTATION ANALYSIS
D71V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 42(20P13) MUTATED    72  54
  DEL PEAK 42(20P13) WILD-TYPE 251 127
  DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE 
                         126                          378 
  DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE 
                          54                          127 
$`DEL PEAK 42(20P13) MUTATED`
TCGA-38-4629 TCGA-38-6178 TCGA-44-2662 TCGA-49-4501 TCGA-49-6745 TCGA-50-6597 
       28.41        14.73        42.08        46.72        17.16        41.69 
TCGA-55-1595 TCGA-55-6978 TCGA-55-7725 TCGA-55-8090 TCGA-55-8207 TCGA-55-A491 
       48.62         5.79        14.53        19.66        32.12        20.58 
TCGA-73-4662 TCGA-78-8660 TCGA-95-7043 TCGA-95-7562 TCGA-95-A4VN TCGA-J2-8192 
       82.68        10.55        16.54         2.86        18.18        24.30 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-05-4395 
       10.09        27.19         5.29        31.23         2.43         0.00 
TCGA-05-4398 TCGA-05-4415 TCGA-05-5423 TCGA-44-2656 TCGA-44-2665 TCGA-44-3917 
       47.05         2.99         4.96        46.98        42.77        38.89 
TCGA-44-3919 TCGA-44-6779 TCGA-44-8117 TCGA-44-A47A TCGA-44-A47G TCGA-49-4505 
       33.73        16.44        12.66        15.32        11.54        14.07 
TCGA-49-4512 TCGA-49-6743 TCGA-49-AAQV TCGA-49-AARO TCGA-49-AARQ TCGA-50-5051 
       29.75        53.29        22.26       123.58       221.33        15.72 
TCGA-50-5072 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5944 TCGA-50-6593 
        8.22        78.67         8.45        15.12        57.53        11.05 
TCGA-50-6594 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-55-1594 TCGA-55-6712 
       12.16        27.25        34.29        30.54        38.73         5.62 
TCGA-55-6975 TCGA-55-6980 TCGA-55-6984 TCGA-55-7283 TCGA-55-7576 TCGA-55-7727 
        3.88        69.34        24.99        20.02        22.03         3.91 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7994 TCGA-55-8092 TCGA-55-8094 TCGA-55-8506 
       18.64        11.28        19.82         5.06        17.79         0.36 
TCGA-55-8616 TCGA-55-A493 TCGA-62-8397 TCGA-62-A46O TCGA-62-A46U TCGA-62-A46V 
        1.58         0.92        42.38        47.80        67.96        72.30 
TCGA-62-A46Y TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1681 
       13.61        40.96        29.92        56.81        39.09        38.37 
TCGA-64-5781 TCGA-67-3773 TCGA-67-6216 TCGA-69-7761 TCGA-69-7974 TCGA-69-8453 
       51.25        14.04         4.64         6.12         6.05        26.73 
TCGA-69-A59K TCGA-73-4666 TCGA-73-4670 TCGA-73-7499 TCGA-75-5125 TCGA-75-6212 
       19.43        26.30         4.31        50.33        66.64        49.84 
TCGA-75-6214 TCGA-78-7143 TCGA-78-7145 TCGA-78-7148 TCGA-78-7158 TCGA-78-7159 
       36.66       163.10        27.16        20.58         5.88        64.90 
TCGA-78-7535 TCGA-78-8662 TCGA-80-5608 TCGA-86-6562 TCGA-86-6851 TCGA-86-7953 
       31.20       110.50        93.11        12.36         5.88        32.78 
TCGA-86-7955 TCGA-86-8278 TCGA-86-8280 TCGA-86-8673 TCGA-91-6828 TCGA-91-6835 
       35.24        31.04        23.05        28.34        10.62         2.60 
TCGA-93-7347 TCGA-95-7039 TCGA-95-7567 TCGA-97-7554 TCGA-97-A4M0 TCGA-99-7458 
       22.45        41.82        18.67        25.48        21.44        24.56 
TCGA-99-8033 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV 
       21.57        18.08        19.00        18.58        38.63        86.14 
TCGA-MP-A4SW TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF TCGA-O1-A52J 
       58.45        14.10        11.15        19.13        71.05        59.11 

$`DEL PEAK 42(20P13) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 
       19.96        14.01         9.96         8.02        20.05         9.01 
TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 TCGA-38-4630 TCGA-38-4631 TCGA-38-7271 
       26.01        15.02        15.02        35.28        11.64        26.30 
TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       43.53        38.10        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 TCGA-49-6761 
       29.00        29.23         9.37        11.08        16.04        11.64 
TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 TCGA-55-6979 
      156.66        37.32        40.60        21.47        23.05         7.79 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7726 TCGA-55-7914 TCGA-55-8091 
        7.99        16.01        23.18        21.44         6.15        19.73 
TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 
       17.98        16.93        19.69        18.15        13.68        16.93 
TCGA-55-A48X TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 
       22.65        19.59        20.19        20.65        13.87        52.60 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 
       39.09         8.48        50.24        85.32        13.71        16.18 
TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
        1.45         6.12        17.29        15.68        15.65        21.40 
TCGA-97-8172 TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 TCGA-J2-8194 
       17.92        20.19        20.52        17.75        20.68        23.80 
TCGA-L9-A443 TCGA-L9-A743 TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4389 
        6.35        21.83        10.09        50.07         3.98        45.01 
TCGA-05-4390 TCGA-05-4397 TCGA-05-4403 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
       37.02        24.03        19.00        14.96        29.98        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-05-5425 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-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2666 TCGA-44-2668 
       44.61         4.37        44.42        44.94         3.19        25.02 
TCGA-44-3396 TCGA-44-3398 TCGA-44-3918 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
       37.15        38.24        34.06        26.56        33.30        28.37 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 
       28.01        23.77        19.56        23.15        21.63        23.18 
TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 
       32.45        61.28        22.72        19.46         7.17        36.07 
TCGA-44-7669 TCGA-44-7672 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47B TCGA-44-A4SS 
       18.87        23.64         8.55        15.98         9.44        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-49-6744 TCGA-49-6767 
       32.84         8.81        29.46        55.89        55.33        22.26 
TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AAR9 TCGA-49-AARE TCGA-49-AARR 
       73.12        62.24        28.90         8.55        40.41       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       101.72        60.16        47.41 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5931 TCGA-50-5941 TCGA-50-5942 TCGA-50-5946 
       49.28         9.27        14.27        48.46        60.72        53.16 
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-55-1596 TCGA-55-5899 
       36.99        36.79        13.94        35.21        67.89        30.58 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 
       14.30        80.52        42.51        40.73        15.25        46.03 
TCGA-55-6972 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
       53.65        45.34        32.71        92.81        40.54       107.21 
TCGA-55-6987 TCGA-55-7281 TCGA-55-7570 TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 
       70.26        28.67        27.09        32.71        23.15        25.41 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       34.19        17.65        18.44        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 
       23.08        23.64        15.65        29.19        22.16        15.42 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
       17.56        15.72        14.47        13.74        20.28        17.72 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 
       19.96        26.01        17.10        17.62        14.66        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A494 TCGA-55-A4DG TCGA-55-A57B 
       20.71        21.40         3.25        15.81        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-A46S TCGA-62-A470 TCGA-64-1679 TCGA-64-1680 TCGA-64-5774 
       56.71        54.35        39.25        81.80        37.02        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 
        2.04        42.90        28.41        28.47        20.05        20.05 
TCGA-67-3772 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-69-7760 TCGA-69-7763 
       18.84        12.66        14.73         5.72         6.64        22.68 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
       13.61         5.42         7.56         4.41        13.41        13.51 
TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 
       14.01        13.45         4.24         8.42        23.38        15.35 
TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-A9RS TCGA-75-5146 TCGA-75-5147 
       30.31         9.24         1.25        11.18        77.85        43.82 
TCGA-75-6206 TCGA-75-7025 TCGA-75-7027 TCGA-78-7146 TCGA-78-7147 TCGA-78-7149 
       85.15       108.66       100.57         5.69        19.27       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
       21.90        39.95       119.51        19.50        38.50        32.09 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       22.92         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
        8.02        53.33        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-83-5908 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
       39.75        77.59        27.09        31.13        34.39        38.04 
TCGA-86-7714 TCGA-86-7954 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
       20.55        19.89        37.74         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        22.82        32.65        31.20        21.47        14.60 
TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 
       11.61        13.91        30.84        27.58         0.62        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
       29.46         3.81        24.23        13.64        26.47        41.36 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        1.97        10.19        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JN 
       16.60        14.27         1.18        19.82        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP 
        1.08        19.00        12.39        27.29         2.76        19.89 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-7938 
       42.25        64.60        63.52        61.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       14.30        21.60        20.58        19.76        20.84        18.67 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AE TCGA-J2-A4AG 
       34.85        36.76         1.45        21.63        35.47        32.48 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SY 
       14.30        14.53         1.91        15.65         2.76        49.35 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE 
       37.35        86.04        58.85         5.49        41.59        29.46 
TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       11.05        24.36        73.91        74.33         0.13         1.64 
TCGA-NJ-A4YQ TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-S2-AA1A 
       47.08         0.49         0.43        19.82        20.28        16.87 

  DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE 
                        0.00                         0.13 
  DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE 
                      221.33                       238.29 
  DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE 
                      22.355                       21.470 
[1] "0.0 - 221.3 (22.4)" "0.1 - 238.3 (21.5)"
[1] "hr=" "1.2"
D71V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 42(20P13) MUTATED         2       29       27        1        13
  DEL PEAK 42(20P13) WILD-TYPE       3      104      112        0        37
                              vv
clus                           STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 42(20P13) MUTATED          25         21          5        6
  DEL PEAK 42(20P13) WILD-TYPE        47         51          6       19
D71V3, multiclass
            clus
vv           DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE
  STAGE I                             2                            3
  STAGE IA                           29                          104
  STAGE IB                           27                          112
  STAGE II                            1                            0
  STAGE IIA                          13                           37
  STAGE IIB                          25                           47
  STAGE IIIA                         21                           51
  STAGE IIIB                          5                            6
  STAGE IV                            6                           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 42(20P13) MUTATED    38  72  12   7
  DEL PEAK 42(20P13) WILD-TYPE 133 206  34  12
D71V4, multiclass
    clus
vv   DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE
  T1                         38                          133
  T2                         72                          206
  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 42(20P13) MUTATED    74  29    25
  DEL PEAK 42(20P13) WILD-TYPE 259  67    51
D71V5, multiclass
       clus
vv      DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE
  N0                            74                          259
  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"
D71V6, binary
                              cls
clus                             0   1
  DEL PEAK 42(20P13) MUTATED    93   6
  DEL PEAK 42(20P13) WILD-TYPE 256  19
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(20P13) MUTATED     93    6
  DEL PEAK 42(20P13) WILD-TYPE  256   19
   clus
vv  DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE
  0                         93                          256
  1                          6                           19
[1] 2 2
[1] FALSE
D71V7, binary
                              cls
clus                             0   1
  DEL PEAK 42(20P13) MUTATED    80  50
  DEL PEAK 42(20P13) WILD-TYPE 196 190
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(20P13) MUTATED     80   50
  DEL PEAK 42(20P13) WILD-TYPE  196  190
        clus
vv       DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE
  FEMALE                         80                          196
  MALE                           50                          190
[1] 2 2
[1] FALSE
D71V8, binary
                              cls
clus                             0   1
  DEL PEAK 42(20P13) MUTATED   109  13
  DEL PEAK 42(20P13) WILD-TYPE 301  47
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(20P13) MUTATED    109   13
  DEL PEAK 42(20P13) WILD-TYPE  301   47
     clus
vv    DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE
  NO                         109                          301
  YES                         13                           47
[1] 2 2
[1] FALSE
D71V9, continuous
                              vv
clus                           LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 42(20P13) MUTATED                            3
  DEL PEAK 42(20P13) WILD-TYPE                         15
                              vv
clus                           LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 42(20P13) MUTATED                                  25
  DEL PEAK 42(20P13) WILD-TYPE                                82
                              vv
clus                           LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 42(20P13) MUTATED                                                   85
  DEL PEAK 42(20P13) WILD-TYPE                                                236
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 42(20P13) MUTATED                                            0
  DEL PEAK 42(20P13) WILD-TYPE                                          5
                              vv
clus                           LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 42(20P13) MUTATED                                               6
  DEL PEAK 42(20P13) WILD-TYPE                                            13
                              vv
clus                           LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 42(20P13) MUTATED                                2
  DEL PEAK 42(20P13) WILD-TYPE                              0
                              vv
clus                           LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 42(20P13) MUTATED                                    1
  DEL PEAK 42(20P13) WILD-TYPE                                  2
                              vv
clus                           LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 42(20P13) MUTATED                              0
  DEL PEAK 42(20P13) WILD-TYPE                            2
                              vv
clus                           LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 42(20P13) MUTATED                               4
  DEL PEAK 42(20P13) WILD-TYPE                            19
                              vv
clus                           LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 42(20P13) MUTATED                                 1
  DEL PEAK 42(20P13) WILD-TYPE                               0
                              vv
clus                           LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 42(20P13) MUTATED                                               1
  DEL PEAK 42(20P13) WILD-TYPE                                             4
                              vv
clus                           MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 42(20P13) MUTATED                              2
  DEL PEAK 42(20P13) WILD-TYPE                            8
D71V10, multiclass
                                                    clus
vv                                                   DEL PEAK 42(20P13) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                  3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                          25
  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 42(20P13) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                   15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            82
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          236
  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"
D71V11, continuous
D71V12, continuous
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 42(20P13) MUTATED    93   5   1   4
  DEL PEAK 42(20P13) WILD-TYPE 251   8   3  22
D71V13, multiclass
    clus
vv   DEL PEAK 42(20P13) MUTATED DEL PEAK 42(20P13) WILD-TYPE
  R0                         93                          251
  R1                          5                            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 42(20P13) MUTATED                                  0     1
  DEL PEAK 42(20P13) WILD-TYPE                                1     6
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(20P13) MUTATED                          10   101
  DEL PEAK 42(20P13) WILD-TYPE                        42   289
D71V14, multiclass
                                  clus
vv                                 DEL PEAK 42(20P13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                10
  WHITE                                                   101
                                  clus
vv                                 DEL PEAK 42(20P13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  42
  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"
D71V15, binary
                              cls
clus                             0   1
  DEL PEAK 42(20P13) MUTATED     1  98
  DEL PEAK 42(20P13) WILD-TYPE   6 286
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 42(20P13) MUTATED      1   98
  DEL PEAK 42(20P13) WILD-TYPE    6  286
                        clus
vv                       DEL PEAK 42(20P13) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         98
                        clus
vv                       DEL PEAK 42(20P13) WILD-TYPE
  HISPANIC OR LATINO                                6
  NOT HISPANIC OR LATINO                          286
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 43(20Q13.12) MUTATION ANALYSIS
D72V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 43(20Q13.12) MUTATED    45  33
  DEL PEAK 43(20Q13.12) WILD-TYPE 278 148
  DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE 
                             78                             426 
  DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE 
                             33                             148 
$`DEL PEAK 43(20Q13.12) MUTATED`
TCGA-05-4402 TCGA-05-4405 TCGA-05-4418 TCGA-49-4501 TCGA-49-6745 TCGA-55-1595 
        8.02        20.05         9.01        46.72        17.16        48.62 
TCGA-55-8090 TCGA-95-A4VK TCGA-97-8172 TCGA-MP-A4TC TCGA-05-4415 TCGA-05-4417 
       19.66        21.40        17.92         2.43         2.99        14.96 
TCGA-05-4422 TCGA-05-5715 TCGA-38-4628 TCGA-44-2656 TCGA-44-3918 TCGA-44-3919 
       12.00         2.04        49.05        46.98        34.06        33.73 
TCGA-44-6779 TCGA-44-A47B TCGA-44-A47G TCGA-49-4506 TCGA-49-4507 TCGA-49-6743 
       16.44         9.44        11.54        32.84         8.81        53.29 
TCGA-49-AARE TCGA-50-5051 TCGA-50-5072 TCGA-50-5936 TCGA-50-6593 TCGA-50-8460 
       40.41        15.72         8.22         8.45        11.05        27.25 
TCGA-53-7624 TCGA-53-A4EZ TCGA-55-8087 TCGA-55-8512 TCGA-55-8615 TCGA-55-A494 
       34.29        35.21        15.19        19.96        14.66        15.81 
TCGA-62-8397 TCGA-62-A46O TCGA-62-A46S TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 
       42.38        47.80        54.35        67.96        40.96        29.92 
TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 
       20.05        14.04        12.66         5.72         4.64        22.68 
TCGA-69-8253 TCGA-69-8453 TCGA-69-A59K TCGA-73-4675 TCGA-75-5146 TCGA-75-6212 
       14.01        26.73        19.43        30.31        77.85        49.84 
TCGA-78-7143 TCGA-78-7146 TCGA-78-7152 TCGA-78-7158 TCGA-78-7160 TCGA-78-7167 
      163.10         5.69        39.95         5.88        22.92        88.14 
TCGA-78-7537 TCGA-86-7953 TCGA-86-8054 TCGA-86-8358 TCGA-91-6828 TCGA-91-6831 
       53.33        32.78        37.74        21.47        10.62        10.19 
TCGA-93-7347 TCGA-97-8174 TCGA-97-8547 TCGA-97-A4M0 TCGA-99-7458 TCGA-99-8025 
       22.45         5.39        21.60        21.44        24.56        34.85 
TCGA-99-8033 TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-MP-A4SW TCGA-MP-A4TH TCGA-MP-A4TI 
       21.57        35.47        19.00        58.45        24.36        14.10 

$`DEL PEAK 43(20Q13.12) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4427 TCGA-05-4434 TCGA-05-5420 
       19.96        14.01         9.96        26.01        15.02        15.02 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 
       28.41        35.28        11.64        14.73        26.30        43.53 
TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-7661 
       38.10        42.08        23.93        27.78        86.01        18.31 
TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 TCGA-49-6761 
       29.00        29.23         9.37        11.08        16.04        11.64 
TCGA-49-AAR0 TCGA-49-AARN TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-1592 
      156.66        37.32        40.60        21.47        41.69        23.05 
TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 
        5.79         7.79         7.99        16.01        23.18        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8091 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 
       21.44         6.15        19.73        17.98        16.93        19.69 
TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       32.12        18.15        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4658 TCGA-73-4662 
       19.59        20.19        20.65        13.87        52.60        82.68 
TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-78-8660 TCGA-80-5611 TCGA-91-6836 
       39.09         8.48        50.24        10.55        85.32        13.71 
TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-93-A4JQ TCGA-95-7043 TCGA-95-7562 
       16.18         1.45         6.12        17.29        16.54         2.86 
TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 
       15.68        15.65        18.18        20.19        20.52        17.75 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 
       20.68        24.30        23.80         6.35        10.09        21.83 
TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 
       27.19         5.29        31.23        10.09        50.07         3.98 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4398 TCGA-05-4403 
       45.01        37.02         0.00        24.03        47.05        19.00 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4430 TCGA-05-4432 
       29.98        30.02        21.99        26.01        25.02        25.02 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-35-3615 
       24.00         4.96        29.00        22.03         9.04         0.46 
TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        7.40         5.98         8.68        97.74       120.79        37.71 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2659 TCGA-44-2665 TCGA-44-2666 
       44.61         4.37        44.42        44.94        42.77         3.19 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-4112 TCGA-44-5643 
       25.02        37.15        38.24        38.89        26.56        33.30 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 
       28.37        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       23.18        32.45        61.28        22.72        19.46         7.17 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 TCGA-44-A479 
       36.07        18.87        23.64        12.66         8.55        15.98 
TCGA-44-A47A TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 
       15.32        13.64        13.45        76.21        28.11        28.57 
TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4510 TCGA-49-4512 TCGA-49-4514 
       12.66        35.54        14.07        29.46        29.75        55.89 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAQV TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AAR4 
       55.33        22.26        22.26        73.12        62.24        28.90 
TCGA-49-AAR9 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR TCGA-4B-A93V TCGA-50-5044 
        8.55       123.58       221.33       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       101.72        60.16        47.41        49.28         9.27 
TCGA-50-5931 TCGA-50-5933 TCGA-50-5939 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
       14.27        78.67        15.12        48.46        60.72        57.53 
TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6594 TCGA-50-6595 
       53.16        42.35         3.91        25.55        12.16         6.21 
TCGA-50-6673 TCGA-50-7109 TCGA-50-8457 TCGA-50-8459 TCGA-53-7626 TCGA-53-7813 
        0.72        10.13        36.99        36.79        30.54        13.94 
TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 
       38.73        67.89        30.58        14.30        80.52         5.62 
TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
       42.51        40.73        15.25        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 
       69.34        45.34        32.71        92.81        24.99        40.54 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
      107.21        70.26        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 
       22.03         3.91        23.15        25.41        18.64        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
       34.19        17.65        18.44        19.82        29.23        29.72 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       23.08         5.06        17.79        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
       22.16        15.42        17.56        15.72        14.47         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
       13.74        20.28        17.72        26.01        17.10        17.62 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 
        1.58        12.33        20.71        21.40         3.25         0.92 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 
       19.99        17.95         4.57        39.98        14.60        88.64 
TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 
       49.25        19.53        56.71        72.30        13.61        39.25 
TCGA-64-1676 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 
       56.81        39.09        81.80        37.02        38.37        87.98 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 TCGA-67-3771 
        2.04        42.90        28.41        51.25        28.47        20.05 
TCGA-67-3772 TCGA-67-4679 TCGA-69-7760 TCGA-69-7761 TCGA-69-7764 TCGA-69-7765 
       18.84        14.73         6.64         6.12        13.61         5.42 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8254 
        7.56         6.05         4.41        13.41        13.51        13.45 
TCGA-69-8255 TCGA-71-6725 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 TCGA-73-4670 
        4.24         8.42        23.38        26.30        15.35         4.31 
TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-73-A9RS TCGA-75-5125 TCGA-75-5147 
        9.24         1.25        50.33        11.18        66.64        43.82 
TCGA-75-6206 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-78-7145 TCGA-78-7147 
       85.15        36.66       108.66       100.57        27.16        19.27 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 
       20.58       129.53        21.90       119.51        19.50        38.50 
TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7220 
       32.09        64.90         9.57       104.19       238.29        26.53 
TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8640 
       31.20         8.02        26.01        39.35        10.55       232.18 
TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 
       39.75        77.59       110.50        93.11        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        38.04        20.55        19.89 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
       35.24         4.08         4.57        24.33         0.79        22.82 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8359 TCGA-86-8585 
       32.65        31.04        31.20        23.05        14.60        11.61 
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        28.34        26.50 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
       29.46         3.81        24.23        13.64        26.47        41.36 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 
        1.97         2.60        12.23        27.68         7.36         1.15 
TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7348 TCGA-93-A4JN 
       16.60        14.27         1.18        19.82        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 
        2.76        19.89        42.25        64.60        63.52        61.48 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 
       25.48        18.54         0.59        15.91        18.67        18.12 
TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 
       15.39        16.41        14.30        20.58        19.76        20.84 
TCGA-97-A4M6 TCGA-99-8028 TCGA-99-8032 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AG 
       18.67        36.76         1.45        21.63        18.08        32.48 
TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N4 
       14.30        14.53         1.91        18.58        15.65        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-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TJ TCGA-MP-A4TK 
        5.49        41.59        29.46        11.05        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        74.33         0.13         1.64        47.08 
TCGA-NJ-A55A TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J TCGA-S2-AA1A 
        0.49         0.43        19.82        20.28        59.11        16.87 

  DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE 
                           2.04                            0.00 
  DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE 
                         163.10                          238.29 
  DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE 
                         21.455                          21.865 
[1] "2.0 - 163.1 (21.5)" "0.0 - 238.3 (21.9)"
[1] "hr=" "1.3"
D72V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 43(20Q13.12) MUTATED         1       15       24        0         4
  DEL PEAK 43(20Q13.12) WILD-TYPE       4      118      115        1        46
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 43(20Q13.12) MUTATED          12         17          2        7
  DEL PEAK 43(20Q13.12) WILD-TYPE        60         55          9       18
D72V3, multiclass
            clus
vv           DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE
  STAGE I                                1                               4
  STAGE IA                              15                             118
  STAGE IB                              24                             115
  STAGE II                               0                               1
  STAGE IIA                              4                              46
  STAGE IIB                             12                              60
  STAGE IIIA                            17                              55
  STAGE IIIB                             2                               9
  STAGE IV                               7                              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 43(20Q13.12) MUTATED    21  47   9   4
  DEL PEAK 43(20Q13.12) WILD-TYPE 150 231  37  15
D72V4, multiclass
    clus
vv   DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE
  T1                            21                             150
  T2                            47                             231
  T3                             9                              37
  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 43(20Q13.12) MUTATED    48  14    18
  DEL PEAK 43(20Q13.12) WILD-TYPE 285  82    58
D72V5, multiclass
       clus
vv      DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE
  N0                               48                             285
  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"
D72V6, binary
                                 cls
clus                                0   1
  DEL PEAK 43(20Q13.12) MUTATED    62   7
  DEL PEAK 43(20Q13.12) WILD-TYPE 287  18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(20Q13.12) MUTATED     62    7
  DEL PEAK 43(20Q13.12) WILD-TYPE  287   18
   clus
vv  DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE
  0                            62                             287
  1                             7                              18
[1] 2 2
[1] FALSE
D72V7, binary
                                 cls
clus                                0   1
  DEL PEAK 43(20Q13.12) MUTATED    48  34
  DEL PEAK 43(20Q13.12) WILD-TYPE 228 206
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(20Q13.12) MUTATED     48   34
  DEL PEAK 43(20Q13.12) WILD-TYPE  228  206
        clus
vv       DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE
  FEMALE                            48                             228
  MALE                              34                             206
[1] 2 2
[1] FALSE
D72V8, binary
                                 cls
clus                                0   1
  DEL PEAK 43(20Q13.12) MUTATED    65   9
  DEL PEAK 43(20Q13.12) WILD-TYPE 345  51
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(20Q13.12) MUTATED     65    9
  DEL PEAK 43(20Q13.12) WILD-TYPE  345   51
     clus
vv    DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE
  NO                             65                             345
  YES                             9                              51
[1] 2 2
[1] FALSE
D72V9, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 43(20Q13.12) MUTATED                            3
  DEL PEAK 43(20Q13.12) WILD-TYPE                         15
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 43(20Q13.12) MUTATED                                  22
  DEL PEAK 43(20Q13.12) WILD-TYPE                                85
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 43(20Q13.12) MUTATED                                                   45
  DEL PEAK 43(20Q13.12) WILD-TYPE                                                276
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 43(20Q13.12) MUTATED                                            0
  DEL PEAK 43(20Q13.12) WILD-TYPE                                          5
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 43(20Q13.12) MUTATED                                               3
  DEL PEAK 43(20Q13.12) WILD-TYPE                                            16
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 43(20Q13.12) MUTATED                                2
  DEL PEAK 43(20Q13.12) WILD-TYPE                              0
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 43(20Q13.12) MUTATED                                    1
  DEL PEAK 43(20Q13.12) WILD-TYPE                                  2
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 43(20Q13.12) MUTATED                              0
  DEL PEAK 43(20Q13.12) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 43(20Q13.12) MUTATED                               4
  DEL PEAK 43(20Q13.12) WILD-TYPE                            19
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 43(20Q13.12) MUTATED                                 0
  DEL PEAK 43(20Q13.12) WILD-TYPE                               1
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 43(20Q13.12) MUTATED                                               0
  DEL PEAK 43(20Q13.12) WILD-TYPE                                             5
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 43(20Q13.12) MUTATED                              2
  DEL PEAK 43(20Q13.12) WILD-TYPE                            8
D72V10, multiclass
                                                    clus
vv                                                   DEL PEAK 43(20Q13.12) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                     3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             22
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            45
  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                                                   2
                                                    clus
vv                                                   DEL PEAK 43(20Q13.12) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      15
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               85
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             276
  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                                                     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"
D72V11, continuous
D72V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 43(20Q13.12) MUTATED    57   2   1   6
  DEL PEAK 43(20Q13.12) WILD-TYPE 287  11   3  20
D72V13, multiclass
    clus
vv   DEL PEAK 43(20Q13.12) MUTATED DEL PEAK 43(20Q13.12) WILD-TYPE
  R0                            57                             287
  R1                             2                              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 43(20Q13.12) MUTATED                                  0     1
  DEL PEAK 43(20Q13.12) WILD-TYPE                                1     6
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(20Q13.12) MUTATED                           4    62
  DEL PEAK 43(20Q13.12) WILD-TYPE                        48   328
D72V14, multiclass
                                  clus
vv                                 DEL PEAK 43(20Q13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       62
                                  clus
vv                                 DEL PEAK 43(20Q13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     48
  WHITE                                                        328
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V15, binary
                                 cls
clus                                0   1
  DEL PEAK 43(20Q13.12) MUTATED     2  55
  DEL PEAK 43(20Q13.12) WILD-TYPE   5 329
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(20Q13.12) MUTATED      2   55
  DEL PEAK 43(20Q13.12) WILD-TYPE    5  329
                        clus
vv                       DEL PEAK 43(20Q13.12) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            55
                        clus
vv                       DEL PEAK 43(20Q13.12) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             329
[1] 2 2
[1] FALSE

Clustering(73) Variable = DEL PEAK 44(21Q11.2) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(21Q11.2) MUTATED   113  64
  DEL PEAK 44(21Q11.2) WILD-TYPE 210 117
  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                           177                            327 
  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                            64                            117 
$`DEL PEAK 44(21Q11.2) MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4402 TCGA-05-4427 TCGA-05-5420 TCGA-38-4630 
       19.96         9.96         8.02        26.01        15.02        35.28 
TCGA-44-7661 TCGA-44-7670 TCGA-44-A47F TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 
       18.31        29.00        11.08        17.16        11.64       156.66 
TCGA-50-5932 TCGA-50-5935 TCGA-55-1592 TCGA-55-6978 TCGA-55-6979 TCGA-55-7724 
       40.60        21.47        23.05         5.79         7.79        23.18 
TCGA-55-8090 TCGA-55-8203 TCGA-55-8204 TCGA-55-8205 TCGA-55-A491 TCGA-55-A4DF 
       19.66        17.98        16.93        19.69        20.58        20.19 
TCGA-64-1677 TCGA-73-4658 TCGA-78-8660 TCGA-91-6836 TCGA-91-7771 TCGA-93-A4JQ 
       20.65        52.60        10.55        13.71        16.18        17.29 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7948 TCGA-97-8172 TCGA-MP-A4T8 TCGA-05-4249 
       16.54         2.86        15.65        17.92         5.29        50.07 
TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 TCGA-05-4417 TCGA-05-4420 
       45.01        37.02         0.00        47.05        14.96        29.98 
TCGA-05-4422 TCGA-05-4424 TCGA-05-4430 TCGA-05-4432 TCGA-05-5425 TCGA-05-5429 
       12.00        30.02        25.02        25.02        29.00         9.04 
TCGA-35-4122 TCGA-35-4123 TCGA-38-4627 TCGA-44-2656 TCGA-44-2659 TCGA-44-2668 
        7.40         5.98        37.71        46.98        44.94        25.02 
TCGA-44-3917 TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6778 
       38.89        33.30        28.37        23.77        19.56        61.28 
TCGA-44-6779 TCGA-44-7667 TCGA-44-7672 TCGA-44-8117 TCGA-44-A479 TCGA-44-A47B 
       16.44        36.07        23.64        12.66        15.98         9.44 
TCGA-44-A4SS TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6767 
       13.64        32.84         8.81        29.46        55.89        22.26 
TCGA-49-AAR2 TCGA-49-AAR4 TCGA-49-AARE TCGA-4B-A93V TCGA-50-5045 TCGA-50-5051 
       73.12        28.90        40.41         9.86        71.47        15.72 
TCGA-50-5068 TCGA-50-5072 TCGA-50-5933 TCGA-50-5944 TCGA-50-5946 TCGA-50-6592 
       49.28         8.22        78.67        57.53        53.16        25.55 
TCGA-50-6595 TCGA-50-7109 TCGA-53-7813 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
        6.21        10.13        13.94        38.73        67.89        30.58 
TCGA-55-6968 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7570 
       42.51        53.65        92.81        40.54       107.21        27.09 
TCGA-55-7576 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
       22.03        23.15        25.41        11.28        34.19        17.65 
TCGA-55-7994 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 TCGA-55-8302 TCGA-55-8506 
       19.82        23.08         5.06        17.79        15.72         0.36 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8514 TCGA-55-8615 TCGA-55-A490 
       13.74        20.28        17.72        17.10        14.66         3.25 
TCGA-62-8402 TCGA-62-A46S TCGA-62-A470 TCGA-62-A471 TCGA-64-1679 TCGA-64-1681 
       49.25        54.35        39.25        40.96        81.80        38.37 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5781 TCGA-69-7760 TCGA-69-7761 TCGA-69-7765 
       87.98         2.04        51.25         6.64         6.12         5.42 
TCGA-69-7974 TCGA-69-7979 TCGA-69-7980 TCGA-73-4659 TCGA-73-4666 TCGA-73-4668 
        6.05        13.41        13.51        23.38        26.30        15.35 
TCGA-73-4670 TCGA-73-4675 TCGA-73-A9RS TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 
        4.31        30.31        11.18       100.57         5.69        20.58 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-8640 
      119.51        19.50        88.14        26.53         8.02       232.18 
TCGA-80-5608 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 TCGA-86-8054 TCGA-86-8278 
       93.11        31.13        34.39        32.78        37.74        31.04 
TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6831 
       14.60        11.61        30.84        24.23        10.62        10.19 
TCGA-91-6840 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7547 TCGA-97-8175 TCGA-97-A4M6 
       12.23         2.76        19.89        64.60        18.12        18.67 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AE TCGA-L9-A7SV 
       34.85        36.76         1.45        21.57        35.47        18.58 
TCGA-L9-A8F4 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4TE TCGA-MP-A4TJ TCGA-NJ-A4YQ 
       15.65        86.14        49.35        29.46        11.15        47.08 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-NJ-A7XG 
        0.43        19.82        20.28 

$`DEL PEAK 44(21Q11.2) WILD-TYPE`
TCGA-05-4384 TCGA-05-4405 TCGA-05-4418 TCGA-05-4434 TCGA-38-4629 TCGA-38-4631 
       14.01        20.05         9.01        15.02        28.41        11.64 
TCGA-38-6178 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6146 
       14.73        26.30        43.53        38.10        42.08        23.93 
TCGA-44-6147 TCGA-44-6776 TCGA-44-7671 TCGA-44-8119 TCGA-49-4501 TCGA-49-6742 
       27.78        86.01        29.23         9.37        46.72        16.04 
TCGA-49-AARN TCGA-50-6597 TCGA-55-1595 TCGA-55-7284 TCGA-55-7573 TCGA-55-7725 
       37.32        41.69        48.62         7.99        16.01        14.53 
TCGA-55-7726 TCGA-55-7914 TCGA-55-8091 TCGA-55-8207 TCGA-55-8511 TCGA-55-8619 
       21.44         6.15        19.73        32.12        18.15        13.68 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-67-6217 TCGA-73-4662 TCGA-73-7498 
       16.93        22.65        19.59        13.87        82.68        39.09 
TCGA-78-7166 TCGA-78-7633 TCGA-80-5611 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7947 
        8.48        50.24        85.32         1.45         6.12        15.68 
TCGA-95-A4VK TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-97-A4M7 
       21.40        18.18        20.19        20.52        17.75        20.68 
TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A743 TCGA-MN-A4N1 
       24.30        23.80         6.35        10.09        21.83        27.19 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4397 TCGA-05-4403 
       31.23         2.43        10.09         3.98        24.03        19.00 
TCGA-05-4415 TCGA-05-4425 TCGA-05-4426 TCGA-05-4433 TCGA-05-5423 TCGA-05-5428 
        2.99        21.99        26.01        24.00         4.96        22.03 
TCGA-05-5715 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4628 
        2.04         0.46         8.68        97.74       120.79        49.05 
TCGA-38-4632 TCGA-38-A44F TCGA-44-2657 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 
       44.61         4.37        44.42        42.77         3.19        37.15 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 TCGA-44-6148 
       38.24        34.06        33.73        26.56        28.01        23.15 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7660 TCGA-44-7662 
       21.63        23.18        32.45        22.72        19.46         7.17 
TCGA-44-7669 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47G TCGA-44-A4SU TCGA-49-4486 
       18.87         8.55        15.32        11.54        13.45        76.21 
TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 TCGA-49-4505 TCGA-49-4512 
       28.11        28.57        12.66        35.54        14.07        29.75 
TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR9 TCGA-49-AARO 
       53.29        55.33        22.26        62.24         8.55       123.58 
TCGA-49-AARQ TCGA-49-AARR TCGA-50-5044 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
      221.33       164.12        20.52       101.72        60.16        47.41 
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        48.46        60.72 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6593 TCGA-50-6594 TCGA-50-6673 TCGA-50-8457 
       42.35         3.91        11.05        12.16         0.72        36.99 
TCGA-50-8459 TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-A4EZ TCGA-55-6543 
       36.79        27.25        34.29        30.54        35.21        14.30 
TCGA-55-6642 TCGA-55-6712 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6975 
       80.52         5.62        40.73        15.25        46.03         3.88 
TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 TCGA-55-6984 TCGA-55-6987 TCGA-55-7281 
       69.34        45.34        32.71        24.99        70.26        28.67 
TCGA-55-7283 TCGA-55-7574 TCGA-55-7727 TCGA-55-7903 TCGA-55-7913 TCGA-55-7995 
       20.02        32.71         3.91        18.64        18.44        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       29.72        15.19        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8301 TCGA-55-8505 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 
       15.42        17.56        14.47        19.96        26.01        17.62 
TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A493 TCGA-55-A494 
        1.58        12.33        20.71        21.40         0.92        15.81 
TCGA-55-A4DG TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
       19.99        17.95         4.57        39.98        42.38        14.60 
TCGA-62-8399 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46U TCGA-62-A46V 
       88.64        47.80        19.53        56.71        67.96        72.30 
TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-1680 TCGA-64-5778 
       13.61        29.92        56.81        39.09        37.02        42.90 
TCGA-64-5779 TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 
       28.41        28.47        20.05        20.05        18.84        14.04 
TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7763 TCGA-69-7764 
       12.66        14.73         5.72         4.64        22.68        13.61 
TCGA-69-7973 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 
        7.56         4.41        14.01        13.45         4.24        26.73 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4676 TCGA-73-4677 TCGA-73-7499 TCGA-75-5125 
       19.43         8.42         9.24         1.25        50.33        66.64 
TCGA-75-5146 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 
       77.85        43.82        85.15        49.84        36.66       108.66 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
      163.10        27.16        19.27       129.53        21.90        39.95 
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        22.92         9.57 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
      104.19       238.29        31.20        53.33        26.01        39.35 
TCGA-78-7542 TCGA-78-8648 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 TCGA-86-6562 
       10.55        39.75        77.59       110.50        27.09        12.36 
TCGA-86-6851 TCGA-86-7713 TCGA-86-7714 TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 
        5.88        38.04        20.55        19.89        35.24         4.08 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8279 
        4.57        24.33         0.79        22.82        32.65        31.20 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8668 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 
       23.05        21.47        13.91        27.58         0.62        28.34 
TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6829 
       26.50        29.46         3.81        13.64        26.47        41.36 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 
        1.97         2.60        27.68         7.36         1.15        16.60 
TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN 
       14.27         1.18        19.82        22.45        17.46        23.61 
TCGA-93-A4JO TCGA-93-A4JP TCGA-95-7039 TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 
        1.08        19.00        41.82        18.67        12.39        27.29 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
       42.25        63.52        61.48        25.48        18.54         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8176 TCGA-97-8177 TCGA-97-8179 
       15.91        18.67         5.39        15.39        16.41        14.30 
TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M0 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 
       21.60        20.58        21.44        19.76        20.84        24.56 
TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A50W 
       21.63        18.08        32.48        19.00        14.30        14.53 
TCGA-L9-A5IP TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 
        1.91        38.63         2.76        58.45        37.35        86.04 
TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TI 
       58.85         5.49        41.59        11.05        24.36        14.10 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YI TCGA-NJ-A4YP 
       19.13        73.91        71.05        74.33         0.13         1.64 
TCGA-NJ-A55A TCGA-O1-A52J TCGA-S2-AA1A 
        0.49        59.11        16.87 

  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                          0.00                           0.13 
  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                        232.18                         238.29 
  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE 
                         21.47                          21.63 
[1] "0.0 - 232.2 (21.5)" "0.1 - 238.3 (21.6)"
[1] "hr=" "1"  
D73V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 44(21Q11.2) MUTATED         1       40       49        0        15
  DEL PEAK 44(21Q11.2) WILD-TYPE       4       93       90        1        35
                                vv
clus                             STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 44(21Q11.2) MUTATED          30         28          5        8
  DEL PEAK 44(21Q11.2) WILD-TYPE        42         44          6       17
D73V3, multiclass
            clus
vv           DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  STAGE I                               1                              4
  STAGE IA                             40                             93
  STAGE IB                             49                             90
  STAGE II                              0                              1
  STAGE IIA                            15                             35
  STAGE IIB                            30                             42
  STAGE IIIA                           28                             44
  STAGE IIIB                            5                              6
  STAGE IV                              8                             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 44(21Q11.2) MUTATED    50 103  17   8
  DEL PEAK 44(21Q11.2) WILD-TYPE 121 175  29  11
D73V4, multiclass
    clus
vv   DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  T1                           50                            121
  T2                          103                            175
  T3                           17                             29
  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 44(21Q11.2) MUTATED   114  36    27
  DEL PEAK 44(21Q11.2) WILD-TYPE 219  60    49
D73V5, multiclass
       clus
vv      DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  N0                             114                            219
  N1                              36                             60
  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"
D73V6, binary
                                cls
clus                               0   1
  DEL PEAK 44(21Q11.2) MUTATED   123   8
  DEL PEAK 44(21Q11.2) WILD-TYPE 226  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(21Q11.2) MUTATED    123    8
  DEL PEAK 44(21Q11.2) WILD-TYPE  226   17
   clus
vv  DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  0                          123                            226
  1                            8                             17
[1] 2 2
[1] FALSE
D73V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(21Q11.2) MUTATED    87  92
  DEL PEAK 44(21Q11.2) WILD-TYPE 189 148
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(21Q11.2) MUTATED     87   92
  DEL PEAK 44(21Q11.2) WILD-TYPE  189  148
        clus
vv       DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  FEMALE                           87                            189
  MALE                             92                            148
[1] 2 2
[1] FALSE
D73V8, binary
                                cls
clus                               0   1
  DEL PEAK 44(21Q11.2) MUTATED   140  26
  DEL PEAK 44(21Q11.2) WILD-TYPE 270  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(21Q11.2) MUTATED    140   26
  DEL PEAK 44(21Q11.2) WILD-TYPE  270   34
     clus
vv    DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  NO                           140                            270
  YES                           26                             34
[1] 2 2
[1] FALSE
D73V9, continuous
                                vv
clus                             LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 44(21Q11.2) MUTATED                            9
  DEL PEAK 44(21Q11.2) WILD-TYPE                          9
                                vv
clus                             LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 44(21Q11.2) MUTATED                                  29
  DEL PEAK 44(21Q11.2) WILD-TYPE                                78
                                vv
clus                             LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 44(21Q11.2) MUTATED                                                  125
  DEL PEAK 44(21Q11.2) WILD-TYPE                                                196
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 44(21Q11.2) MUTATED                                            0
  DEL PEAK 44(21Q11.2) WILD-TYPE                                          5
                                vv
clus                             LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 44(21Q11.2) MUTATED                                               2
  DEL PEAK 44(21Q11.2) WILD-TYPE                                            17
                                vv
clus                             LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 44(21Q11.2) MUTATED                                0
  DEL PEAK 44(21Q11.2) WILD-TYPE                              2
                                vv
clus                             LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 44(21Q11.2) MUTATED                                    1
  DEL PEAK 44(21Q11.2) WILD-TYPE                                  2
                                vv
clus                             LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 44(21Q11.2) MUTATED                              0
  DEL PEAK 44(21Q11.2) WILD-TYPE                            2
                                vv
clus                             LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 44(21Q11.2) MUTATED                               6
  DEL PEAK 44(21Q11.2) WILD-TYPE                            17
                                vv
clus                             LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 44(21Q11.2) MUTATED                                 1
  DEL PEAK 44(21Q11.2) WILD-TYPE                               0
                                vv
clus                             LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 44(21Q11.2) MUTATED                                               2
  DEL PEAK 44(21Q11.2) WILD-TYPE                                             3
                                vv
clus                             MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 44(21Q11.2) MUTATED                              4
  DEL PEAK 44(21Q11.2) WILD-TYPE                            6
D73V10, multiclass
                                                    clus
vv                                                   DEL PEAK 44(21Q11.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                            29
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          125
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                    0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 2
  LUNG CLEAR CELL ADENOCARCINOMA                                                0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                            1
  LUNG MUCINOUS ADENOCARCINOMA                                                  0
  LUNG PAPILLARY ADENOCARCINOMA                                                 6
  LUNG SIGNET RING ADENOCARCINOMA                                               1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                 2
  MUCINOUS (COLLOID) CARCINOMA                                                  4
                                                    clus
vv                                                   DEL PEAK 44(21Q11.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                      9
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                              78
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                            196
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                      5
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                  17
  LUNG CLEAR CELL ADENOCARCINOMA                                                  2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                              2
  LUNG MUCINOUS ADENOCARCINOMA                                                    2
  LUNG PAPILLARY ADENOCARCINOMA                                                  17
  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"
D73V11, continuous
D73V12, continuous
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(21Q11.2) MUTATED   120   3   1   7
  DEL PEAK 44(21Q11.2) WILD-TYPE 224  10   3  19
D73V13, multiclass
    clus
vv   DEL PEAK 44(21Q11.2) MUTATED DEL PEAK 44(21Q11.2) WILD-TYPE
  R0                          120                            224
  R1                            3                             10
  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 44(21Q11.2) MUTATED                                  1     1
  DEL PEAK 44(21Q11.2) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(21Q11.2) MUTATED                          23   126
  DEL PEAK 44(21Q11.2) WILD-TYPE                        29   264
D73V14, multiclass
                                  clus
vv                                 DEL PEAK 44(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  23
  WHITE                                                     126
                                  clus
vv                                 DEL PEAK 44(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    29
  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"
D73V15, binary
                                cls
clus                               0   1
  DEL PEAK 44(21Q11.2) MUTATED     2 130
  DEL PEAK 44(21Q11.2) WILD-TYPE   5 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(21Q11.2) MUTATED      2  130
  DEL PEAK 44(21Q11.2) WILD-TYPE    5  254
                        clus
vv                       DEL PEAK 44(21Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          130
                        clus
vv                       DEL PEAK 44(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            254
[1] 2 2
[1] FALSE

Clustering(74) Variable = DEL PEAK 45(22Q13.32) MUTATION ANALYSIS
D74V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 45(22Q13.32) MUTATED   159  86
  DEL PEAK 45(22Q13.32) WILD-TYPE 164  95
  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                            245                             259 
  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                             86                              95 
$`DEL PEAK 45(22Q13.32) MUTATED`
TCGA-05-4396 TCGA-05-4418 TCGA-05-4427 TCGA-05-5420 TCGA-38-4630 TCGA-38-6178 
        9.96         9.01        26.01        15.02        35.28        14.73 
TCGA-44-2662 TCGA-44-6147 TCGA-44-7671 TCGA-49-4501 TCGA-49-6761 TCGA-49-AARN 
       42.08        27.78        29.23        46.72        11.64        37.32 
TCGA-50-5932 TCGA-50-5935 TCGA-50-6597 TCGA-55-8203 TCGA-55-8205 TCGA-55-8207 
       40.60        21.47        41.69        17.98        19.69        32.12 
TCGA-55-8511 TCGA-55-A4DF TCGA-64-1677 TCGA-67-6217 TCGA-73-4662 TCGA-78-8660 
       18.15        20.19        20.65        13.87        82.68        10.55 
TCGA-80-5611 TCGA-91-6836 TCGA-91-7771 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7562 
       85.32        13.71        16.18         1.45         6.12         2.86 
TCGA-95-A4VN TCGA-97-A4M3 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA 
       18.18        17.75        10.09        27.19         5.29        31.23 
TCGA-05-4249 TCGA-05-4389 TCGA-05-4390 TCGA-05-4395 TCGA-05-4397 TCGA-05-4415 
       50.07        45.01        37.02         0.00        24.03         2.99 
TCGA-05-4420 TCGA-05-4424 TCGA-05-4426 TCGA-05-4432 TCGA-05-4433 TCGA-05-5425 
       29.98        30.02        26.01        25.02        24.00        29.00 
TCGA-05-5428 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 TCGA-38-4628 TCGA-38-4632 
       22.03         7.40         5.98         8.68        49.05        44.61 
TCGA-44-2656 TCGA-44-2659 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 
       46.98        44.94        38.89        34.06        33.73        26.56 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6774 TCGA-44-6778 
       33.30        28.37        23.77        19.56        21.63        61.28 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SS 
        7.17        36.07        18.87        12.66         8.55        13.64 
TCGA-44-A4SU TCGA-49-4488 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
       13.45        28.57        14.07        32.84         8.81        29.46 
TCGA-49-6744 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR9 TCGA-49-AARE TCGA-4B-A93V 
       55.33        22.26        73.12         8.55        40.41         9.86 
TCGA-50-5051 TCGA-50-5930 TCGA-50-5933 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
       15.72         9.27        78.67         8.45        15.12        48.46 
TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 TCGA-50-6593 TCGA-50-6673 TCGA-50-7109 
       42.35         3.91        25.55        11.05         0.72        10.13 
TCGA-50-8457 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6642 
       36.99        34.29        13.94        35.21        38.73        80.52 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 
        5.62        42.51        40.73        46.03        53.65         3.88 
TCGA-55-6980 TCGA-55-6985 TCGA-55-7281 TCGA-55-7283 TCGA-55-7570 TCGA-55-7574 
       69.34        40.54        28.67        20.02        27.09        32.71 
TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 
       22.03         3.91        18.64        34.19        17.65        18.44 
TCGA-55-7994 TCGA-55-8092 TCGA-55-8094 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
       19.82         5.06        17.79        14.47         0.36        13.74 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8512 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 
       20.28        17.72        19.96        14.66         1.58        12.33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DG TCGA-62-8399 
       20.71        21.40         3.25         0.92        19.99        88.64 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46Y TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
       54.35        67.96        13.61        29.92        56.81        39.09 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
       81.80        38.37        87.98         2.04        42.90        28.41 
TCGA-64-5781 TCGA-67-3771 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
       51.25        20.05         6.64         6.12        22.68        13.61 
TCGA-69-7973 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8255 
        7.56         4.41        13.41        13.51        14.01         4.24 
TCGA-69-8453 TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-4668 TCGA-73-4670 
       26.73        19.43         8.42        23.38        15.35         4.31 
TCGA-73-A9RS TCGA-75-5147 TCGA-75-6214 TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 
       11.18        43.82        36.66       100.57       163.10        27.16 
TCGA-78-7146 TCGA-78-7152 TCGA-78-7159 TCGA-78-7163 TCGA-78-7167 TCGA-78-7535 
        5.69        39.95        64.90       238.29        88.14        31.20 
TCGA-78-7536 TCGA-78-8640 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        8.02       232.18       110.50        93.11        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        32.78        19.89        35.24        37.74 
TCGA-86-8056 TCGA-86-8074 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
        4.57         0.79        31.20        21.47        14.60        11.61 
TCGA-86-8672 TCGA-86-A4D0 TCGA-86-A4JF TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
        0.62         3.81        24.23        10.62        41.36         1.97 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-8499 TCGA-93-A4JN TCGA-95-7039 
       10.19        12.23        27.68         1.18        23.61        41.82 
TCGA-95-7567 TCGA-95-7944 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VP TCGA-97-7546 
       18.67        12.39        27.29         2.76        19.89        42.25 
TCGA-97-7552 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 TCGA-97-A4M0 TCGA-99-7458 
       63.52        25.48        18.54         0.59        21.44        24.56 
TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A50W 
       36.76         1.45        21.57        32.48        19.00        14.53 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SY TCGA-MP-A4T2 
       18.58        15.65         2.76        86.14        49.35        37.35 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-NJ-A4YF 
       29.46        11.05        24.36        11.15        19.13        71.05 
TCGA-NJ-A4YI TCGA-NJ-A4YQ TCGA-NJ-A55R TCGA-NJ-A7XG TCGA-O1-A52J 
        0.13        47.08        19.82        20.28        59.11 

$`DEL PEAK 45(22Q13.32) WILD-TYPE`
TCGA-05-4382 TCGA-05-4384 TCGA-05-4402 TCGA-05-4405 TCGA-05-4434 TCGA-38-4629 
       19.96        14.01         8.02        20.05        15.02        28.41 
TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-6146 TCGA-44-6776 
       11.64        26.30        43.53        38.10        23.93        86.01 
TCGA-44-7661 TCGA-44-7670 TCGA-44-8119 TCGA-44-A47F TCGA-49-6742 TCGA-49-6745 
       18.31        29.00         9.37        11.08        16.04        17.16 
TCGA-49-AAR0 TCGA-55-1592 TCGA-55-1595 TCGA-55-6978 TCGA-55-6979 TCGA-55-7284 
      156.66        23.05        48.62         5.79         7.79         7.99 
TCGA-55-7573 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7914 TCGA-55-8090 
       16.01        23.18        14.53        21.44         6.15        19.66 
TCGA-55-8091 TCGA-55-8204 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 
       19.73        16.93        13.68        16.93        22.65        20.58 
TCGA-55-A492 TCGA-73-4658 TCGA-73-7498 TCGA-78-7166 TCGA-78-7633 TCGA-93-A4JQ 
       19.59        52.60        39.09         8.48        50.24        17.29 
TCGA-95-7043 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-8172 TCGA-97-A4LX 
       16.54        15.68        15.65        21.40        17.92        20.19 
TCGA-97-A4M2 TCGA-97-A4M7 TCGA-J2-8192 TCGA-J2-8194 TCGA-L9-A443 TCGA-L9-A743 
       20.52        20.68        24.30        23.80         6.35        21.83 
TCGA-MP-A4TC TCGA-MP-A4TD TCGA-05-4250 TCGA-05-4398 TCGA-05-4403 TCGA-05-4417 
        2.43        10.09         3.98        47.05        19.00        14.96 
TCGA-05-4422 TCGA-05-4425 TCGA-05-4430 TCGA-05-5423 TCGA-05-5429 TCGA-05-5715 
       12.00        21.99        25.02         4.96         9.04         2.04 
TCGA-35-3615 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-A44F TCGA-44-2657 
        0.46        97.74       120.79        37.71         4.37        44.42 
TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-5645 
       42.77         3.19        25.02        37.15        38.24        28.01 
TCGA-44-6148 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 
       23.15        23.18        32.45        16.44        22.72        19.46 
TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-49-4486 
       23.64        15.98        15.32         9.44        11.54        76.21 
TCGA-49-4487 TCGA-49-4490 TCGA-49-4494 TCGA-49-4512 TCGA-49-4514 TCGA-49-6743 
       28.11        12.66        35.54        29.75        55.89        53.29 
TCGA-49-AAQV TCGA-49-AAR3 TCGA-49-AAR4 TCGA-49-AARO TCGA-49-AARQ TCGA-49-AARR 
       22.26        62.24        28.90       123.58       221.33       164.12 
TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 
       20.52        71.47       101.72        60.16        47.41        49.28 
TCGA-50-5072 TCGA-50-5931 TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6594 
        8.22        14.27        60.72        57.53        53.16        12.16 
TCGA-50-6595 TCGA-50-8459 TCGA-50-8460 TCGA-53-7626 TCGA-55-1596 TCGA-55-5899 
        6.21        36.79        27.25        30.54        67.89        30.58 
TCGA-55-6543 TCGA-55-6970 TCGA-55-6981 TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 
       14.30        15.25        45.34        32.71        92.81        24.99 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7995 
      107.21        70.26        23.15        25.41        11.28        29.23 
TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 
       29.72        15.19        23.08        23.64        15.65        29.19 
TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8513 TCGA-55-8514 
       22.16        15.42        17.56        15.72        26.01        17.10 
TCGA-55-8614 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
       17.62        15.81        17.95         4.57        39.98        42.38 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46V 
       14.60        49.25        47.80        19.53        56.71        72.30 
TCGA-62-A470 TCGA-62-A471 TCGA-64-1680 TCGA-64-5815 TCGA-67-3770 TCGA-67-3772 
       39.25        40.96        37.02        28.47        20.05        18.84 
TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-69-7765 
       14.04        12.66        14.73         5.72         4.64         5.42 
TCGA-69-7974 TCGA-69-8254 TCGA-73-4666 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 
        6.05        13.45        26.30        30.31         9.24         1.25 
TCGA-73-7499 TCGA-75-5125 TCGA-75-5146 TCGA-75-6206 TCGA-75-6212 TCGA-75-7025 
       50.33        66.64        77.85        85.15        49.84       108.66 
TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7153 TCGA-78-7154 
       19.27        20.58       129.53        21.90       119.51        19.50 
TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 
       38.50        32.09         5.88        22.92         9.57       104.19 
TCGA-78-7220 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-8648 
       26.53        53.33        26.01        39.35        10.55        39.75 
TCGA-78-8655 TCGA-86-6562 TCGA-86-7713 TCGA-86-7714 TCGA-86-8055 TCGA-86-8073 
       77.59        12.36        38.04        20.55         4.08        24.33 
TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8668 TCGA-86-8669 
       22.82        32.65        31.04        23.05        13.91        30.84 
TCGA-86-8671 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
       27.58        28.34        26.50        29.46        13.64        26.47 
TCGA-91-6835 TCGA-91-6848 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
        2.60         7.36         1.15        16.60        14.27        19.82 
TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JO TCGA-93-A4JP TCGA-97-7547 TCGA-97-7553 
       22.45        17.46         1.08        19.00        64.60        61.48 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-97-A4M6 
       14.30        21.60        20.58        19.76        20.84        18.67 
TCGA-99-8025 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-L4-A4E6 TCGA-L9-A5IP 
       34.85        21.63        18.08        35.47        14.30         1.91 
TCGA-MN-A4N4 TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T9 
       38.63        58.45        86.04        58.85         5.49        41.59 
TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A55A TCGA-NJ-A55O 
       14.10        73.91        74.33         1.64         0.49         0.43 
TCGA-S2-AA1A 
       16.87 

  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                           0.00                            0.43 
  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                         238.29                          221.33 
  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE 
                          21.47                           21.83 
[1] "0.0 - 238.3 (21.5)" "0.4 - 221.3 (21.8)"
[1] "hr=" "1"  
D74V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 45(22Q13.32) MUTATED         3       60       65        0        28
  DEL PEAK 45(22Q13.32) WILD-TYPE       2       73       74        1        22
                                 vv
clus                              STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 45(22Q13.32) MUTATED          35         38          6       14
  DEL PEAK 45(22Q13.32) WILD-TYPE        37         34          5       11
D74V3, multiclass
            clus
vv           DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE
  STAGE I                                3                               2
  STAGE IA                              60                              73
  STAGE IB                              65                              74
  STAGE II                               0                               1
  STAGE IIA                             28                              22
  STAGE IIB                             35                              37
  STAGE IIIA                            38                              34
  STAGE IIIB                             6                               5
  STAGE IV                              14                              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 45(22Q13.32) MUTATED    82 135  22  10
  DEL PEAK 45(22Q13.32) WILD-TYPE  89 143  24   9
D74V4, multiclass
    clus
vv   DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE
  T1                            82                              89
  T2                           135                             143
  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 45(22Q13.32) MUTATED   163  46    38
  DEL PEAK 45(22Q13.32) WILD-TYPE 170  50    38
D74V5, multiclass
       clus
vv      DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE
  N0                              163                             170
  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"
D74V6, binary
                                 cls
clus                                0   1
  DEL PEAK 45(22Q13.32) MUTATED   168  14
  DEL PEAK 45(22Q13.32) WILD-TYPE 181  11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(22Q13.32) MUTATED    168   14
  DEL PEAK 45(22Q13.32) WILD-TYPE  181   11
   clus
vv  DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE
  0                           168                             181
  1                            14                              11
[1] 2 2
[1] FALSE
D74V7, binary
                                 cls
clus                                0   1
  DEL PEAK 45(22Q13.32) MUTATED   122 128
  DEL PEAK 45(22Q13.32) WILD-TYPE 154 112
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(22Q13.32) MUTATED    122  128
  DEL PEAK 45(22Q13.32) WILD-TYPE  154  112
        clus
vv       DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE
  FEMALE                           122                             154
  MALE                             128                             112
[1] 2 2
[1] FALSE
D74V8, binary
                                 cls
clus                                0   1
  DEL PEAK 45(22Q13.32) MUTATED   195  33
  DEL PEAK 45(22Q13.32) WILD-TYPE 215  27
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(22Q13.32) MUTATED    195   33
  DEL PEAK 45(22Q13.32) WILD-TYPE  215   27
     clus
vv    DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE
  NO                            195                             215
  YES                            33                              27
[1] 2 2
[1] FALSE
D74V9, continuous
                                 vv
clus                              LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 45(22Q13.32) MUTATED                           11
  DEL PEAK 45(22Q13.32) WILD-TYPE                          7
                                 vv
clus                              LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 45(22Q13.32) MUTATED                                  44
  DEL PEAK 45(22Q13.32) WILD-TYPE                                63
                                 vv
clus                              LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 45(22Q13.32) MUTATED                                                  165
  DEL PEAK 45(22Q13.32) WILD-TYPE                                                156
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 45(22Q13.32) MUTATED                                            1
  DEL PEAK 45(22Q13.32) WILD-TYPE                                          4
                                 vv
clus                              LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 45(22Q13.32) MUTATED                                              10
  DEL PEAK 45(22Q13.32) WILD-TYPE                                             9
                                 vv
clus                              LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 45(22Q13.32) MUTATED                                0
  DEL PEAK 45(22Q13.32) WILD-TYPE                              2
                                 vv
clus                              LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 45(22Q13.32) MUTATED                                    2
  DEL PEAK 45(22Q13.32) WILD-TYPE                                  1
                                 vv
clus                              LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(22Q13.32) MUTATED                              0
  DEL PEAK 45(22Q13.32) WILD-TYPE                            2
                                 vv
clus                              LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 45(22Q13.32) MUTATED                               9
  DEL PEAK 45(22Q13.32) WILD-TYPE                            14
                                 vv
clus                              LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 45(22Q13.32) MUTATED                                 1
  DEL PEAK 45(22Q13.32) WILD-TYPE                               0
                                 vv
clus                              LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 45(22Q13.32) MUTATED                                               4
  DEL PEAK 45(22Q13.32) WILD-TYPE                                             1
                                 vv
clus                              MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 45(22Q13.32) MUTATED                              3
  DEL PEAK 45(22Q13.32) WILD-TYPE                            7
D74V10, multiclass
                                                    clus
vv                                                   DEL PEAK 45(22Q13.32) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             44
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                           165
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                     1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                 10
  LUNG CLEAR CELL ADENOCARCINOMA                                                 0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                             2
  LUNG MUCINOUS ADENOCARCINOMA                                                   0
  LUNG PAPILLARY ADENOCARCINOMA                                                  9
  LUNG SIGNET RING ADENOCARCINOMA                                                1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                  4
  MUCINOUS (COLLOID) CARCINOMA                                                   3
                                                    clus
vv                                                   DEL PEAK 45(22Q13.32) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                       7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                               63
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                             156
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                       4
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                    9
  LUNG CLEAR CELL ADENOCARCINOMA                                                   2
  LUNG MICROPAPILLARY ADENOCARCINOMA                                               1
  LUNG MUCINOUS ADENOCARCINOMA                                                     2
  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"
D74V11, continuous
D74V12, continuous
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 45(22Q13.32) MUTATED   166   7   1  12
  DEL PEAK 45(22Q13.32) WILD-TYPE 178   6   3  14
D74V13, multiclass
    clus
vv   DEL PEAK 45(22Q13.32) MUTATED DEL PEAK 45(22Q13.32) WILD-TYPE
  R0                           166                             178
  R1                             7                               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
  DEL PEAK 45(22Q13.32) MUTATED                                  1     2
  DEL PEAK 45(22Q13.32) WILD-TYPE                                0     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(22Q13.32) MUTATED                          30   183
  DEL PEAK 45(22Q13.32) WILD-TYPE                        22   207
D74V14, multiclass
                                  clus
vv                                 DEL PEAK 45(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   30
  WHITE                                                      183
                                  clus
vv                                 DEL PEAK 45(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     22
  WHITE                                                        207
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V15, binary
                                 cls
clus                                0   1
  DEL PEAK 45(22Q13.32) MUTATED     4 189
  DEL PEAK 45(22Q13.32) WILD-TYPE   3 195
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 45(22Q13.32) MUTATED      4  189
  DEL PEAK 45(22Q13.32) WILD-TYPE    3  195
                        clus
vv                       DEL PEAK 45(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           189
                        clus
vv                       DEL PEAK 45(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             195
[1] 2 2
[1] FALSE

Clustering(75) Variable = DEL PEAK 46(XP22.2) MUTATION ANALYSIS
D75V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 46(XP22.2) MUTATED    96  45
  DEL PEAK 46(XP22.2) WILD-TYPE 227 136
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                          141                           363 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                           45                           136 
$`DEL PEAK 46(XP22.2) MUTATED`
TCGA-05-4382 TCGA-05-4396 TCGA-05-4405 TCGA-05-4427 TCGA-05-4434 TCGA-38-6178 
       19.96         9.96        20.05        26.01        15.02        14.73 
TCGA-44-6146 TCGA-50-5932 TCGA-50-6597 TCGA-55-1592 TCGA-55-6979 TCGA-55-7726 
       23.93        40.60        41.69        23.05         7.79        21.44 
TCGA-55-8090 TCGA-55-8203 TCGA-55-A48X TCGA-55-A492 TCGA-67-6217 TCGA-78-7166 
       19.66        17.98        22.65        19.59        13.87         8.48 
TCGA-78-8660 TCGA-91-7771 TCGA-93-A4JQ TCGA-95-7043 TCGA-97-8172 TCGA-97-A4M7 
       10.55        16.18        17.29        16.54        17.92        20.68 
TCGA-L9-A444 TCGA-05-4389 TCGA-05-4397 TCGA-05-4426 TCGA-05-5428 TCGA-05-5715 
       10.09        45.01        24.03        26.01        22.03         2.04 
TCGA-35-4122 TCGA-35-4123 TCGA-44-2659 TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 
        7.40         5.98        44.94        34.06        33.30        28.37 
TCGA-44-6778 TCGA-44-6779 TCGA-44-7660 TCGA-44-8117 TCGA-44-8120 TCGA-49-4490 
       61.28        16.44        19.46        12.66         8.55        12.66 
TCGA-49-4505 TCGA-49-4512 TCGA-49-6767 TCGA-49-AAR2 TCGA-49-AAR3 TCGA-49-AARQ 
       14.07        29.75        22.26        73.12        62.24       221.33 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5933 TCGA-50-5936 TCGA-50-5941 TCGA-50-5946 
       47.41        49.28        78.67         8.45        48.46        53.16 
TCGA-50-6593 TCGA-50-6594 TCGA-50-7109 TCGA-53-7624 TCGA-53-7626 TCGA-55-1596 
       11.05        12.16        10.13        34.29        30.54        67.89 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6712 TCGA-55-6968 TCGA-55-6987 TCGA-55-7281 
       30.58        14.30         5.62        42.51        70.26        28.67 
TCGA-55-7570 TCGA-55-7903 TCGA-55-7994 TCGA-55-8094 TCGA-55-8301 TCGA-55-8510 
       27.09        18.64        19.82        17.79        17.56        17.72 
TCGA-55-8616 TCGA-55-A48Z TCGA-55-A4DG TCGA-62-8397 TCGA-62-A46O TCGA-62-A46U 
        1.58        21.40        19.99        42.38        47.80        67.96 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 
       29.92        56.81        39.09        42.90        28.47        20.05 
TCGA-67-3772 TCGA-67-3773 TCGA-67-4679 TCGA-69-7764 TCGA-69-7765 TCGA-69-7979 
       18.84        14.04        14.73        13.61         5.42        13.41 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4666 TCGA-73-4668 TCGA-73-7499 TCGA-73-A9RS 
       19.43         8.42        26.30        15.35        50.33        11.18 
TCGA-75-5125 TCGA-75-5146 TCGA-75-7025 TCGA-78-7146 TCGA-78-7154 TCGA-78-7160 
       66.64        77.85       108.66         5.69        19.50        22.92 
TCGA-78-7535 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-86-7954 TCGA-86-7955 
       31.20        10.55       232.18        77.59        19.89        35.24 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8075 TCGA-86-8358 TCGA-86-8359 TCGA-86-8673 
       37.74         4.08        22.82        21.47        14.60        28.34 
TCGA-86-A4P7 TCGA-91-6848 TCGA-91-8496 TCGA-93-A4JO TCGA-95-7039 TCGA-95-7567 
       13.64         7.36        16.60         1.08        41.82        18.67 
TCGA-95-8039 TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 TCGA-97-8179 TCGA-97-8547 
       27.29         2.76        25.48        18.54        14.30        21.60 
TCGA-97-A4M0 TCGA-97-A4M6 TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV TCGA-MN-A4N5 
       21.44        18.67        19.00        14.53        18.58         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 
        0.49        20.28        16.87 

$`DEL PEAK 46(XP22.2) WILD-TYPE`
TCGA-05-4384 TCGA-05-4402 TCGA-05-4418 TCGA-05-5420 TCGA-38-4629 TCGA-38-4630 
       14.01         8.02         9.01        15.02        28.41        35.28 
TCGA-38-4631 TCGA-38-7271 TCGA-44-2655 TCGA-44-2661 TCGA-44-2662 TCGA-44-6147 
       11.64        26.30        43.53        38.10        42.08        27.78 
TCGA-44-6776 TCGA-44-7661 TCGA-44-7670 TCGA-44-7671 TCGA-44-8119 TCGA-44-A47F 
       86.01        18.31        29.00        29.23         9.37        11.08 
TCGA-49-4501 TCGA-49-6742 TCGA-49-6745 TCGA-49-6761 TCGA-49-AAR0 TCGA-49-AARN 
       46.72        16.04        17.16        11.64       156.66        37.32 
TCGA-50-5935 TCGA-55-1595 TCGA-55-6978 TCGA-55-7284 TCGA-55-7573 TCGA-55-7724 
       21.47        48.62         5.79         7.99        16.01        23.18 
TCGA-55-7725 TCGA-55-7914 TCGA-55-8091 TCGA-55-8204 TCGA-55-8205 TCGA-55-8207 
       14.53         6.15        19.73        16.93        19.69        32.12 
TCGA-55-8511 TCGA-55-8619 TCGA-55-8621 TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 
       18.15        13.68        16.93        20.58        20.19        20.65 
TCGA-73-4658 TCGA-73-4662 TCGA-73-7498 TCGA-78-7633 TCGA-80-5611 TCGA-91-6836 
       52.60        82.68        39.09        50.24        85.32        13.71 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-7562 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK 
        1.45         6.12         2.86        15.68        15.65        21.40 
TCGA-95-A4VN TCGA-97-A4LX TCGA-97-A4M2 TCGA-97-A4M3 TCGA-J2-8192 TCGA-J2-8194 
       18.18        20.19        20.52        17.75        24.30        23.80 
TCGA-L9-A443 TCGA-L9-A743 TCGA-MN-A4N1 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TC 
        6.35        21.83        27.19         5.29        31.23         2.43 
TCGA-MP-A4TD TCGA-05-4249 TCGA-05-4250 TCGA-05-4390 TCGA-05-4395 TCGA-05-4398 
       10.09        50.07         3.98        37.02         0.00        47.05 
TCGA-05-4403 TCGA-05-4415 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 
       19.00         2.99        14.96        29.98        12.00        30.02 
TCGA-05-4425 TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5423 TCGA-05-5425 
       21.99        25.02        25.02        24.00         4.96        29.00 
TCGA-05-5429 TCGA-35-3615 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 
        9.04         0.46         8.68        97.74       120.79        37.71 
TCGA-38-4628 TCGA-38-4632 TCGA-38-A44F TCGA-44-2656 TCGA-44-2657 TCGA-44-2665 
       49.05        44.61         4.37        46.98        44.42        42.77 
TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 TCGA-44-3917 TCGA-44-3919 
        3.19        25.02        37.15        38.24        38.89        33.73 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 
       26.56        28.01        23.77        19.56        23.15        21.63 
TCGA-44-6775 TCGA-44-6777 TCGA-44-7659 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
       23.18        32.45        22.72         7.17        36.07        18.87 
TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47G TCGA-44-A4SS 
       23.64        15.98        15.32         9.44        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-49-4507 TCGA-49-4510 TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-49-AAQV 
        8.81        29.46        55.89        53.29        55.33        22.26 
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-50-5049 TCGA-50-5051 TCGA-50-5055 TCGA-50-5072 
       20.52        71.47       101.72        15.72        60.16         8.22 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5939 TCGA-50-5942 TCGA-50-5944 TCGA-50-6590 
        9.27        14.27        15.12        60.72        57.53        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        36.99        36.79 
TCGA-50-8460 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1594 TCGA-55-6642 TCGA-55-6969 
       27.25        13.94        35.21        38.73        80.52        40.73 
TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 TCGA-55-6975 TCGA-55-6980 TCGA-55-6981 
       15.25        46.03        53.65         3.88        69.34        45.34 
TCGA-55-6982 TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-7283 
       32.71        92.81        24.99        40.54       107.21        20.02 
TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
       32.71        22.03         3.91        23.15        25.41        11.28 
TCGA-55-7910 TCGA-55-7911 TCGA-55-7913 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 
       34.19        17.65        18.44        29.23        29.72        15.19 
TCGA-55-8089 TCGA-55-8092 TCGA-55-8096 TCGA-55-8097 TCGA-55-8206 TCGA-55-8208 
       23.08         5.06        23.64        15.65        29.19        22.16 
TCGA-55-8299 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
       15.42        15.72        14.47         0.36        13.74        20.28 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 
       19.96        26.01        17.10        17.62        14.66        12.33 
TCGA-55-A48Y TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A57B TCGA-62-8394 
       20.71         3.25         0.92        15.81        17.95         4.57 
TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46P TCGA-62-A46R 
       39.98        14.60        88.64        49.25        19.53        56.71 
TCGA-62-A46S TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-64-1679 
       54.35        72.30        13.61        39.25        40.96        81.80 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-64-5781 
       37.02        38.37        87.98         2.04        28.41        51.25 
TCGA-67-3771 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7760 TCGA-69-7761 
       20.05        12.66         5.72         4.64         6.64         6.12 
TCGA-69-7763 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7980 TCGA-69-8253 
       22.68         7.56         6.05         4.41        13.51        14.01 
TCGA-69-8254 TCGA-69-8255 TCGA-69-8453 TCGA-73-4659 TCGA-73-4670 TCGA-73-4675 
       13.45         4.24        26.73        23.38         4.31        30.31 
TCGA-73-4676 TCGA-73-4677 TCGA-75-5147 TCGA-75-6206 TCGA-75-6212 TCGA-75-6214 
        9.24         1.25        43.82        85.15        49.84        36.66 
TCGA-75-7027 TCGA-78-7143 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
      100.57       163.10        27.16        19.27        20.58       129.53 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 
       21.90        39.95       119.51        38.50        32.09         5.88 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7220 
       64.90         9.57       104.19       238.29        88.14        26.53 
TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-8648 TCGA-78-8662 
        8.02        53.33        26.01        39.35        39.75       110.50 
TCGA-80-5608 TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 
       93.11        27.09        12.36         5.88        31.13        34.39 
TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 
       38.04        20.55        32.78         4.57        24.33         0.79 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 TCGA-86-8585 TCGA-86-8668 
       32.65        31.04        31.20        23.05        11.61        13.91 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
       30.84        27.58         0.62        26.50        29.46         3.81 
TCGA-86-A4JF TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 
       24.23        26.47        10.62        41.36         1.97        10.19 
TCGA-91-6835 TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8497 TCGA-91-8499 
        2.60        12.23        27.68         1.15        14.27         1.18 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-A4JN TCGA-93-A4JP TCGA-95-7944 
       19.82        22.45        17.46        23.61        19.00        12.39 
TCGA-95-A4VP TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7938 
       19.89        42.25        64.60        63.52        61.48         0.59 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8174 TCGA-97-8175 TCGA-97-8176 TCGA-97-8177 
       15.91        18.67         5.39        18.12        15.39        16.41 
TCGA-97-8552 TCGA-97-A4M1 TCGA-97-A4M5 TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 
       20.58        19.76        20.84        24.56        34.85        36.76 
TCGA-99-8032 TCGA-99-8033 TCGA-99-AA5R TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG 
        1.45        21.57        21.63        18.08        35.47        32.48 
TCGA-L4-A4E6 TCGA-L9-A5IP TCGA-L9-A8F4 TCGA-MN-A4N4 TCGA-MP-A4SY TCGA-MP-A4T6 
       14.30         1.91        15.65        38.63        49.35        58.85 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TJ 
        5.49        41.59        29.46        11.05        24.36        11.15 
TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-NJ-A4YF TCGA-NJ-A4YG TCGA-NJ-A4YP TCGA-NJ-A4YQ 
       19.13        73.91        71.05        74.33         1.64        47.08 
TCGA-NJ-A55O TCGA-NJ-A55R TCGA-O1-A52J 
        0.43        19.82        59.11 

  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                         0.13                          0.00 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                       232.18                        238.29 
  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE 
                        19.99                         22.68 
[1] "0.1 - 232.2 (20.0)" "0.0 - 238.3 (22.7)"
[1] "hr=" "1.1"
D75V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  DEL PEAK 46(XP22.2) MUTATED         2       34       38        0        11
  DEL PEAK 46(XP22.2) WILD-TYPE       3       99      101        1        39
                               vv
clus                            STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  DEL PEAK 46(XP22.2) MUTATED          29         17          3        7
  DEL PEAK 46(XP22.2) WILD-TYPE        43         55          8       18
D75V3, multiclass
            clus
vv           DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  STAGE I                              2                             3
  STAGE IA                            34                            99
  STAGE IB                            38                           101
  STAGE II                             0                             1
  STAGE IIA                           11                            39
  STAGE IIB                           29                            43
  STAGE IIIA                          17                            55
  STAGE IIIB                           3                             8
  STAGE IV                             7                            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 46(XP22.2) MUTATED    45  80  14   6
  DEL PEAK 46(XP22.2) WILD-TYPE 126 198  32  13
D75V4, multiclass
    clus
vv   DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  T1                          45                           126
  T2                          80                           198
  T3                          14                            32
  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 46(XP22.2) MUTATED    88  35    20
  DEL PEAK 46(XP22.2) WILD-TYPE 245  61    56
D75V5, multiclass
       clus
vv      DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  N0                             88                           245
  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"
D75V6, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED   101   7
  DEL PEAK 46(XP22.2) WILD-TYPE 248  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED    101    7
  DEL PEAK 46(XP22.2) WILD-TYPE  248   18
   clus
vv  DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  0                         101                           248
  1                           7                            18
[1] 2 2
[1] FALSE
D75V7, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED    66  79
  DEL PEAK 46(XP22.2) WILD-TYPE 210 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED     66   79
  DEL PEAK 46(XP22.2) WILD-TYPE  210  161
        clus
vv       DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  FEMALE                          66                           210
  MALE                            79                           161
[1] 2 2
[1] FALSE
D75V8, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED   112  14
  DEL PEAK 46(XP22.2) WILD-TYPE 298  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED    112   14
  DEL PEAK 46(XP22.2) WILD-TYPE  298   46
     clus
vv    DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  NO                          112                           298
  YES                          14                            46
[1] 2 2
[1] FALSE
D75V9, continuous
                               vv
clus                            LUNG ACINAR ADENOCARCINOMA
  DEL PEAK 46(XP22.2) MUTATED                            7
  DEL PEAK 46(XP22.2) WILD-TYPE                         11
                               vv
clus                            LUNG ADENOCARCINOMA MIXED SUBTYPE
  DEL PEAK 46(XP22.2) MUTATED                                  32
  DEL PEAK 46(XP22.2) WILD-TYPE                                75
                               vv
clus                            LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  DEL PEAK 46(XP22.2) MUTATED                                                   93
  DEL PEAK 46(XP22.2) WILD-TYPE                                                228
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  DEL PEAK 46(XP22.2) MUTATED                                            2
  DEL PEAK 46(XP22.2) WILD-TYPE                                          3
                               vv
clus                            LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  DEL PEAK 46(XP22.2) MUTATED                                               4
  DEL PEAK 46(XP22.2) WILD-TYPE                                            15
                               vv
clus                            LUNG CLEAR CELL ADENOCARCINOMA
  DEL PEAK 46(XP22.2) MUTATED                                0
  DEL PEAK 46(XP22.2) WILD-TYPE                              2
                               vv
clus                            LUNG MICROPAPILLARY ADENOCARCINOMA
  DEL PEAK 46(XP22.2) MUTATED                                    2
  DEL PEAK 46(XP22.2) WILD-TYPE                                  1
                               vv
clus                            LUNG MUCINOUS ADENOCARCINOMA
  DEL PEAK 46(XP22.2) MUTATED                              1
  DEL PEAK 46(XP22.2) WILD-TYPE                            1
                               vv
clus                            LUNG PAPILLARY ADENOCARCINOMA
  DEL PEAK 46(XP22.2) MUTATED                               3
  DEL PEAK 46(XP22.2) WILD-TYPE                            20
                               vv
clus                            LUNG SIGNET RING ADENOCARCINOMA
  DEL PEAK 46(XP22.2) MUTATED                                 0
  DEL PEAK 46(XP22.2) WILD-TYPE                               1
                               vv
clus                            LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  DEL PEAK 46(XP22.2) MUTATED                                               0
  DEL PEAK 46(XP22.2) WILD-TYPE                                             5
                               vv
clus                            MUCINOUS (COLLOID) CARCINOMA
  DEL PEAK 46(XP22.2) MUTATED                              1
  DEL PEAK 46(XP22.2) WILD-TYPE                            9
D75V10, multiclass
                                                    clus
vv                                                   DEL PEAK 46(XP22.2) MUTATED
  LUNG ACINAR ADENOCARCINOMA                                                   7
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                           32
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)                          93
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                                   2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS                                4
  LUNG CLEAR CELL ADENOCARCINOMA                                               0
  LUNG MICROPAPILLARY ADENOCARCINOMA                                           2
  LUNG MUCINOUS ADENOCARCINOMA                                                 1
  LUNG PAPILLARY ADENOCARCINOMA                                                3
  LUNG SIGNET RING ADENOCARCINOMA                                              0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA                                0
  MUCINOUS (COLLOID) CARCINOMA                                                 1
                                                    clus
vv                                                   DEL PEAK 46(XP22.2) WILD-TYPE
  LUNG ACINAR ADENOCARCINOMA                                                    11
  LUNG ADENOCARCINOMA MIXED SUBTYPE                                             75
  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                                                   1
  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"
D75V11, continuous
D75V12, continuous
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 46(XP22.2) MUTATED    92   3   1   6
  DEL PEAK 46(XP22.2) WILD-TYPE 252  10   3  20
D75V13, multiclass
    clus
vv   DEL PEAK 46(XP22.2) MUTATED DEL PEAK 46(XP22.2) WILD-TYPE
  R0                          92                           252
  R1                           3                            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 46(XP22.2) MUTATED                                  1     2
  DEL PEAK 46(XP22.2) WILD-TYPE                                0     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(XP22.2) MUTATED                          16   105
  DEL PEAK 46(XP22.2) WILD-TYPE                        36   285
D75V14, multiclass
                                  clus
vv                                 DEL PEAK 46(XP22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 16
  WHITE                                                    105
                                  clus
vv                                 DEL PEAK 46(XP22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      285
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V15, binary
                               cls
clus                              0   1
  DEL PEAK 46(XP22.2) MUTATED     1 105
  DEL PEAK 46(XP22.2) WILD-TYPE   6 279
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 46(XP22.2) MUTATED      1  105
  DEL PEAK 46(XP22.2) WILD-TYPE    6  279
                        clus
vv                       DEL PEAK 46(XP22.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                         105
                        clus
vv                       DEL PEAK 46(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                           279
[1] 2 2
[1] FALSE
